RnoINT0038658 @ rn6
Intron Retention
Gene
ENSRNOG00000005286 | Coch
Description
cochlin [Source:RGD Symbol;Acc:1308536]
Coordinates
chr6:72364758-72369964:+
Coord C1 exon
chr6:72364758-72364905
Coord A exon
chr6:72364906-72369860
Coord C2 exon
chr6:72369861-72369964
Length
4955 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
TTCTTTTTTCATTTTTATAGTGA
3' ss Score
8.06
Exon sequences
Seq C1 exon
ACTGCAAGGCAGACATTGCATTTCTCATCGATGGAAGCTTTAATATAGGGCAGCGCCGATTTAATTTGCAGAAGAATTTTGTTGGGAAGGTGGCACTAATGTTGGGAGTTGGAACCGAAGGACCACACGTGGGCCTCGTTCAAGCCAG
Seq A exon
GTACCAACTTTAATAAAATAAAGAGATTACAGATGTCTTGAATGGTGATAACTTACCATTTCATTTCAGTTGAACATAACTTAAATCTGGGCAAGTTGCCAAACTATGCACAGTCAGGATTTAAGAATGTCTATACATGGCTGGGCATGGTGGTGCCTACCTTTAATCCCAGCACTCAGGAGGCAGAGGCAGGCAATTGCCTTATGTTAGCTTTCTACTCATCTCTGTGAGTTCAAGACTAGCCTGGGCTACCTAGCAAATAGACCAGCCAGGGCTGCATAGTGAGACCCAGTCTTTCAAATAGAAAAATCTCTGAAAGCACTTGCATGCACACATCATGCAAGTTCTCAATCTCCAACACTGCAAACAACAATATCAAAGACTGCCTGGGTAGACTGTGCAGGGCTCAGTGAGCCATTGCATAAAAGGACTTAATGAACTGTAGGAGATGCAGAAAGGGGGCAGAATAGCTTGGGAACCTTACATGAATACCTTTCTCGGCTTCACTTAGTTCTTGAGTTTTCCTTTTGGAAGGGAGCAGCCATGAACTTTGTTCTCTGCTGCTGGTGTTGTTGTTGTTGTTGTTGTTGTTGTTGCCCTTTCTATATTCCTTCATTGGGGATCCAAGCTGGCTGTTACCACTCTAGTTGGCAATGCGAACCTGGGAGAGTAGAGCCTAAAAAACATGAGGTGTACTAGAGTCTCATCCAGTAGGCAACTTTATTCAGGGTATCAGACAATTTATAGTCTGAGGGCATTCTGAGGATTAAGAAAGGTCATATGAGCAAAGCTGACTTTGAGTTCAAGCTGTATACAGTCACGACTGCAGTGTCACATGAGTTTAGGCTGTATACAGCCATGAAGGCAGCCCTCACCTGCAAATGTCATTCTGAATACAAATGGGTAAAATGATCGATAATCTAAAGTAAAACCCACTCCTATGATTACACCCTGGAGAGGCATGAGAGCGGGTTCCAAGAGCAACCCATGTGATGGAGGAACAGAAATCACAAGCCTCCTGTCTTGTTTACATGGCGTTTTCTAATAAGCTCTTAGAAATCTCCTCAGGCAGCTTCATTCACAGACCATGTTCTGACACATAACCTCTTACACTTCCTGCCTGTAAAAATAATATTGGTGGGTTTTAGCACTGTAGTATGTTCCTTACAGGAGGCTTCCAAAGCTAGGTACAAAGAAATACATTTCTCAGAGCAAGCCTTTATAAAGTTGTTTCCTTTCTGCATTTGAGAAGATGTTCCTCTAAACACATGCTCCCCTTTCCTACAATTCAGTCTATAAACGTGTTGAACCCTGTTTGTCTCCCCCACCCTTGGTGTTTTAGCATTTTCTTGAGGCAGATGTGCACTTTCCTTTGCATACTCGTGTAGACATTCTTCCCTTGCCTTTCACGGTTACACAGCGTCCTGTGATAAAGCCTTCTGTCAGCTTTCTGTCCATCTTTGATTATTTCACTCAACTGAATTCCTGGGCGTGGAGTTCAGTCACTTTCAAAGTCTTTGACAAAATTACTAAGTGGCTTTCTAGACAGTTGACCAGCTAATATTATCAGCAGTGTGTAGCCCCACACAACCACAAACACTAATATTCCGATTGTTACATTTTTGTTGTTTGTTTTTCAAGACCAAGTTTCTCTGTGTAGGCTTGGCTGTCCCGGAATTTGCTCTGTAGACCAGGCTGGCCTTCAGTGCAAGAGATCCCCTTGACTCTGCCTTCCAAGTCTGCTTGTTACCTTTTATAGTCAGCTCTGCTTAGAAGTTATTTAACTTTTCTATATAATACAGCCATCCCCCTTGTTTTTAAAACACTGAGCCCCTTATGTATTGATTTAAAATGAAATATCAATTTCATGAATACCTAGGCAAGTTTCTTTGTCTCAGGGGCTGATTTTTTTCTTTCTTTTTCCCTTGTGATGCTGCTGGTTTGGTTGGTTGGTTGGTTGGCTGGCTGGCTGACTGGTTTTTGTTTTTGTTTTTGTTTTTTGTTTTGTTTTATAGACCAGGGTGGACTTGAACACAAAGCTCCTCCTCTGCCTCTCAGGCACTGGGATTACCAGCATACCACCATGTCTGGCTTAGGTAGTGATACTTATATTTTCGAGGTATTTTGATTATTATAGCTCTACTGGATTTAAACATCCCCTGAGGCAATTCAGCACGACTTCCTTTCTAATATTGTTTTGTTTGGGCTAATTAACCCCATGCATTTTCAAAATGAAAGCTGCATTAACTTATGTATTCAGAGTTTTTCTGCTTAAGGAAATACTAGAATAAAGAGCTCATATTTGAATAGAACAGAATGACCCTTGCATCATTAACAAAGCAAAAAAAAAAAAAAAAGATGAATCTCCTTAGGTTAGAATTTAAGTAGTTGGAAGTGGCTACAAACTGAAAAGTTTGTACCATGAAATGAGATTCTGTGACCTAGCATTCCACTAGGAATGCTGATAGAAACCAGCAGGCATGCAGAGGTGAAGTCTGTGCTTTTCTTGTCACTTGAAGAGTTGAAGGAGAATAGATCTTATCTTAAACAAACGAACAAACAAAACTGGACAAAAAATTGGCTACTTATGCTAAAAGCTTAAATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGAAAGGGAATAACACTCGAAATGTATATAAGAAATACTCAAGTTAATAAAAATAAAATAAAATAAAATAAAATGTCTTCTGACCTGAGAGACCGGCTTAGACTGCTGATGTACTCTCATATCCAACTGTTTGCTTCCTACTTGGTGCCTTCTACTAAAGGCAGAACCCAGAGCCGACCTACTTTAACATGCTGCATCCATGTAGTCTGTTATTCCTGTTCCAACCTAGATTTGGAATGGTTTTGGAGCCAGTTGAGTCTGAATTTAAAAGGCAGCCATGTTTTCTTAGACATATTACCTAAGTGTTCTGAACCTGTTTCAGTGATTGGGATAATTCTACCTTGTGAAAATATGAAACAAAACTGTGTATGCTTGGCCATTATGAGAAATACAATAAATGCTGCACAAGGCAACTGTACTTGTCGCATCTGCTGCACTCTTGTTGTTGTACTTGCAACATTCCCAGGGAGGAGAAGCAATGTGCTAGCTGATTGTGGTTTAAGAAAGACCTGGGTCTGACTTTTTTATTCATCTTATGCTTTTCCCCCTGAATGTAGGTCTTTGAGTCATGTGTGGTGCTGGTGCCCACAGAGGTCAGAAGGGGTGTTAGGTCCTCTGGACGTGAGTTAGATGGTTGTGAGCCATTATGTTGCTTCTGGAAATGGAACCTGGGTTCTCTGCTAGTAAACTTTTTAAAGGTCATCTGTTTATTTGCCTTTCCTGAAAAACTTTCTTTTTTCATTTTTATAG
Seq C2 exon
TGAACACCCCAAAATAGAATTTTACTTGAAAAACTTTACTTCGGCCAAAGATGTCTTGTTTGCCATAAAAGAAGTAGGTTTCCGAGGGGGTAACTCCAACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005286:ENSRNOT00000007365:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(27.8=90.0)
A:
NA
C2:
PF0009223=VWA=FE(21.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]