RnoINT0038651 @ rn6
Intron Retention
Gene
ENSRNOG00000005286 | Coch
Description
cochlin [Source:RGD Symbol;Acc:1308536]
Coordinates
chr6:72371154-72373695:+
Coord C1 exon
chr6:72371154-72371670
Coord A exon
chr6:72371671-72372799
Coord C2 exon
chr6:72372800-72373695
Length
1129 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
AAAATATTTCCACTTTTTAGGTA
3' ss Score
8.59
Exon sequences
Seq C1 exon
GCTGTGTGCAGGAATAATGGCTTCTTCTCTTATCACATGCCCAACTGGTTTGGCACTACAAAATATGTAAAGCCTCTGGTGCAGAAGCTCTGTACTCATGAACAGATGATGTGCAGCAAAACCTGTTACAACTCAGTCAATATTGCCTTTCTGATTGATGGCTCCAGCAGCGTTGGAGATAGCAATTTCCGCCTCATGCTTGAATTTGTTTCTAACATAGCGAAGACATTTGAAATCTCAGACATTGGAGCCAAGATAGCAGCTGTACAGTTCACTTATGATCAGCGCACAGAATTCAGTTTCACTGACTATAACACCAAAGAGAACGTCCTAGCTGTCCTAGCGAATATACGCTACATGAGTGGTGGGACAGCTACGGGTGATGCCATTTCCTTTACTGTTAGAAATGTATTTGGTCCCATAAGGGACAGCCCCAACAAAAACTTCCTGGTTATTGTCACAGATGGACAGTCCTACGATGATGTCCGAGGTCCAGCTGCAGCTGCCCATGATGCAG
Seq A exon
GTAAGATGGTTGTCCTTTGGATTAAGATTAAGGAAGGGGTCCTGTGAAGTCTAGGAGTCAGCATCTTTGTAGAAAGGATCCTTTAGTGGAATTTATATATTCTATGAGCTTTGGAGTCTGAATGAGTTGAAATTCTTCCAAGCTCCACTGAAATCCCTTTGGGAGGCTTTGCTGTTGTTTTTCTGTGTAACATCTCTGGCTGTCCTGGAACTCACTCTGTGGACTAGGCGGACTTCAAACTCAGAGATCCTCCTGCCTCTGCCTCTTAAGTGCTGAGATTAAAGGCCTGTGCCACCAACATGTAGCTCAAGGGGAGTTTTTATTAGATTATTATTATTCACCAAATTGATTTAAAGACTAGCAATTTTAAAAAATGACTTTTTTTCAAAAAATTTGAGTGTTTTTCCTGTGTTTATGTATGTGCACAGTGTGTAACTGATGCCCATAAAGGTCACGAGGGGGCATTGGATGTCCTGGAACTGGAGTCATGGATGTCTGTAAACTATGTGGGTGCAGGAAGTAGAACATAGGTCTGGTGCAAGAACAACAAATGTTCTTACCTGGGGAGCCATTTCTCCAGCTCTTAAGATTTACAATTTTTAAGTACTGGATTTGTACATATAACTTCAAAGACTGAAGTAGAACAAATAAAATTATCACTAGTTCCTATTCCTCAGACAATGCAACCTTCCCCATTTACCTGTCCTCTTGTGCCAGTCTCACTTTAATGTGCTAATTAGGACCTCAAGATGATATCTGAAAGTGACAATAGCAGGGAGTCCCTTCTGTCAAACATGTGCCTGCTACAATAACTCCATAAACTATCAGCTTAATTCACTTTCTTTTAAGAGTTCCTTTCTTTTCCTAGCTTGTTCAGTGCAGTCTTGAGTAAGGTGACAATCTCAGTGTTTTCATCAGGTTATTAATAAACAGCTGATAGCAAAGCTTCTGGTTTTGACCAATTTTTCTTGCCATAATCAAAATGACTGTGGTCTACCTAAAAACAGCATAAATTTCACTTAAAAATTAGGCAGTTTCCTCTGCAGCTATGTATTAATGTGTGAAATATATAACTTTATATGTAAGCTAAGCCTATTTTTAACTTATTTAAAATATTTCCACTTTTTAG
Seq C2 exon
GTATCACCATCTTCTCTGTTGGTGTGGCTTGGGCACCTCTGGATGACCTGAAAGACATGGCCTCTAAACCCAAAGAGTCCCACGCCTTCTTTACCAGAGAGTTTACAGGATTGGAACCGATTGTCTCTGATGTCATTAGAGGCATCTGTAGAGATTTCTTAGAATCCCAGCAATAACCGATACTCTGACAACGCAAGGAATACGTACAAGGGATCTAATGTTCAAATTGTGTTCTCAATGCCTATATAACTTTTAGCTTACCAGTGTCAAAAAGTATGTCAACAGCTGTTTAAAGGAAATGTACATTCATTTGAAGCTCACAATTTAGATTGGCTTGATAATCAGGTCCTTAGAAACTCAGGAAAGAGGAGATGTCATGGCTTAAAGTTGGGAGGTCAAATATGCATACAAGTGCATAGGTAAGCTACTTAGCTTAATAAAAGAACCTGACGCTTAGACACAACGCACTGTTCCTTCTTTAATCACTCTGCATTGACCATGCAAGGAAACAAGACAGCTTTTAAACACAGATCAAGTCTAAGTATTTTGCCCCACGTTGATGTTTTCTTAAAATCAGCCAAGGACAGCTGTTATTCTGTGTACTAGTCATAACTACACATTTTATATACTCATGTATCTAGCTTCTTTTGTAGTGTTTTCATAACTTAATGGCTGAAATATTACATTGAGTAAATGTAGGATTGCGGTATTTTTCTATTTATATCCTTAACTTTATGTGTACAGACAGGCATATACTCCAAGGACTAAGAAAATGTTTAAGCAGGTAACGTTTCTTTTTTTTTTTTGGAAAAAAAAATGTTTCAAGTATTGTAACAGGAAAAATACTTGGTATAATAGCTTGGCTATGTCAGCAATAAAATGACTAGTGACTGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005286:ENSRNOT00000007365:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(3.1=2.9),PF0009223=VWA=PU(72.8=72.8)
A:
NA
C2:
PF0009223=VWA=PD(26.6=78.0)
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:
TGGAGCCAAGATAGCAGCTGT
R:
GCGTGGGACTCTTTGGGTTTA
Band lengths:
357-1486
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]