Non-Coding RNA Search

Ss1.1-rpgl08_i17.5

Sequence:


               
               GTCGGAGGACTAAAGCCAAGGGTATCCAAGTTGGACTGGGTTGCGTCCTGACGGCGCCCC
CAGTGTGCACGAGTGGGAAGGACTTGGCTCGCCCTCCCTCGGCGCGGAGCCAGGGAGCGG
CAGCCCGCGGGCTGCCCCGCTTTGCGAACGGGCTGTCCCCGCGCAAACAGAACGTTAAGA
CTTTTCTTTAACACTGACCAAGAACTGCATGGACCTAACATTCGATCTCATTCAGTATTA
AGGGGGGGGAGGGGGGAGGGTTGCAAACTGCAATAGAGACTGTAGATTGCTTCTGTAGTA
CTCCTTAACACAAAGGGGGGGGTGGGGGAGGGGAGGCGGGAGGGAGGTTTGTGAGAGCGA
GGCCCAGCCTGCAGATGAACTCTTTCTGGCCTGCCTTCCATTACTGTGTATGTACATATA
TATATTTTTTAATTTGATGAAAGCTGATTACTGTCAATAAACAGCTTCATGCCTTTGTAA
GTTATTTCATGTTTGTTTGTTTGGGTGTCCTGCCCAGTTGTTGTTTGTAAATAAGAAATT
TTGAGCACTCTGAGTTTACCATTTGTAATAAAGTATATAATTTTTTTATGTTTTGTTTCT
GAAAATTCCAGAAAGGATATTTAAGAAAATACAATAAAATATTGAAAAAGTTACCCCTCC
AAAAAAAAAAAA

Sequence:

Distiller database | Help | Less info

Blue-coloured subsequences are predicted RNA structures by RNAz


               
               GTCGGAGGACTAAAGCCAAGGGTATCCAAGTTGGACTGGGTTGCGTCCTGACGGCGCCCC
CAGTGTGCACGAGTGGGAAGGACTTGGCTCGCCCTCCCTCGGCGCGGAGCCAGGGAGCGG
CAGCCCGCGGGCTGCCCCGCTTTGCGAACGGGCTGTCCCCGCGCAAACAGAACGTTAAGA
CTTTTCTTTAACACTGACCAAGAACTGCATGGACCTAACATTCGATCTCATTCAGTATTA
AGGGGGGGGAGGGGGGAGGGTTGCAAACTGCAATAGAGACTGTAGATTGCTTCTGTAGTA
CTCCTTAACACAAAGGGGGGGGTGGGGGAGGGGAGGCGGGAGGGAGGTTTGTGAGAGCGA
GGCCCAGCCTGCAGATGAACTCTTTCTGGCCTGCCTTCCATTACTGTGTATGTACATATA
TATATTTTTTAATTTGATGAAAGCTGATTACTGTCAATAAACAGCTTCATGCCTTTGTAA
GTTATTTCATGTTTGTTTGTTTGGGTGTCCTGCCCAGTTGTTGTTTGTAAATAAGAAATT
TTGAGCACTCTGAGTTTACCATTTGTAATAAAGTATATAATTTTTTTATGTTTTGTTTCT
GAAAATTCCAGAAAGGATATTTAAGAAAATACAATAAAATATTGAAAAAGTTACCCCTCC
AAAAAAAAAAAA

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

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

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               80-197, - strand, RNAz p=0.513022
               

               
               314-427, + strand, RNAz p=0.999127

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


               
               80-197, - strand, RNAz p=0.513022
               

               
               314-427, + strand, RNAz p=0.999127

Predicted microRNA(s): 2 entry(ies)

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Predicted microRNA(s): 2 entry(ies)

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               328-421, + strand, RNAmicro p=0.999996
               

               
               56-153, + strand, RNAmicro p=0.970679

Predicted microRNA(s): 2 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


               
               328-421, + strand, RNAmicro p=0.999996
               

               
               56-153, + strand, RNAmicro p=0.970679

Similar Transcript(s): 6 entry(ies)

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Similar Transcript(s): 6 entry(ies)

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               334-427, AJ691430 KN261 Bos taurus cDNA clone KN261-024_G18, mRNA sequence 
(emb|AJ691430.1|), blast E-value=6e-40, identity=97.87% 
               

               
               334-427, 245447 MARC 2BOV Bos taurus cDNA 5', mRNA sequence (gb|BF193765.1|), 
blast E-value=6e-40, identity=97.87% 
               

               
               334-427, 531039 MARC 3BOV Bos taurus cDNA 5', mRNA sequence (gb|BM480462.1|), 
blast E-value=6e-40, identity=97.87% 
               

               
               334-427, UMC-bend_0A02-024-g03 Day 16 Uterus from a pregnant animal bend Bos 
(gb|CO727846.1|), blast E-value=6e-40, identity=97.87% 
               

               
               334-427, 001004BEMN037741HT BEMN Bos taurus cDNA, mRNA sequence 
(gb|DY094874.1|), blast E-value=6e-40, identity=97.87% 
               

               
               337-427, PADT0811028_O01F porcine adipose tissue cDNA library (PADT) Sus 
(gb|EB422410.1|), blast E-value=7.00649e-43, identity=100%

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


               
               334-427, AJ691430 KN261 Bos taurus cDNA clone KN261-024_G18, mRNA sequence 
(emb|AJ691430.1|), blast E-value=6e-40, identity=97.87% 
               

               
               334-427, 245447 MARC 2BOV Bos taurus cDNA 5', mRNA sequence (gb|BF193765.1|), 
blast E-value=6e-40, identity=97.87% 
               

               
               334-427, 531039 MARC 3BOV Bos taurus cDNA 5', mRNA sequence (gb|BM480462.1|), 
blast E-value=6e-40, identity=97.87% 
               

               
               334-427, UMC-bend_0A02-024-g03 Day 16 Uterus from a pregnant animal bend Bos 
(gb|CO727846.1|), blast E-value=6e-40, identity=97.87% 
               

               
               334-427, 001004BEMN037741HT BEMN Bos taurus cDNA, mRNA sequence 
(gb|DY094874.1|), blast E-value=6e-40, identity=97.87% 
               

               
               337-427, PADT0811028_O01F porcine adipose tissue cDNA library (PADT) Sus 
(gb|EB422410.1|), blast E-value=7.00649e-43, identity=100%

Homologous human UTR: 1 entry(ies)

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Homologous human UTR: 1 entry(ies)

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               5' of NM_002228, +

Homologous human UTR: 1 entry(ies)

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Human gene identifier and UTR site,
human gene reading direction


               
               5' of NM_002228, +

Aligned organism(s): 3 entry(ies)

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Aligned organism(s): 3 entry(ies)

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               1-660, gnl|bosTau2|chr3 (65484463-65485123)
               

               
               1-660, gnl|Hg17|chr1 (58959668-58959009)
               

               
               1-660, gnl|Mm7|chr4 (94442779-94442137)

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


               
               1-660, gnl|bosTau2|chr3 (65484463-65485123)
               

               
               1-660, gnl|Hg17|chr1 (58959668-58959009)
               

               
               1-660, gnl|Mm7|chr4 (94442779-94442137)

Expressed library(ies): 13 entry(ies)

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Expressed library(ies): 13 entry(ies)

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               bla (0.248694)
               

               
               pgl (0.236967)
               

               
               ece (0.229305)
               

               
               nms (0.213858)
               

               
               hea (0.204499)
               

               
               sto (0.179824)
               

               
               nco (0.161734)
               

               
               ctl (0.153069)
               

               
               cag (0.151194)
               

               
               hlv (0.139256)
               

               
               ute (0.132784)
               

               
               ecc (0.115035)
               

               
               ldo (0.0970026)

Expressed library(ies): 13 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


               
               bla (0.248694)
               

               
               pgl (0.236967)
               

               
               ece (0.229305)
               

               
               nms (0.213858)
               

               
               hea (0.204499)
               

               
               sto (0.179824)
               

               
               nco (0.161734)
               

               
               ctl (0.153069)
               

               
               cag (0.151194)
               

               
               hlv (0.139256)
               

               
               ute (0.132784)
               

               
               ecc (0.115035)
               

               
               ldo (0.0970026)

	80-197, - strand, RNAz p=0.513022
	314-427, + strand, RNAz p=0.999127

	328-421, + strand, RNAmicro p=0.999996
	56-153, + strand, RNAmicro p=0.970679

	334-427, AJ691430 KN261 Bos taurus cDNA clone KN261-024_G18, mRNA sequence (emb\|AJ691430.1\|), blast E-value=6e-40, identity=97.87%
	334-427, 245447 MARC 2BOV Bos taurus cDNA 5', mRNA sequence (gb\|BF193765.1\|), blast E-value=6e-40, identity=97.87%
	334-427, 531039 MARC 3BOV Bos taurus cDNA 5', mRNA sequence (gb\|BM480462.1\|), blast E-value=6e-40, identity=97.87%
	334-427, UMC-bend_0A02-024-g03 Day 16 Uterus from a pregnant animal bend Bos (gb\|CO727846.1\|), blast E-value=6e-40, identity=97.87%
	334-427, 001004BEMN037741HT BEMN Bos taurus cDNA, mRNA sequence (gb\|DY094874.1\|), blast E-value=6e-40, identity=97.87%
	337-427, PADT0811028_O01F porcine adipose tissue cDNA library (PADT) Sus (gb\|EB422410.1\|), blast E-value=7.00649e-43, identity=100%

	1-660, gnl\|bosTau2\|chr3 (65484463-65485123)
	1-660, gnl\|Hg17\|chr1 (58959668-58959009)
	1-660, gnl\|Mm7\|chr4 (94442779-94442137)

	bla (0.248694)
	pgl (0.236967)
	ece (0.229305)
	nms (0.213858)
	hea (0.204499)
	sto (0.179824)
	nco (0.161734)
	ctl (0.153069)
	cag (0.151194)
	hlv (0.139256)
	ute (0.132784)
	ecc (0.115035)
	ldo (0.0970026)