Non-Coding RNA Search

Ss1.1-rmed03c_n7.5

Sequence:


               
               CAGGTCTAGAGGCAGCTCCTGAGACATAACATTGCAAACGAAGGGCTCTGGGGGATTCAG
AAGGTTACTGAGTAAGTTACTGGACGTCCTCCTATGGGAAGCTGGTCACACAGGCAAGTT
AGATATTGGGGTTCATTTCATTCATTCCAGTTGCTGCTTGGAATAAGGAACTAGAAGGCT
GCTCCCCACAGTGTGAAAGCCTTTCACTCCTGCCTTCTAGCCTCAAGCGTACTACCCTGA
CTATGGATTCCTGCTCTGCCCTGTCTATCCGTTTTTTCCTGCCGGTTCTATCTCCTCCCT
GAGGTTTTTCCTTTCTCTCTGGAGGGCAGGCCTCCTTTGGGAGTATGCAAAGGCAGTGAT
GGCTGCTGCTCTACAGGCAGCTTCCTCTCCCACAGTCAGAATGCTCAGGGTCACTGAACC
ACTGTTTCTCTTCACAAAGGTGAGCTAGCTGCCACCTCCACGTGGCCTCCAGAGTCTCCA
CCTGCACCCTTGTGCTCCCCTGCCACTCCAATGATTCAAGACAAGGCGGGCAAACCCTCC
TAGAAACATCCCGGGCACGGGCATCCTTTCTCATAAGGCACAGCCAAGCCAAATGCTCAC
GTTGTGCCAGTGAGTCAGCCACAGAGCAAAAGAGGGTTTGTGGTTAGTCTCCTCTATCTG
GGTCAGAACCAGAGAGCAGGCTGGATGCCCCCTGCTTGCTCGGTAAGCCTGCCCAGCCTG
AGTCAATGCTCACGGCTGACAGTGCAATGCTTGCAGAAACAGGAGGGAGCCCGGTCTTCA
CTGGGAAGCACAAGAGGCCAAGACAAGTTCCAAAGTGCCTCACTCGAAAGGGAACCCTGT
CCCCTGGAGCTAGGGTGTACCACAAAGCTTTGGCTGAGTCTTGGGCTGAACAGCGTCTCT
GTTCAGCAAACTAACCAGCATTCCCTACAGCACAGCCCAAGGCAGACAAGAGAATAGAAG
AGGGCTGGAAAACAAAAAATAAGAACCTTGGCCCACTCCTGTCCCTGTAACCTCAGTCGT
CAACACAGAAGCCTGTCTTTACTCTAAAGATTGGAAATATACAATACCAGATGCTCTGTC
CACTGTTGAGCCCCAGGAGTGGAAGGGCAGAGAGCA

Sequence:

Distiller database | Help | Less info

Blue-coloured subsequences are predicted RNA structures by RNAz


               
               CAGGTCTAGAGGCAGCTCCTGAGACATAACATTGCAAACGAAGGGCTCTGGGGGATTCAG
AAGGTTACTGAGTAAGTTACTGGACGTCCTCCTATGGGAAGCTGGTCACACAGGCAAGTT
AGATATTGGGGTTCATTTCATTCATTCCAGTTGCTGCTTGGAATAAGGAACTAGAAGGCT
GCTCCCCACAGTGTGAAAGCCTTTCACTCCTGCCTTCTAGCCTCAAGCGTACTACCCTGA
CTATGGATTCCTGCTCTGCCCTGTCTATCCGTTTTTTCCTGCCGGTTCTATCTCCTCCCT
GAGGTTTTTCCTTTCTCTCTGGAGGGCAGGCCTCCTTTGGGAGTATGCAAAGGCAGTGAT
GGCTGCTGCTCTACAGGCAGCTTCCTCTCCCACAGTCAGAATGCTCAGGGTCACTGAACC
ACTGTTTCTCTTCACAAAGGTGAGCTAGCTGCCACCTCCACGTGGCCTCCAGAGTCTCCA
CCTGCACCCTTGTGCTCCCCTGCCACTCCAATGATTCAAGACAAGGCGGGCAAACCCTCC
TAGAAACATCCCGGGCACGGGCATCCTTTCTCATAAGGCACAGCCAAGCCAAATGCTCAC
GTTGTGCCAGTGAGTCAGCCACAGAGCAAAAGAGGGTTTGTGGTTAGTCTCCTCTATCTG
GGTCAGAACCAGAGAGCAGGCTGGATGCCCCCTGCTTGCTCGGTAAGCCTGCCCAGCCTG
AGTCAATGCTCACGGCTGACAGTGCAATGCTTGCAGAAACAGGAGGGAGCCCGGTCTTCA
CTGGGAAGCACAAGAGGCCAAGACAAGTTCCAAAGTGCCTCACTCGAAAGGGAACCCTGT
CCCCTGGAGCTAGGGTGTACCACAAAGCTTTGGCTGAGTCTTGGGCTGAACAGCGTCTCT
GTTCAGCAAACTAACCAGCATTCCCTACAGCACAGCCCAAGGCAGACAAGAGAATAGAAG
AGGGCTGGAAAACAAAAAATAAGAACCTTGGCCCACTCCTGTCCCTGTAACCTCAGTCGT
CAACACAGAAGCCTGTCTTTACTCTAAAGATTGGAAATATACAATACCAGATGCTCTGTC
CACTGTTGAGCCCCAGGAGTGGAAGGGCAGAGAGCA

Predicted RNA structure(s): 3 entry(ies)

More info

Predicted RNA structure(s): 3 entry(ies)

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               394-737, - strand, RNAz p=0.998434
               

               
               521-730, - strand, RNAz p=0.994664
               

               
               764-888, - strand, RNAz p=0.998753

Predicted RNA structure(s): 3 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


               
               394-737, - strand, RNAz p=0.998434
               

               
               521-730, - strand, RNAz p=0.994664
               

               
               764-888, - strand, RNAz p=0.998753

Similar Transcript(s): 6 entry(ies)

More info

Similar Transcript(s): 6 entry(ies)

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               569-730, DKFZp459J1224_r1 459 (synonym (emb|CR544679.1|), blast 
E-value=4.99983e-42, identity=88.89% 
               

               
               521-730, LB0285.CR_E16 GC_BGC-28 Bos taurus cDNA clone IMAGE (gb|DV914676.1|), 
blast E-value=8e-38, identity=85.71% 
               

               
               521-726, 000330BMPA004817HT BMPA Bos taurus cDNA, mRNA sequence 
(gb|DY138846.1|), blast E-value=8e-38, identity=85.92% 
               

               
               532-730, PADT0811026_N08R porcine adipose tissue cDNA library (PADT) Sus 
(gb|EB421648.1|), blast E-value=0, identity=99.5% 
               

               
               525-730, PADT0811027_M22R porcine adipose tissue cDNA library (PADT) Sus 
(gb|EB422097.1|), blast E-value=0, identity=98.06% 
               

               
               521-730, LB02538.CR_O02 GC_BGC-25 Bos taurus cDNA clone IMAGE (gb|EE342064.1|), 
blast E-value=8e-38, identity=85.71%

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


               
               569-730, DKFZp459J1224_r1 459 (synonym (emb|CR544679.1|), blast 
E-value=4.99983e-42, identity=88.89% 
               

               
               521-730, LB0285.CR_E16 GC_BGC-28 Bos taurus cDNA clone IMAGE (gb|DV914676.1|), 
blast E-value=8e-38, identity=85.71% 
               

               
               521-726, 000330BMPA004817HT BMPA Bos taurus cDNA, mRNA sequence 
(gb|DY138846.1|), blast E-value=8e-38, identity=85.92% 
               

               
               532-730, PADT0811026_N08R porcine adipose tissue cDNA library (PADT) Sus 
(gb|EB421648.1|), blast E-value=0, identity=99.5% 
               

               
               525-730, PADT0811027_M22R porcine adipose tissue cDNA library (PADT) Sus 
(gb|EB422097.1|), blast E-value=0, identity=98.06% 
               

               
               521-730, LB02538.CR_O02 GC_BGC-25 Bos taurus cDNA clone IMAGE (gb|EE342064.1|), 
blast E-value=8e-38, identity=85.71%

Aligned organism(s): 13 entry(ies)

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Aligned organism(s): 13 entry(ies)

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               241-888, gnl|bosTau2|chr26 (12716874-12717519)
               

               
               241-888, gnl|canFam2|chr28 (16122916-16123622)
               

               
               241-888, gnl|dasNov1|scaffold_25440 (2574-1924)
               

               
               241-888, gnl|echTel1|scaffold_279548 (48112-47475)
               

               
               241-888, gnl|Hg17|chr10 (102112217-102112874)
               

               
               241-888, gnl|hg17|chr17 (20631000-20631728)
               

               
               241-888, gnl|loxAfr1|scaffold_10678 (8855-8105)
               

               
               241-888, gnl|mm7|chr19 (44290562-44289948)
               

               
               241-888, gnl|monDom2|scaffold_41 (10613287-10613852)
               

               
               241-888, gnl|oryCun1|scaffold_163381 (16297-16954)
               

               
               241-888, gnl|panTro1|chr19_random (5536795-5536068)
               

               
               241-888, gnl|rheMac2|chr3 (134751277-134752017)
               

               
               241-888, gnl|rn3|chr1 (249719839-249719182)

Aligned organism(s): 13 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


               
               241-888, gnl|bosTau2|chr26 (12716874-12717519)
               

               
               241-888, gnl|canFam2|chr28 (16122916-16123622)
               

               
               241-888, gnl|dasNov1|scaffold_25440 (2574-1924)
               

               
               241-888, gnl|echTel1|scaffold_279548 (48112-47475)
               

               
               241-888, gnl|Hg17|chr10 (102112217-102112874)
               

               
               241-888, gnl|hg17|chr17 (20631000-20631728)
               

               
               241-888, gnl|loxAfr1|scaffold_10678 (8855-8105)
               

               
               241-888, gnl|mm7|chr19 (44290562-44289948)
               

               
               241-888, gnl|monDom2|scaffold_41 (10613287-10613852)
               

               
               241-888, gnl|oryCun1|scaffold_163381 (16297-16954)
               

               
               241-888, gnl|panTro1|chr19_random (5536795-5536068)
               

               
               241-888, gnl|rheMac2|chr3 (134751277-134752017)
               

               
               241-888, gnl|rn3|chr1 (249719839-249719182)

Expressed library(ies): 5 entry(ies)

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Expressed library(ies): 5 entry(ies)

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               cga (0.279096)
               

               
               ute (0.265569)
               

               
               jca (0.22792)
               

               
               cli (0.152812)
               

               
               med (0.116252)

Expressed library(ies): 5 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


               
               cga (0.279096)
               

               
               ute (0.265569)
               

               
               jca (0.22792)
               

               
               cli (0.152812)
               

               
               med (0.116252)

	394-737, - strand, RNAz p=0.998434
	521-730, - strand, RNAz p=0.994664
	764-888, - strand, RNAz p=0.998753

	569-730, DKFZp459J1224_r1 459 (synonym (emb\|CR544679.1\|), blast E-value=4.99983e-42, identity=88.89%
	521-730, LB0285.CR_E16 GC_BGC-28 Bos taurus cDNA clone IMAGE (gb\|DV914676.1\|), blast E-value=8e-38, identity=85.71%
	521-726, 000330BMPA004817HT BMPA Bos taurus cDNA, mRNA sequence (gb\|DY138846.1\|), blast E-value=8e-38, identity=85.92%
	532-730, PADT0811026_N08R porcine adipose tissue cDNA library (PADT) Sus (gb\|EB421648.1\|), blast E-value=0, identity=99.5%
	525-730, PADT0811027_M22R porcine adipose tissue cDNA library (PADT) Sus (gb\|EB422097.1\|), blast E-value=0, identity=98.06%
	521-730, LB02538.CR_O02 GC_BGC-25 Bos taurus cDNA clone IMAGE (gb\|EE342064.1\|), blast E-value=8e-38, identity=85.71%

	241-888, gnl\|bosTau2\|chr26 (12716874-12717519)
	241-888, gnl\|canFam2\|chr28 (16122916-16123622)
	241-888, gnl\|dasNov1\|scaffold_25440 (2574-1924)
	241-888, gnl\|echTel1\|scaffold_279548 (48112-47475)
	241-888, gnl\|Hg17\|chr10 (102112217-102112874)
	241-888, gnl\|hg17\|chr17 (20631000-20631728)
	241-888, gnl\|loxAfr1\|scaffold_10678 (8855-8105)
	241-888, gnl\|mm7\|chr19 (44290562-44289948)
	241-888, gnl\|monDom2\|scaffold_41 (10613287-10613852)
	241-888, gnl\|oryCun1\|scaffold_163381 (16297-16954)
	241-888, gnl\|panTro1\|chr19_random (5536795-5536068)
	241-888, gnl\|rheMac2\|chr3 (134751277-134752017)
	241-888, gnl\|rn3\|chr1 (249719839-249719182)

	cga (0.279096)
	ute (0.265569)
	jca (0.22792)
	cli (0.152812)
	med (0.116252)