Non-Coding RNA Search

Ss1.1-Pig4-TMW8042I03.3

Sequence:


               
               ATCAGACTCTGGTATCAGTGTTAGAATGTTCTTAAGTGCTGTTGCTTTTTAGGTATCAAT
TCCACTTGACATGGTAGAAGGTATTTTTCTCTTGTTACTCTAGTGTAAGGGGAAGGGTGG
CCTTAGGCATTACCAGCTGATATAGGTGGTCTAGCTGCCTTTCCTTGGTTACCTAGAGAG
CTGTCACCACTTACAAAACTATGATGCTTTTCTTCTCCAAGCGCATATTAACTGTATTGT
TGACAGATTGAGTCAGGATAATTGTCCTTGACTGTTGATCAGAAAAAAATTAATGGAATG
CTCTTTATTTCTCTAATTTTAAGAAATGGTGATAGGTGTCATATCCATTAATTTATTTTA
GCTCTTCTTAAGCGTCTCCGTTTATATCTATTCTCAGGGTTATAACTCCATGTTTACCAT
CATCCGCAAAAAGGTACCAAAAAAATCCATAAATAAATATGGAATGTATTCATAAATACA
TCAGTTCTTTTGGTAAAATGATACTTTGACCATTTAGGCTTCATCAGTAGAACTATTCTT
ATTTTTTGGACTGAATTAACTGAATTGATTGGCTGGTCAACCAATTCCTAACATTTCATT
TTGTCCCAAATGGTGAGATTCTTGTGTGTAGAAACAGTATTTTGGTTTCATCTGAAAAAA
GAGGAGAATTGGCCTGATGACTTTGAAGCATGAAAGCATGATTGGCAATGGTAGCTTCTT
GAGTTCTGAAGTTAAAACCAAGGGATTATAGAGAGAATCATTTTTATGGGTTTTTTTGGT
CATGGTGCTATTCCTAAGGTTAATTTTGAATATGTGACACACACTCCTAAGTATCTTTAA
GAAAAACCAATAAATAATTAATACTTCAAAATGTTTACATTGAGCACTAGAACACGGTTG
ACTTTTTTCTATTTCTGTTTATGCGAAATGAGCAGGGATTTAATGCACAGATGTACTTTA
ATATGTTTGGGATCAGTTTGTATTTTTCTCATGAGAAAAGATAAAAAGTTAAAAATTGAT
TGTGAACTGATCCAGAAGTAAGTGCTATAGCTTTCCATTGCACTTGAAGTAACTTAATGA

Sequence:

Distiller database | Help | Less info

Blue-coloured subsequences are predicted RNA structures by RNAz


               
               ATCAGACTCTGGTATCAGTGTTAGAATGTTCTTAAGTGCTGTTGCTTTTTAGGTATCAAT
TCCACTTGACATGGTAGAAGGTATTTTTCTCTTGTTACTCTAGTGTAAGGGGAAGGGTGG
CCTTAGGCATTACCAGCTGATATAGGTGGTCTAGCTGCCTTTCCTTGGTTACCTAGAGAG
CTGTCACCACTTACAAAACTATGATGCTTTTCTTCTCCAAGCGCATATTAACTGTATTGT
TGACAGATTGAGTCAGGATAATTGTCCTTGACTGTTGATCAGAAAAAAATTAATGGAATG
CTCTTTATTTCTCTAATTTTAAGAAATGGTGATAGGTGTCATATCCATTAATTTATTTTA
GCTCTTCTTAAGCGTCTCCGTTTATATCTATTCTCAGGGTTATAACTCCATGTTTACCAT
CATCCGCAAAAAGGTACCAAAAAAATCCATAAATAAATATGGAATGTATTCATAAATACA
TCAGTTCTTTTGGTAAAATGATACTTTGACCATTTAGGCTTCATCAGTAGAACTATTCTT
ATTTTTTGGACTGAATTAACTGAATTGATTGGCTGGTCAACCAATTCCTAACATTTCATT
TTGTCCCAAATGGTGAGATTCTTGTGTGTAGAAACAGTATTTTGGTTTCATCTGAAAAAA
GAGGAGAATTGGCCTGATGACTTTGAAGCATGAAAGCATGATTGGCAATGGTAGCTTCTT
GAGTTCTGAAGTTAAAACCAAGGGATTATAGAGAGAATCATTTTTATGGGTTTTTTTGGT
CATGGTGCTATTCCTAAGGTTAATTTTGAATATGTGACACACACTCCTAAGTATCTTTAA
GAAAAACCAATAAATAATTAATACTTCAAAATGTTTACATTGAGCACTAGAACACGGTTG
ACTTTTTTCTATTTCTGTTTATGCGAAATGAGCAGGGATTTAATGCACAGATGTACTTTA
ATATGTTTGGGATCAGTTTGTATTTTTCTCATGAGAAAAGATAAAAAGTTAAAAATTGAT
TGTGAACTGATCCAGAAGTAAGTGCTATAGCTTTCCATTGCACTTGAAGTAACTTAATGA

Predicted RNA structure(s): 4 entry(ies)

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Predicted RNA structure(s): 4 entry(ies)

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               80-397, - strand, RNAz p=0.998783
               

               
               396-553, - strand, RNAz p=0.70592
               

               
               435-620, - strand, RNAz p=0.99548
               

               
               930-1080, + strand, RNAz p=0.933561

Predicted RNA structure(s): 4 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


               
               80-397, - strand, RNAz p=0.998783
               

               
               396-553, - strand, RNAz p=0.70592
               

               
               435-620, - strand, RNAz p=0.99548
               

               
               930-1080, + strand, RNAz p=0.933561

Similar Transcript(s): 6 entry(ies)

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Similar Transcript(s): 6 entry(ies)

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               446-614, AJ815573 KN206 Bos sp. cDNA clone C0005198b21, mRNA sequence 
(emb|AJ815573.1|), blast E-value=5e-39, identity=86.98% 
               

               
               446-555, 226135 MARC 2BOV Bos taurus cDNA 5', mRNA sequence (gb|BF076546.1|), 
blast E-value=3e-37, identity=93.64% 
               

               
               446-614, 696350 MARC 6BOV Bos taurus cDNA 5', mRNA sequence (gb|CB445101.1|), 
blast E-value=5e-39, identity=86.98% 
               

               
               446-614, 696830 MARC 6BOV Bos taurus cDNA 3', mRNA sequence (gb|CB445471.1|), 
blast E-value=5e-39, identity=86.98% 
               

               
               446-614, 700281 MARC 6BOV Bos taurus cDNA 3', mRNA sequence (gb|CB446565.1|), 
blast E-value=5e-39, identity=86.98% 
               

               
               446-614, 000812BPSA001006HT BPSA Bos taurus cDNA, mRNA sequence 
(gb|DY141760.1|), blast E-value=5e-39, identity=86.98%

Similar Transcript(s): 6 entry(ies)

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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


               
               446-614, AJ815573 KN206 Bos sp. cDNA clone C0005198b21, mRNA sequence 
(emb|AJ815573.1|), blast E-value=5e-39, identity=86.98% 
               

               
               446-555, 226135 MARC 2BOV Bos taurus cDNA 5', mRNA sequence (gb|BF076546.1|), 
blast E-value=3e-37, identity=93.64% 
               

               
               446-614, 696350 MARC 6BOV Bos taurus cDNA 5', mRNA sequence (gb|CB445101.1|), 
blast E-value=5e-39, identity=86.98% 
               

               
               446-614, 696830 MARC 6BOV Bos taurus cDNA 3', mRNA sequence (gb|CB445471.1|), 
blast E-value=5e-39, identity=86.98% 
               

               
               446-614, 700281 MARC 6BOV Bos taurus cDNA 3', mRNA sequence (gb|CB446565.1|), 
blast E-value=5e-39, identity=86.98% 
               

               
               446-614, 000812BPSA001006HT BPSA Bos taurus cDNA, mRNA sequence 
(gb|DY141760.1|), blast E-value=5e-39, identity=86.98%

Homologous human UTR: 1 entry(ies)

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Homologous human UTR: 1 entry(ies)

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               5' of AB080587, +

Homologous human UTR: 1 entry(ies)

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Human gene identifier and UTR site,
human gene reading direction


               
               5' of AB080587, +

Aligned organism(s): 12 entry(ies)

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Aligned organism(s): 12 entry(ies)

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               1-1080, gnl|bosTau2|chr1 (89268218-89269309)
               

               
               1-1080, gnl|canFam2|chr31 (36290853-36291568)
               

               
               1-1080, gnl|dasNov1|scaffold_29498 (12532-13281)
               

               
               1-1080, gnl|echTel1|scaffold_208656 (7175-6514)
               

               
               1-1080, gnl|Hg17|chr21 (39488498-39487421)
               

               
               1-1080, gnl|hg17|chr3 (6496333-6497051)
               

               
               1-1080, gnl|loxAfr1|scaffold_1015 (104603-103925)
               

               
               1-1080, gnl|mm7|chr16 (96336792-96337358)
               

               
               1-1080, gnl|oryCun1|scaffold_191798 (19894-20560)
               

               
               1-1080, gnl|panTro1|chr2 (6712330-6713048)
               

               
               1-1080, gnl|rheMac2|chr2 (54495568-54494853)
               

               
               1-1080, gnl|rn3|chr11 (36358654-36359178)

Aligned organism(s): 12 entry(ies)

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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


               
               1-1080, gnl|bosTau2|chr1 (89268218-89269309)
               

               
               1-1080, gnl|canFam2|chr31 (36290853-36291568)
               

               
               1-1080, gnl|dasNov1|scaffold_29498 (12532-13281)
               

               
               1-1080, gnl|echTel1|scaffold_208656 (7175-6514)
               

               
               1-1080, gnl|Hg17|chr21 (39488498-39487421)
               

               
               1-1080, gnl|hg17|chr3 (6496333-6497051)
               

               
               1-1080, gnl|loxAfr1|scaffold_1015 (104603-103925)
               

               
               1-1080, gnl|mm7|chr16 (96336792-96337358)
               

               
               1-1080, gnl|oryCun1|scaffold_191798 (19894-20560)
               

               
               1-1080, gnl|panTro1|chr2 (6712330-6713048)
               

               
               1-1080, gnl|rheMac2|chr2 (54495568-54494853)
               

               
               1-1080, gnl|rn3|chr11 (36358654-36359178)

Expressed library(ies): 4 entry(ies)

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Expressed library(ies): 4 entry(ies)

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               tes (0.207814)
               

               
               fco (0.157208)
               

               
               lnt (0.142308)
               

               
               ret (0.128733)

Expressed library(ies): 4 entry(ies)

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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


               
               tes (0.207814)
               

               
               fco (0.157208)
               

               
               lnt (0.142308)
               

               
               ret (0.128733)

	80-397, - strand, RNAz p=0.998783
	396-553, - strand, RNAz p=0.70592
	435-620, - strand, RNAz p=0.99548
	930-1080, + strand, RNAz p=0.933561

	446-614, AJ815573 KN206 Bos sp. cDNA clone C0005198b21, mRNA sequence (emb\|AJ815573.1\|), blast E-value=5e-39, identity=86.98%
	446-555, 226135 MARC 2BOV Bos taurus cDNA 5', mRNA sequence (gb\|BF076546.1\|), blast E-value=3e-37, identity=93.64%
	446-614, 696350 MARC 6BOV Bos taurus cDNA 5', mRNA sequence (gb\|CB445101.1\|), blast E-value=5e-39, identity=86.98%
	446-614, 696830 MARC 6BOV Bos taurus cDNA 3', mRNA sequence (gb\|CB445471.1\|), blast E-value=5e-39, identity=86.98%
	446-614, 700281 MARC 6BOV Bos taurus cDNA 3', mRNA sequence (gb\|CB446565.1\|), blast E-value=5e-39, identity=86.98%
	446-614, 000812BPSA001006HT BPSA Bos taurus cDNA, mRNA sequence (gb\|DY141760.1\|), blast E-value=5e-39, identity=86.98%

	1-1080, gnl\|bosTau2\|chr1 (89268218-89269309)
	1-1080, gnl\|canFam2\|chr31 (36290853-36291568)
	1-1080, gnl\|dasNov1\|scaffold_29498 (12532-13281)
	1-1080, gnl\|echTel1\|scaffold_208656 (7175-6514)
	1-1080, gnl\|Hg17\|chr21 (39488498-39487421)
	1-1080, gnl\|hg17\|chr3 (6496333-6497051)
	1-1080, gnl\|loxAfr1\|scaffold_1015 (104603-103925)
	1-1080, gnl\|mm7\|chr16 (96336792-96337358)
	1-1080, gnl\|oryCun1\|scaffold_191798 (19894-20560)
	1-1080, gnl\|panTro1\|chr2 (6712330-6713048)
	1-1080, gnl\|rheMac2\|chr2 (54495568-54494853)
	1-1080, gnl\|rn3\|chr11 (36358654-36359178)