Non-Coding RNA Search

Ss1.1-rfbs3919b_k4.5

Sequence:


               
               CCTTAATTGGATGTCGTGCCCTTCCCAGCTCCCCATCCCTGTGCACATCTCCAGGCTCAT
CCGAGCAAGTGTGCTTTTGCAGCTCCCCTTCCTTAGCCAGAACTGCTCCCCTCACTTTCC
CCGGTCCCTTCTCCAGGTGATAATGCACTCAGGGGAAAGTTGCTCTGGCAGGTGGGAGAT
GCAGGACTTAAGAGTACATGCTGTCAGCCTTGAGAGGCAAGGGTAAAGATTGAAGTGAAA
TGAGGGCAAGTTGTACTCCCAGCCCTGGTGCTGCATCCCTGAGGGGCCAGCTTCCCGGTC
TCAAGCCAAATCTGCCTTAAATCAGAGGTAGGGGGGTTGGGGGGTATAAGCAATGAAGTG
GTTTTGTTTTTGTTTTGTTTGATCTTCATCTTTGTATTACAGGCATCTAGCAGAGTGCCT
AGCACATACAGGATGCTCAATAAAATTTTGATGAAATCAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAA

Sequence:

Distiller database | Help | Less info

Blue-coloured subsequences are predicted RNA structures by RNAz


               
               CCTTAATTGGATGTCGTGCCCTTCCCAGCTCCCCATCCCTGTGCACATCTCCAGGCTCAT
CCGAGCAAGTGTGCTTTTGCAGCTCCCCTTCCTTAGCCAGAACTGCTCCCCTCACTTTCC
CCGGTCCCTTCTCCAGGTGATAATGCACTCAGGGGAAAGTTGCTCTGGCAGGTGGGAGAT
GCAGGACTTAAGAGTACATGCTGTCAGCCTTGAGAGGCAAGGGTAAAGATTGAAGTGAAA
TGAGGGCAAGTTGTACTCCCAGCCCTGGTGCTGCATCCCTGAGGGGCCAGCTTCCCGGTC
TCAAGCCAAATCTGCCTTAAATCAGAGGTAGGGGGGTTGGGGGGTATAAGCAATGAAGTG
GTTTTGTTTTTGTTTTGTTTGATCTTCATCTTTGTATTACAGGCATCTAGCAGAGTGCCT
AGCACATACAGGATGCTCAATAAAATTTTGATGAAATCAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAA

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

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

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               196-330, - strand, RNAz p=0.989796
               

               
               266-467, - strand, RNAz p=0.998405

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


               
               196-330, - strand, RNAz p=0.989796
               

               
               266-467, - strand, RNAz p=0.998405

Predicted microRNA(s): 1 entry(ies)

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Predicted microRNA(s): 1 entry(ies)

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               277-349, + strand, RNAmicro p=0.962716

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


               
               277-349, + strand, RNAmicro p=0.962716

Similar Transcript(s): 6 entry(ies)

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Similar Transcript(s): 6 entry(ies)

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               381-457, BovGen_09123 normal cattle brain Bos taurus cDNA clone 
(gb|CO880798.1|), blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1242103 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb|DN287769.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1252732 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb|DN515481.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1373562 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb|DN537388.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, LB0196.CR_C03 GC_BGC-19 Bos taurus cDNA clone IMAGE (gb|DV834693.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1591889 MARC 11BOV Bos taurus cDNA 3', mRNA sequence (gb|DY459987.1|), 
blast E-value=1e-24, identity=94.81%

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


               
               381-457, BovGen_09123 normal cattle brain Bos taurus cDNA clone 
(gb|CO880798.1|), blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1242103 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb|DN287769.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1252732 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb|DN515481.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1373562 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb|DN537388.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, LB0196.CR_C03 GC_BGC-19 Bos taurus cDNA clone IMAGE (gb|DV834693.1|), 
blast E-value=1e-24, identity=94.81% 
               

               
               381-457, 1591889 MARC 11BOV Bos taurus cDNA 3', mRNA sequence (gb|DY459987.1|), 
blast E-value=1e-24, identity=94.81%

Homologous human UTR: 1 entry(ies)

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Homologous human UTR: 1 entry(ies)

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               5' of AY275431, -

Homologous human UTR: 1 entry(ies)

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Human gene identifier and UTR site,
human gene reading direction


               
               5' of AY275431, -

Aligned organism(s): 15 entry(ies)

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Aligned organism(s): 15 entry(ies)

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               1-147, gnl|bosTau2|chr29 (20703412-20703560)
               

               
               1-147, gnl|Hg17|chr11 (124294788-124294661)
               

               
               1-147, gnl|Mm7|chr9 (37314728-37314872)
               


               
               157-467, gnl|bosTau2|chr29 (20703605-20703914)
               

               
               157-467, gnl|canFam2|chr5 (12538554-12538199)
               

               
               157-467, gnl|echTel1|scaffold_320545 (68728-68357)
               

               
               157-467, gnl|hg17|chr11 (124294263-124294596)
               

               
               157-467, gnl|Hg17|chr11 (124294650-124294344)
               

               
               157-467, gnl|loxAfr1|scaffold_39346 (34189-34502)
               

               
               157-467, gnl|mm7|chr9 (37315273-37314930)
               

               
               157-467, gnl|Mm7|chr9 (37314882-37315193)
               

               
               157-467, gnl|oryCun1|scaffold_95928 (1114-1435)
               

               
               157-467, gnl|panTro1|chr9 (126377590-126377927)
               

               
               157-467, gnl|rheMac2|chr14 (123060067-123060417)
               

               
               157-467, gnl|rn3|chr8 (38650967-38650624)

Aligned organism(s): 15 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


               
               1-147, gnl|bosTau2|chr29 (20703412-20703560)
               

               
               1-147, gnl|Hg17|chr11 (124294788-124294661)
               

               
               1-147, gnl|Mm7|chr9 (37314728-37314872)
               


               
               157-467, gnl|bosTau2|chr29 (20703605-20703914)
               

               
               157-467, gnl|canFam2|chr5 (12538554-12538199)
               

               
               157-467, gnl|echTel1|scaffold_320545 (68728-68357)
               

               
               157-467, gnl|hg17|chr11 (124294263-124294596)
               

               
               157-467, gnl|Hg17|chr11 (124294650-124294344)
               

               
               157-467, gnl|loxAfr1|scaffold_39346 (34189-34502)
               

               
               157-467, gnl|mm7|chr9 (37315273-37314930)
               

               
               157-467, gnl|Mm7|chr9 (37314882-37315193)
               

               
               157-467, gnl|oryCun1|scaffold_95928 (1114-1435)
               

               
               157-467, gnl|panTro1|chr9 (126377590-126377927)
               

               
               157-467, gnl|rheMac2|chr14 (123060067-123060417)
               

               
               157-467, gnl|rn3|chr8 (38650967-38650624)

Expressed library(ies): 3 entry(ies)

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Expressed library(ies): 3 entry(ies)

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               fbs (0.526039)
               

               
               fhi (0.508733)
               

               
               hyp (0.142837)

Expressed library(ies): 3 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


               
               fbs (0.526039)
               

               
               fhi (0.508733)
               

               
               hyp (0.142837)

	196-330, - strand, RNAz p=0.989796
	266-467, - strand, RNAz p=0.998405

	381-457, BovGen_09123 normal cattle brain Bos taurus cDNA clone (gb\|CO880798.1\|), blast E-value=1e-24, identity=94.81%
	381-457, 1242103 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb\|DN287769.1\|), blast E-value=1e-24, identity=94.81%
	381-457, 1252732 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb\|DN515481.1\|), blast E-value=1e-24, identity=94.81%
	381-457, 1373562 MARC 7BOV Bos taurus cDNA 3', mRNA sequence (gb\|DN537388.1\|), blast E-value=1e-24, identity=94.81%
	381-457, LB0196.CR_C03 GC_BGC-19 Bos taurus cDNA clone IMAGE (gb\|DV834693.1\|), blast E-value=1e-24, identity=94.81%
	381-457, 1591889 MARC 11BOV Bos taurus cDNA 3', mRNA sequence (gb\|DY459987.1\|), blast E-value=1e-24, identity=94.81%

	1-147, gnl\|bosTau2\|chr29 (20703412-20703560)
	1-147, gnl\|Hg17\|chr11 (124294788-124294661)
	1-147, gnl\|Mm7\|chr9 (37314728-37314872)

	157-467, gnl\|bosTau2\|chr29 (20703605-20703914)
	157-467, gnl\|canFam2\|chr5 (12538554-12538199)
	157-467, gnl\|echTel1\|scaffold_320545 (68728-68357)
	157-467, gnl\|hg17\|chr11 (124294263-124294596)
	157-467, gnl\|Hg17\|chr11 (124294650-124294344)
	157-467, gnl\|loxAfr1\|scaffold_39346 (34189-34502)
	157-467, gnl\|mm7\|chr9 (37315273-37314930)
	157-467, gnl\|Mm7\|chr9 (37314882-37315193)
	157-467, gnl\|oryCun1\|scaffold_95928 (1114-1435)
	157-467, gnl\|panTro1\|chr9 (126377590-126377927)
	157-467, gnl\|rheMac2\|chr14 (123060067-123060417)
	157-467, gnl\|rn3\|chr8 (38650967-38650624)