Non-Coding RNA Search

Ss1.1-Tra1-TCH01E120020.5

Sequence:


               
               CCCCGCCCCCACCACGTCCCTCCGTCCAGCCACCATTGCCACCAGGAGAACCACTACGTG
CAGCCCACCGCTACCCACCCCTCACAGGGTTGGGCCTAACCTGGTCCCCTGCAGTTAGTT
TCTAGAATCTACCATGCTTCTGTGAGAGCCGCCTTCCCCAACACCTCAGTTCTCCTGGCC
TCAAAACCCACAAAGTTTCCCCCAAATCTGCCCCATGGAAGCTGGCAGGTGCCAGGGTGG
TGGAGGGATTGTGGCAGGGGCCAGAATTCCCTGCCTAATAGGTGGAGCCCCTCCCCCAGC
CTCCCAGAGAATGCTCTCCTGCCCAGGACACAGAGAGCTTTCTGACCCTTTTCCCCAGAA
AAAGAGACTAGATTGCCTTCGTTTTGATGTTTGTGGCCTCAGAATTGATCATTTCCTGTC
TTCCCCCTCCCGGACCTGGGCTCCCCTTCCTTTCATGCCCACCCTCCAAGAGCTACTTAG
GGCCACTTCTGACTAATTACGGATTCAGGCTGCTTGGGAGAAAGTAAAAAGGACCAGGAC
CCTCTCCCCACCTCTGGCCTGGCCAAAGTCCCTACCCCCAAATCCCAGTGTCCACTAGAG
GCCTCTGGCTAGAGGTCAGCCCCACCTGGGATGGAGGGGGCTGTAGCTGCAGGAAGCACC
CCACGCCAAAGCTCGGGTGGCCCTCGCGGTTTAGCACCACCTCCGCTCCCTTCCCCTTCC
TCTTCCCCAGCTCCCATGACCATGACTGAGGGACCAACTGGGCCCTAGACAGGTGCCCCA
GAGCTGTTTATGGCCTCAGCTGCCTCACTTCCTGCAAGGAGATCAGCCTGTGGCATCTTT
GCCTTGGGCTGCTGCCCATGGGGGTCAGGAGCCTCAGCCAGAGGTGAGGGGAGCTACAGG
GAGCAGCTGTGGGAGCCCTAGGGTCTTCCCTACCTCAGGCAGGAAGGGCAGGAAGGAGAG
CCTCATGCTGCCGTGAAGGGAGGGCTGCTGGAGGGGCCAGACCTGCCTGCCTGGCCCAAA
CGATTTGTGCACCACCCTCGTTCAGCCTGGGCAGCCGGGCTGCCGAGGTCAGAGTGGCCT
GGCCAGGAGCTCTTCAGGCCTCCTTCTCTCCTCTGCTCCACCCATGGCCTGTCTCATCCC
TGGGGGTCCCGGCCTAGCCCCGGCCACCCCGGGCTCTCTGCTGTACATATTTGAGACTAG
TTTTTATTCCTTGTGAAGATGATATACTATTTTTGTTAAGCGTGTCTGTATTTATGTGTG
AGGAGCTGCTGGCTTGCTGTGCGTGTGCACGTGGAGAGCTGGTGCCCGGAGGTCAAACAG
CCTGATGCTCCCTCCCCTGCCCTGGTCCGGGGAAGCCAGCCGGGGGTCCTGGCTCCTGAG
GGACACCTGTCCCTCCCCCAACCCCCACCCCACACTTGTTCCAGCTCTTTGAAATAGTCT
GTGTGAAGGTGAAAGTGCAGTTCAGTAATAAACTGTGTTGATTCAGTGAAAAAAAAAAAA
AAAAAAAAAAAA

Sequence:

Distiller database | Help | Less info

Blue-coloured subsequences are predicted RNA structures by RNAz


               
               CCCCGCCCCCACCACGTCCCTCCGTCCAGCCACCATTGCCACCAGGAGAACCACTACGTG
CAGCCCACCGCTACCCACCCCTCACAGGGTTGGGCCTAACCTGGTCCCCTGCAGTTAGTT
TCTAGAATCTACCATGCTTCTGTGAGAGCCGCCTTCCCCAACACCTCAGTTCTCCTGGCC
TCAAAACCCACAAAGTTTCCCCCAAATCTGCCCCATGGAAGCTGGCAGGTGCCAGGGTGG
TGGAGGGATTGTGGCAGGGGCCAGAATTCCCTGCCTAATAGGTGGAGCCCCTCCCCCAGC
CTCCCAGAGAATGCTCTCCTGCCCAGGACACAGAGAGCTTTCTGACCCTTTTCCCCAGAA
AAAGAGACTAGATTGCCTTCGTTTTGATGTTTGTGGCCTCAGAATTGATCATTTCCTGTC
TTCCCCCTCCCGGACCTGGGCTCCCCTTCCTTTCATGCCCACCCTCCAAGAGCTACTTAG
GGCCACTTCTGACTAATTACGGATTCAGGCTGCTTGGGAGAAAGTAAAAAGGACCAGGAC
CCTCTCCCCACCTCTGGCCTGGCCAAAGTCCCTACCCCCAAATCCCAGTGTCCACTAGAG
GCCTCTGGCTAGAGGTCAGCCCCACCTGGGATGGAGGGGGCTGTAGCTGCAGGAAGCACC
CCACGCCAAAGCTCGGGTGGCCCTCGCGGTTTAGCACCACCTCCGCTCCCTTCCCCTTCC
TCTTCCCCAGCTCCCATGACCATGACTGAGGGACCAACTGGGCCCTAGACAGGTGCCCCA
GAGCTGTTTATGGCCTCAGCTGCCTCACTTCCTGCAAGGAGATCAGCCTGTGGCATCTTT
GCCTTGGGCTGCTGCCCATGGGGGTCAGGAGCCTCAGCCAGAGGTGAGGGGAGCTACAGG
GAGCAGCTGTGGGAGCCCTAGGGTCTTCCCTACCTCAGGCAGGAAGGGCAGGAAGGAGAG
CCTCATGCTGCCGTGAAGGGAGGGCTGCTGGAGGGGCCAGACCTGCCTGCCTGGCCCAAA
CGATTTGTGCACCACCCTCGTTCAGCCTGGGCAGCCGGGCTGCCGAGGTCAGAGTGGCCT
GGCCAGGAGCTCTTCAGGCCTCCTTCTCTCCTCTGCTCCACCCATGGCCTGTCTCATCCC
TGGGGGTCCCGGCCTAGCCCCGGCCACCCCGGGCTCTCTGCTGTACATATTTGAGACTAG
TTTTTATTCCTTGTGAAGATGATATACTATTTTTGTTAAGCGTGTCTGTATTTATGTGTG
AGGAGCTGCTGGCTTGCTGTGCGTGTGCACGTGGAGAGCTGGTGCCCGGAGGTCAAACAG
CCTGATGCTCCCTCCCCTGCCCTGGTCCGGGGAAGCCAGCCGGGGGTCCTGGCTCCTGAG
GGACACCTGTCCCTCCCCCAACCCCCACCCCACACTTGTTCCAGCTCTTTGAAATAGTCT
GTGTGAAGGTGAAAGTGCAGTTCAGTAATAAACTGTGTTGATTCAGTGAAAAAAAAAAAA
AAAAAAAAAAAA

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

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

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               238-352, - strand, RNAz p=0.999468
               

               
               617-1202, - strand, RNAz p=0.999963
               

               
               1323-1462, - strand, RNAz p=0.966477

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


               
               238-352, - strand, RNAz p=0.999468
               

               
               617-1202, - strand, RNAz p=0.999963
               

               
               1323-1462, - strand, RNAz p=0.966477

Similar Transcript(s): 6 entry(ies)

More info

Similar Transcript(s): 6 entry(ies)

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               617-850, BP167895 full-length enriched swine cDNA library, adult thymus Sus 
(dbj|BP167895.1|), blast E-value=0, identity=100% 
               

               
               617-1069, CJ023922 full-length enriched swine cDNA library, adult trachea Sus 
(dbj|CJ023922.1|), blast E-value=0, identity=100% 
               

               
               617-1161, CJ026492 full-length enriched swine cDNA library, adult trachea Sus 
(dbj|CJ026492.1|), blast E-value=0, identity=99.82% 
               

               
               927-1202, DB818803 full-length enriched swine cDNA library, adult thymus Sus 
(dbj|DB818803.1|), blast E-value=0, identity=98.55% 
               

               
               734-1202, LB02527.CR_E21 GC_BGC-25 Bos taurus cDNA clone IMAGE (gb|DV875411.1|), 
blast E-value=0, identity=88.94% 
               

               
               734-963, 000923BEMN016630HT BEMN Bos taurus cDNA, mRNA sequence 
(gb|DY084513.1|), blast E-value=0, identity=92.24%

Similar Transcript(s): 6 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


               
               617-850, BP167895 full-length enriched swine cDNA library, adult thymus Sus 
(dbj|BP167895.1|), blast E-value=0, identity=100% 
               

               
               617-1069, CJ023922 full-length enriched swine cDNA library, adult trachea Sus 
(dbj|CJ023922.1|), blast E-value=0, identity=100% 
               

               
               617-1161, CJ026492 full-length enriched swine cDNA library, adult trachea Sus 
(dbj|CJ026492.1|), blast E-value=0, identity=99.82% 
               

               
               927-1202, DB818803 full-length enriched swine cDNA library, adult thymus Sus 
(dbj|DB818803.1|), blast E-value=0, identity=98.55% 
               

               
               734-1202, LB02527.CR_E21 GC_BGC-25 Bos taurus cDNA clone IMAGE (gb|DV875411.1|), 
blast E-value=0, identity=88.94% 
               

               
               734-963, 000923BEMN016630HT BEMN Bos taurus cDNA, mRNA sequence 
(gb|DY084513.1|), blast E-value=0, identity=92.24%

Aligned organism(s): 3 entry(ies)

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Aligned organism(s): 3 entry(ies)

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               2-1494, gnl|bosTau2|chr13 (43374431-43372938)
               

               
               2-1494, gnl|Hg17|chr20 (29717374-29715918)
               

               
               2-1494, gnl|Mm7|chr2 (152522964-152521521)

Aligned organism(s): 3 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


               
               2-1494, gnl|bosTau2|chr13 (43374431-43372938)
               

               
               2-1494, gnl|Hg17|chr20 (29717374-29715918)
               

               
               2-1494, gnl|Mm7|chr2 (152522964-152521521)

Expressed library(ies): 10 entry(ies)

More info

Expressed library(ies): 10 entry(ies)

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               nbm (0.496623)
               

               
               ece (0.45861)
               

               
               cga (0.279096)
               

               
               cly (0.241284)
               

               
               fhi (0.169578)
               

               
               eli (0.151814)
               

               
               lnt (0.142308)
               

               
               pla (0.133672)
               

               
               pgl (0.118483)
               

               
               med (0.116252)

Expressed library(ies): 10 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


               
               nbm (0.496623)
               

               
               ece (0.45861)
               

               
               cga (0.279096)
               

               
               cly (0.241284)
               

               
               fhi (0.169578)
               

               
               eli (0.151814)
               

               
               lnt (0.142308)
               

               
               pla (0.133672)
               

               
               pgl (0.118483)
               

               
               med (0.116252)

	238-352, - strand, RNAz p=0.999468
	617-1202, - strand, RNAz p=0.999963
	1323-1462, - strand, RNAz p=0.966477

	617-850, BP167895 full-length enriched swine cDNA library, adult thymus Sus (dbj\|BP167895.1\|), blast E-value=0, identity=100%
	617-1069, CJ023922 full-length enriched swine cDNA library, adult trachea Sus (dbj\|CJ023922.1\|), blast E-value=0, identity=100%
	617-1161, CJ026492 full-length enriched swine cDNA library, adult trachea Sus (dbj\|CJ026492.1\|), blast E-value=0, identity=99.82%
	927-1202, DB818803 full-length enriched swine cDNA library, adult thymus Sus (dbj\|DB818803.1\|), blast E-value=0, identity=98.55%
	734-1202, LB02527.CR_E21 GC_BGC-25 Bos taurus cDNA clone IMAGE (gb\|DV875411.1\|), blast E-value=0, identity=88.94%
	734-963, 000923BEMN016630HT BEMN Bos taurus cDNA, mRNA sequence (gb\|DY084513.1\|), blast E-value=0, identity=92.24%

	2-1494, gnl\|bosTau2\|chr13 (43374431-43372938)
	2-1494, gnl\|Hg17\|chr20 (29717374-29715918)
	2-1494, gnl\|Mm7\|chr2 (152522964-152521521)

	nbm (0.496623)
	ece (0.45861)
	cga (0.279096)
	cly (0.241284)
	fhi (0.169578)
	eli (0.151814)
	lnt (0.142308)
	pla (0.133672)
	pgl (0.118483)
	med (0.116252)