Non-Coding RNA Search

Ss1.1-rova002_c2.5

Sequence:


               
               GAGTTCAGAAATAGGACACTAGGCTTGGATAATGCTGCAGACTCTTTTTCTTTTGTATGA
AAAGCTGGGGAGATGAGAGTTCTCGTTTTGGAAGAGAATATCCCAAAATTGGTTAGGCTC
AGCCTTGGGAATAATACAACAGGTTTAACATCCCAAGCCTAACCTGACATGGTTGGGAAA
GGTAGATTGAATGAGATCTGTTTTCTGTGCTTCTAAGTGTTTTGTGTATTGGGCTGCTGT
TGCTTCATGTGTTCATTATGGCAGGTTTAATGAATCCTCAAAAAGAAAAACTGGTTTGCT
TGCCTAAAACTGTAATGCCCACTTAACCTCCTTCACTCAGTCAGTGTCTTTTATGGTTTA
CCCTGGCTCTTAAATAATGTAAAGATTTGAGAATGTTATTCACATAAAATGGGCACCTTC
TCTCTCTCCCTTCCAGCATGTTGCTTTTGAAACTATCATGTGATAATGGAAAGAGCCCTG
AGTTAGGAGTCAAGATATCTGGGTTCTGGTTCCACTCAGTCTAGGCAGAACCGACATGTA
ACCTTGGTCAAATAATTTAACCTCTCTGGATTTCTA

Sequence:

Distiller database | Help | Less info

Blue-coloured subsequences are predicted RNA structures by RNAz


               
               GAGTTCAGAAATAGGACACTAGGCTTGGATAATGCTGCAGACTCTTTTTCTTTTGTATGA
AAAGCTGGGGAGATGAGAGTTCTCGTTTTGGAAGAGAATATCCCAAAATTGGTTAGGCTC
AGCCTTGGGAATAATACAACAGGTTTAACATCCCAAGCCTAACCTGACATGGTTGGGAAA
GGTAGATTGAATGAGATCTGTTTTCTGTGCTTCTAAGTGTTTTGTGTATTGGGCTGCTGT
TGCTTCATGTGTTCATTATGGCAGGTTTAATGAATCCTCAAAAAGAAAAACTGGTTTGCT
TGCCTAAAACTGTAATGCCCACTTAACCTCCTTCACTCAGTCAGTGTCTTTTATGGTTTA
CCCTGGCTCTTAAATAATGTAAAGATTTGAGAATGTTATTCACATAAAATGGGCACCTTC
TCTCTCTCCCTTCCAGCATGTTGCTTTTGAAACTATCATGTGATAATGGAAAGAGCCCTG
AGTTAGGAGTCAAGATATCTGGGTTCTGGTTCCACTCAGTCTAGGCAGAACCGACATGTA
ACCTTGGTCAAATAATTTAACCTCTCTGGATTTCTA

Predicted RNA structure(s): 2 entry(ies)

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Predicted RNA structure(s): 2 entry(ies)

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               43-198, + strand, RNAz p=0.999645
               

               
               95-185, - strand, RNAz p=0.985131

Predicted RNA structure(s): 2 entry(ies)

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PigEST conread start position and end position of the predicted RNA structure by RNAz,
PigEST conread reading direction of predicted structure,
ncRNA classificator p of RNAz


               
               43-198, + strand, RNAz p=0.999645
               

               
               95-185, - strand, RNAz p=0.985131

Predicted microRNA(s): 1 entry(ies)

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Predicted microRNA(s): 1 entry(ies)

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               86-201, + strand, RNAmicro p=0.940044

Predicted microRNA(s): 1 entry(ies)

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PigEST conread start position and end position of the predicted microRNA,
PigEST conread reading direction of prediction,
miRNA classificator p of RNAmicro


               
               86-201, + strand, RNAmicro p=0.940044

Similar Transcript(s): 12 entry(ies)

More info

Similar Transcript(s): 12 entry(ies)

Help | Less info


               
               51-196, DB229385 TRACH3 Homo sapiens cDNA clone TRACH3022495 5', mRNA 
(dbj|DB229385.1|), blast E-value=8e-28, identity=86.3% 
               

               
               51-196, BX347039 Homo sapiens HELA CELLS COT 25-NORMALIZED Homo sapiens 
(emb|BX347039.2|), blast E-value=8e-28, identity=86.3% 
               

               
               51-196, BX388655 Homo sapiens PLACENTA COT 25-NORMALIZED Homo sapiens cDNA 
(emb|BX388655.2|), blast E-value=8e-28, identity=86.3% 
               

               
               65-196, QV3-GN0201-081100-468-a10 GN0201 Homo sapiens cDNA, mRNA sequence 
(gb|BF996973.1|), blast E-value=5e-29, identity=87.88% 
               

               
               51-196, 17000599949077 GRN_PRENEU Homo sapiens cDNA 5', mRNA sequence 
(gb|CN429581.1|), blast E-value=8e-28, identity=86.3% 
               

               
               51-196, ILLUMIGEN_MCQ_29642 Katze_MMPB Macaca mulatta cDNA clone IBIUW 
(gb|CN648058.1|), blast E-value=3e-30, identity=86.99% 
               

               
               95-185, DB229385 TRACH3 Homo sapiens cDNA clone TRACH3022495 5', mRNA 
(dbj|DB229385.1|), blast E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, DKFZp459I188_r1 459 (synonym (emb|CR543425.1|), blast 
E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, DKFZp459O188_r1 459 (synonym (emb|CR543534.1|), blast 
E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, DKFZp459F0945_r1 459 (synonym (emb|CR547515.1|), blast 
E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, QV3-GN0201-081100-468-a10 GN0201 Homo sapiens cDNA, mRNA sequence 
(gb|BF996973.1|), blast E-value=9e-17, identity=87.91% 
               

               
               95-185, ILLUMIGEN_MCQ_29642 Katze_MMPB Macaca mulatta cDNA clone IBIUW 
(gb|CN648058.1|), blast E-value=9e-17, identity=87.91%

Similar Transcript(s): 12 entry(ies)

Help | Less info

PigEST conread start position and end position of sequence similarity to another annotated EST (NCBI dbEST),
transcript identifier and annotation,
blast E-value,
PigEST conread identity to the similar transcript


               
               51-196, DB229385 TRACH3 Homo sapiens cDNA clone TRACH3022495 5', mRNA 
(dbj|DB229385.1|), blast E-value=8e-28, identity=86.3% 
               

               
               51-196, BX347039 Homo sapiens HELA CELLS COT 25-NORMALIZED Homo sapiens 
(emb|BX347039.2|), blast E-value=8e-28, identity=86.3% 
               

               
               51-196, BX388655 Homo sapiens PLACENTA COT 25-NORMALIZED Homo sapiens cDNA 
(emb|BX388655.2|), blast E-value=8e-28, identity=86.3% 
               

               
               65-196, QV3-GN0201-081100-468-a10 GN0201 Homo sapiens cDNA, mRNA sequence 
(gb|BF996973.1|), blast E-value=5e-29, identity=87.88% 
               

               
               51-196, 17000599949077 GRN_PRENEU Homo sapiens cDNA 5', mRNA sequence 
(gb|CN429581.1|), blast E-value=8e-28, identity=86.3% 
               

               
               51-196, ILLUMIGEN_MCQ_29642 Katze_MMPB Macaca mulatta cDNA clone IBIUW 
(gb|CN648058.1|), blast E-value=3e-30, identity=86.99% 
               

               
               95-185, DB229385 TRACH3 Homo sapiens cDNA clone TRACH3022495 5', mRNA 
(dbj|DB229385.1|), blast E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, DKFZp459I188_r1 459 (synonym (emb|CR543425.1|), blast 
E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, DKFZp459O188_r1 459 (synonym (emb|CR543534.1|), blast 
E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, DKFZp459F0945_r1 459 (synonym (emb|CR547515.1|), blast 
E-value=0.00000000000002, identity=86.81% 
               

               
               95-185, QV3-GN0201-081100-468-a10 GN0201 Homo sapiens cDNA, mRNA sequence 
(gb|BF996973.1|), blast E-value=9e-17, identity=87.91% 
               

               
               95-185, ILLUMIGEN_MCQ_29642 Katze_MMPB Macaca mulatta cDNA clone IBIUW 
(gb|CN648058.1|), blast E-value=9e-17, identity=87.91%

Homologous human UTR: 1 entry(ies)

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Homologous human UTR: 1 entry(ies)

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               5' of CR749580, +

Homologous human UTR: 1 entry(ies)

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Human gene identifier and UTR site,
human gene reading direction


               
               5' of CR749580, +

Aligned organism(s): 47 entry(ies)

More info

Aligned organism(s): 47 entry(ies)

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               6-366, gnl|bosTau2|chr3 (16919451-16919811)
               

               
               6-366, gnl|canFam2|chr17 (62883940-62883428)
               

               
               6-366, gnl|dasNov1|scaffold_50290 (4432-3933)
               

               
               6-366, gnl|echTel1|scaffold_324356 (180704-181196)
               

               
               6-366, gnl|Hg17|chr1 (147410963-147410608)
               

               
               6-366, gnl|hg17|chr2 (215388360-215388863)
               

               
               6-366, gnl|loxAfr1|scaffold_6272 (59590-60116)
               

               
               6-366, gnl|mm7|chr3 (95502720-95503186)
               

               
               6-366, gnl|Mm7|chr3 (95502856-95503219)
               

               
               6-366, gnl|monDom2|scaffold_44 (3817810-3817225)
               

               
               6-366, gnl|oryCun1|scaffold_84320 (2750-2258)
               

               
               6-366, gnl|panTro1|chr13 (105542065-105542568)
               

               
               6-366, gnl|rheMac2|chr12 (78519414-78519915)
               

               
               6-366, gnl|rn3|chr2_random (2925464-2924998)
               


               
               397-576, gnl|bosTau2|chr3 (16919819-16919998)
               

               
               397-576, gnl|canFam2|chr17 (62883119-62883427)
               

               
               397-576, gnl|canFam2|chr17 (62883192-62883427)
               

               
               397-576, gnl|canFam2|chr17 (62883427-62883119)
               

               
               397-576, gnl|dasNov1|scaffold_50290 (3646-3932)
               

               
               397-576, gnl|dasNov1|scaffold_50290 (3719-3932)
               

               
               397-576, gnl|dasNov1|scaffold_50290 (3932-3646)
               

               
               397-576, gnl|echTel1|scaffold_324356 (181478-181197)
               

               
               397-576, gnl|echTel1|scaffold_324356 (181421-181197)
               

               
               397-576, gnl|echTel1|scaffold_324356 (181197-181478)
               

               
               397-576, gnl|hg17|chr1 (147410381-147410616)
               

               
               397-576, gnl|Hg17|chr1 (147410577-147410400)
               

               
               397-576, gnl|hg17|chr14 (82227923-82228229)
               

               
               397-576, gnl|hg17|chr2 (215388864-215389171)
               

               
               397-576, gnl|mm7|chr3 (95503486-95503187)
               

               
               397-576, gnl|mm7|chr3 (95503421-95503187)
               

               
               397-576, gnl|mm7|chr3 (95503187-95503486)
               

               
               397-576, gnl|Mm7|chr3 (95503228-95503401)
               

               
               397-576, gnl|monDom2|scaffold_44 (3816991-3817218)
               

               
               397-576, gnl|monDom2|scaffold_44 (3817052-3817218)
               

               
               397-576, gnl|monDom2|scaffold_44 (3817224-3816991)
               

               
               397-576, gnl|oryCun1|scaffold_202897 (52551-52313)
               

               
               397-576, gnl|oryCun1|scaffold_84320 (1966-2257)
               

               
               397-576, gnl|oryCun1|scaffold_84320 (2257-1967)
               

               
               397-576, gnl|panTro1|chr1 (129141309-129141544)
               

               
               397-576, gnl|panTro1|chr13 (105542569-105542874)
               

               
               397-576, gnl|panTro1|chr15 (82342848-82343153)
               

               
               397-576, gnl|rheMac2|chr1 (129019351-129019657)
               

               
               397-576, gnl|rheMac2|chr1 (129019422-129019657)
               

               
               397-576, gnl|rheMac2|chr12 (78519916-78520225)
               

               
               397-576, gnl|rn3|chr2_random (2924700-2924997)
               

               
               397-576, gnl|rn3|chr2_random (2924764-2924997)
               

               
               397-576, gnl|rn3|chr2_random (2924997-2924700)

Aligned organism(s): 47 entry(ies)

Help | Less info

PigEST conread start position and end position of the aligned locus,
aligned organism with chromosome (chromosome position)
closely related Artiodactyla cow is linked to the PigEST - Genome Map


               
               6-366, gnl|bosTau2|chr3 (16919451-16919811)
               

               
               6-366, gnl|canFam2|chr17 (62883940-62883428)
               

               
               6-366, gnl|dasNov1|scaffold_50290 (4432-3933)
               

               
               6-366, gnl|echTel1|scaffold_324356 (180704-181196)
               

               
               6-366, gnl|Hg17|chr1 (147410963-147410608)
               

               
               6-366, gnl|hg17|chr2 (215388360-215388863)
               

               
               6-366, gnl|loxAfr1|scaffold_6272 (59590-60116)
               

               
               6-366, gnl|mm7|chr3 (95502720-95503186)
               

               
               6-366, gnl|Mm7|chr3 (95502856-95503219)
               

               
               6-366, gnl|monDom2|scaffold_44 (3817810-3817225)
               

               
               6-366, gnl|oryCun1|scaffold_84320 (2750-2258)
               

               
               6-366, gnl|panTro1|chr13 (105542065-105542568)
               

               
               6-366, gnl|rheMac2|chr12 (78519414-78519915)
               

               
               6-366, gnl|rn3|chr2_random (2925464-2924998)
               


               
               397-576, gnl|bosTau2|chr3 (16919819-16919998)
               

               
               397-576, gnl|canFam2|chr17 (62883119-62883427)
               

               
               397-576, gnl|canFam2|chr17 (62883192-62883427)
               

               
               397-576, gnl|canFam2|chr17 (62883427-62883119)
               

               
               397-576, gnl|dasNov1|scaffold_50290 (3646-3932)
               

               
               397-576, gnl|dasNov1|scaffold_50290 (3719-3932)
               

               
               397-576, gnl|dasNov1|scaffold_50290 (3932-3646)
               

               
               397-576, gnl|echTel1|scaffold_324356 (181478-181197)
               

               
               397-576, gnl|echTel1|scaffold_324356 (181421-181197)
               

               
               397-576, gnl|echTel1|scaffold_324356 (181197-181478)
               

               
               397-576, gnl|hg17|chr1 (147410381-147410616)
               

               
               397-576, gnl|Hg17|chr1 (147410577-147410400)
               

               
               397-576, gnl|hg17|chr14 (82227923-82228229)
               

               
               397-576, gnl|hg17|chr2 (215388864-215389171)
               

               
               397-576, gnl|mm7|chr3 (95503486-95503187)
               

               
               397-576, gnl|mm7|chr3 (95503421-95503187)
               

               
               397-576, gnl|mm7|chr3 (95503187-95503486)
               

               
               397-576, gnl|Mm7|chr3 (95503228-95503401)
               

               
               397-576, gnl|monDom2|scaffold_44 (3816991-3817218)
               

               
               397-576, gnl|monDom2|scaffold_44 (3817052-3817218)
               

               
               397-576, gnl|monDom2|scaffold_44 (3817224-3816991)
               

               
               397-576, gnl|oryCun1|scaffold_202897 (52551-52313)
               

               
               397-576, gnl|oryCun1|scaffold_84320 (1966-2257)
               

               
               397-576, gnl|oryCun1|scaffold_84320 (2257-1967)
               

               
               397-576, gnl|panTro1|chr1 (129141309-129141544)
               

               
               397-576, gnl|panTro1|chr13 (105542569-105542874)
               

               
               397-576, gnl|panTro1|chr15 (82342848-82343153)
               

               
               397-576, gnl|rheMac2|chr1 (129019351-129019657)
               

               
               397-576, gnl|rheMac2|chr1 (129019422-129019657)
               

               
               397-576, gnl|rheMac2|chr12 (78519916-78520225)
               

               
               397-576, gnl|rn3|chr2_random (2924700-2924997)
               

               
               397-576, gnl|rn3|chr2_random (2924764-2924997)
               

               
               397-576, gnl|rn3|chr2_random (2924997-2924700)

Expressed library(ies): 4 entry(ies)

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Expressed library(ies): 4 entry(ies)

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               cst (0.140036)
               

               
               ova (0.129132)
               

               
               clu (0.119646)
               

               
               pgl (0.118483)

Expressed library(ies): 4 entry(ies)

Help | Less info

Short name of the library (expression score),
see https://rth.dk/resources/pigest/download/pigest_kvl_1.0.1/cDNA_names.html for library description


               
               cst (0.140036)
               

               
               ova (0.129132)
               

               
               clu (0.119646)
               

               
               pgl (0.118483)

	43-198, + strand, RNAz p=0.999645
	95-185, - strand, RNAz p=0.985131

	51-196, DB229385 TRACH3 Homo sapiens cDNA clone TRACH3022495 5', mRNA (dbj\|DB229385.1\|), blast E-value=8e-28, identity=86.3%
	51-196, BX347039 Homo sapiens HELA CELLS COT 25-NORMALIZED Homo sapiens (emb\|BX347039.2\|), blast E-value=8e-28, identity=86.3%
	51-196, BX388655 Homo sapiens PLACENTA COT 25-NORMALIZED Homo sapiens cDNA (emb\|BX388655.2\|), blast E-value=8e-28, identity=86.3%
	65-196, QV3-GN0201-081100-468-a10 GN0201 Homo sapiens cDNA, mRNA sequence (gb\|BF996973.1\|), blast E-value=5e-29, identity=87.88%
	51-196, 17000599949077 GRN_PRENEU Homo sapiens cDNA 5', mRNA sequence (gb\|CN429581.1\|), blast E-value=8e-28, identity=86.3%
	51-196, ILLUMIGEN_MCQ_29642 Katze_MMPB Macaca mulatta cDNA clone IBIUW (gb\|CN648058.1\|), blast E-value=3e-30, identity=86.99%
	95-185, DB229385 TRACH3 Homo sapiens cDNA clone TRACH3022495 5', mRNA (dbj\|DB229385.1\|), blast E-value=0.00000000000002, identity=86.81%
	95-185, DKFZp459I188_r1 459 (synonym (emb\|CR543425.1\|), blast E-value=0.00000000000002, identity=86.81%
	95-185, DKFZp459O188_r1 459 (synonym (emb\|CR543534.1\|), blast E-value=0.00000000000002, identity=86.81%
	95-185, DKFZp459F0945_r1 459 (synonym (emb\|CR547515.1\|), blast E-value=0.00000000000002, identity=86.81%
	95-185, QV3-GN0201-081100-468-a10 GN0201 Homo sapiens cDNA, mRNA sequence (gb\|BF996973.1\|), blast E-value=9e-17, identity=87.91%
	95-185, ILLUMIGEN_MCQ_29642 Katze_MMPB Macaca mulatta cDNA clone IBIUW (gb\|CN648058.1\|), blast E-value=9e-17, identity=87.91%

	6-366, gnl\|bosTau2\|chr3 (16919451-16919811)
	6-366, gnl\|canFam2\|chr17 (62883940-62883428)
	6-366, gnl\|dasNov1\|scaffold_50290 (4432-3933)
	6-366, gnl\|echTel1\|scaffold_324356 (180704-181196)
	6-366, gnl\|Hg17\|chr1 (147410963-147410608)
	6-366, gnl\|hg17\|chr2 (215388360-215388863)
	6-366, gnl\|loxAfr1\|scaffold_6272 (59590-60116)
	6-366, gnl\|mm7\|chr3 (95502720-95503186)
	6-366, gnl\|Mm7\|chr3 (95502856-95503219)
	6-366, gnl\|monDom2\|scaffold_44 (3817810-3817225)
	6-366, gnl\|oryCun1\|scaffold_84320 (2750-2258)
	6-366, gnl\|panTro1\|chr13 (105542065-105542568)
	6-366, gnl\|rheMac2\|chr12 (78519414-78519915)
	6-366, gnl\|rn3\|chr2_random (2925464-2924998)

	397-576, gnl\|bosTau2\|chr3 (16919819-16919998)
	397-576, gnl\|canFam2\|chr17 (62883119-62883427)
	397-576, gnl\|canFam2\|chr17 (62883192-62883427)
	397-576, gnl\|canFam2\|chr17 (62883427-62883119)
	397-576, gnl\|dasNov1\|scaffold_50290 (3646-3932)
	397-576, gnl\|dasNov1\|scaffold_50290 (3719-3932)
	397-576, gnl\|dasNov1\|scaffold_50290 (3932-3646)
	397-576, gnl\|echTel1\|scaffold_324356 (181478-181197)
	397-576, gnl\|echTel1\|scaffold_324356 (181421-181197)
	397-576, gnl\|echTel1\|scaffold_324356 (181197-181478)
	397-576, gnl\|hg17\|chr1 (147410381-147410616)
	397-576, gnl\|Hg17\|chr1 (147410577-147410400)
	397-576, gnl\|hg17\|chr14 (82227923-82228229)
	397-576, gnl\|hg17\|chr2 (215388864-215389171)
	397-576, gnl\|mm7\|chr3 (95503486-95503187)
	397-576, gnl\|mm7\|chr3 (95503421-95503187)
	397-576, gnl\|mm7\|chr3 (95503187-95503486)
	397-576, gnl\|Mm7\|chr3 (95503228-95503401)
	397-576, gnl\|monDom2\|scaffold_44 (3816991-3817218)
	397-576, gnl\|monDom2\|scaffold_44 (3817052-3817218)
	397-576, gnl\|monDom2\|scaffold_44 (3817224-3816991)
	397-576, gnl\|oryCun1\|scaffold_202897 (52551-52313)
	397-576, gnl\|oryCun1\|scaffold_84320 (1966-2257)
	397-576, gnl\|oryCun1\|scaffold_84320 (2257-1967)
	397-576, gnl\|panTro1\|chr1 (129141309-129141544)
	397-576, gnl\|panTro1\|chr13 (105542569-105542874)
	397-576, gnl\|panTro1\|chr15 (82342848-82343153)
	397-576, gnl\|rheMac2\|chr1 (129019351-129019657)
	397-576, gnl\|rheMac2\|chr1 (129019422-129019657)
	397-576, gnl\|rheMac2\|chr12 (78519916-78520225)
	397-576, gnl\|rn3\|chr2_random (2924700-2924997)
	397-576, gnl\|rn3\|chr2_random (2924764-2924997)
	397-576, gnl\|rn3\|chr2_random (2924997-2924700)