RnoINT0040013 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6495475-6500655:+
Coord C1 exon
chr3:6495475-6495531
Coord A exon
chr3:6495532-6500613
Coord C2 exon
chr3:6500614-6500655
Length
5082 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
CTTTCTCTTCCTCTCTGCAGGGA
3' ss Score
12.94
Exon sequences
Seq C1 exon
ATTGGAGGACCCCGAGGTGAGAAAGGGCAAAAGGGAGAACCAGCCATCATTGAGCCG
Seq A exon
GTAAGGATTTCTTCTGTTGTTGTTGGTGGTGGTGGTGGTGGTGGTGGAGGAGGAGGTGTGTGTATTTGTGTCTGTCTGCCTGTCTGAGTTGTGGTATCCTCTGCTTAGCTCATGATGGTTTGTAGGGTGTGATCAGATTGTGGGTCCCACCGTCTGCCTACCTGGCTCTACAAGAATTCACAGTTATGTATTCTGTATTCTTTACATCACAGATTCTTGGGAGAGGCTCTGGGGCTCTGGGAAAATCCTAGAGTTTAGCCAAGGTGATAGATCACAGGTGTTTGTACTGGTAGAGAAGGCGGAGAGTCAGAGCACCTCTGCAAAGATTTCCTCAGAAGAAGTGAGAGGAAGGCTGGGCCCAGGGCTGAGTAGGAACTCCTAGTGTAGGTGGCAGGCAGGGGGACAGTTAAGGACTTCACCTCTCTGTGCCCTTTATGCTGCCATTTGAGTCTATTTGCTGCAACCACTGAGACAGGGAAGACCTTGAAGCCATGCCAAGGGAATGTACGAGGCTTTGAGGTAGGGTTCCCTTTTGAGTCAAGCCGCATGCCATTAGGCAGCGGAGTCCTGGGTAAGTCAGACAAGGGCCTGTAGGGAACGTGTGATTGTGCAATCCATGGCCCTCCTGGGTCAGAGTTTTGTGGAAGCCAGGCCTTGGGTAGGGCATCCTTGTCCAGCTAGGTGCTGCAGCCTGCTTGGGTCTCAGAACCGTTGAGGTCAGGGCCTTGGCCCCAGAGAACAAAAAGCTATGTGATTGGCTGGGCTGGGCTTGGTAGACATGGGAATATGGACTCAGAATTGGCTTTGCCCAGAGGAGCTGACCACTGAGGTCATCCACCCTAGCATCCTGTGAGTACCCAAGGGAGGAAGGACTTGTCCTACATCATGGCCATTACGCTGATGAACAGCTGGTAGCTGCACTGCCAGGATTGGCTGCTGGGGCTGAGTTTATAACGTGACTTTGGGGCTTCCTAGGAGAGAGAACCAGCCTCATAGGCCCCCACCCTCCTGCAGGGTAGGAACCTTGCTTGGCAGTGCTTAGTAGGCCAGTGGGCCAGGGCAAGCTCCCCGGCTTGACCTCTCCTGGCCAAAGGGAGCCTTGGATGGAAGCCTCTTTCTGGTTCCAAGGGCTCTGCCTGCTACTTGTGCCCCTGGCTCCCCCTGGCTCCCCCAGCTCCCTCTGGCAGTGAGCCTGAGGACACAAATCCTCTTCTCAGATCCCTGTGAGTCCAAAGAAGAGAATCCTTACCCAAGGCTATAGAATCAGGGCACACATCGGGGCATGGATTGCACACTGCAAAGGCTGCAGAGCATGACATTAGCCCAACCTGGAGGCTTTTTGCTCAACCCCATGAGAAATTTCAACCCAAGTTCATGTTCATGGGAGGAGGAAAGTCCTGAAGAAAAGCATGTTAAGCGACTGGAGCAGACTCATCCCCTGGAACATATCTGGGGCTTTTCTCTTCCACACCATAGAAGGGTGCAGCACAGATGGCTTCCCTGCTATGCTGGACCTCCTTAGAGCACCACCTCAACTGGGCTTGCCCCCAGGTGGACTTGGGCATCATGAGGAAAGGGTCCTCTTTCCTGAGTCAGGGCAGCGAGATTCTGGAGAAGGGAGGTGCCTGAGGCTCAGTGGGCGTCAACGTTGGTCCCCAGTTTCAGAAGAGCTTGGGTTGTACCTTTGAATAAGGCTTACTTAAGCTTATTGTGTGTGGAGTTGGCACCCCAGTTCTGGGAGCAGCGAGTTTCACTAAAGGGCTGCCCTGAAGGGGGCTGTGGGTGAGGGTGGGCCAGAGACAGCACTGAGAACGTAGAGGTGGTCTGCCAGACACCCATCTCTTCTCTGGGAACAGCACAAGCCATCTGGAAGCAGTTACAGAAGGGCCCACCCCCATCTGATGCTTGCTTCTTCCCGGCTTCCTCAGAGTGTCCACAGGGCCTTTGGTGAGTCCCCATGGAGAAAAATATAAACATTTGGAATTGTCAACCTGGAGAATCGCCAGATGTCTTTACAGTCTTAGCCATACATAAACAGATGGAGGCCCTGGGGACTGGTGGTGCATACCCTGCCCTGTGCTGGGGTGGCTGCTATCCCCTGTTCACCACATCTGTCCCACAGAATGGATTTACAGCAACTGCTGGGCACAGGGTCGGTTCATCCCTGCATCCAGGAGGACCTGGAAGGCCTTTCTCATTGAGGTTCAACTCCTCTAAGTTGTCAGCAAGACAAGGGGTTCCTCCAAAGGACAGATCTGGCTTGGCTGAGATGAGGCAGAGTTAGCAATGCCCTTGGCATCAGCCCACACTAGGGTCAGGGACCACCAAATCCTGATTTGATACCTCCTACCTGTTGGACCCCAAGCCATTCCTGGTTTATCTATTTTTTTTTTTTTTGAGACCGAGTTTCAAGTATCCCAGGCTGGCCTTGTATGTGGTTGAGGATGAGTTTGAACTCCTGCTTCTTATTCCTTCCTCTTCCGAGTCCTGGGATTATGGACCATACCCAGCAACTACAGTTCAAACCCAGGGCTTTGAGTATGCTAGGCAATCCCTACCATGCAAGCCTCGTCCCCAGACTCTGGCATTGCTTTTAGTTCTGCTTAGCAGATGGATGGACCACCATTAAGGTCTGGAGCTGCAAATGACAGCACACACATGTGATACCAGGGAGGCTGAGGCAGGAGGATCTGAGCTCTGGGATAGCCTTGCCTACTGGGATAGCCTAGGCTACAGAGTGAAAAGTAAACAACCACCTTCAGTATGTATTTAAAGTAATAAAACAGCACGGCTTTTTATTTTAATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATTTTGGTATGTGCAGTGCATGCCTGTACATCCTGTGGATGTATGTACATATAGGCAGAGGCCTGAGGTAAATGTCGATTGGCTTTCTCAACAGCTCTGTGCTTTATTTCCTAAAGATAATAATAATAATAATAATAATAATAATAAATATGTCATAAGTGTCTGCTGTATATGTGCAGGTGCCCTCAGCATCCTGAAGAGGGCTCCCCTAGAATTAGGATGGTTGTGAGCTTGGCAACTGGCTAGACTGCCGGGAGAGCGAGTCCCTGGGTTCCACCGATCTCCAGTTACAGGTGCATACCACCATGCCTGGCTCTTAGTTTTATTTTTTATTATTATTGTTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTGATACTGGGGATCTAGACTCAGGTTCTCATGCTCATGTACTTTATTGACTGAGCCATCTCTGCAGCCTTCAGGCAAGACGCTTTGACACTCCTGAAGTACATACAGTAAAGAGCTGAGTCTGTCACCTGGTGTCACGGCCTCCCTTGGTGTGAACTCGGGGCAGCATGTGCGTGTCTGTGTCGGGAGTTAATGAGGGTAGCTGAGTTCGCCTCAGACAGGCCACCAGTGAGTGCAGCCCTGTAAGCCCACGGAGGCTGCGTCCTGTAGTTCCGAGCCCAGATCGGCCGATGAGGTACAAGGTAGGGATAGCATGGCCACGGGACCAGGGCTGGTTCCTTTCTTTTCTGACCTGGGGTGATCCAGGACTGGCCTCCTGTGAGATCCAGCAATGCTGCCCCCCACTCTGCAGAACAACAGTGTGTGTATCTGGAAAGACAGCTGCTGTCTCCTGGGCCCTGCCAGTGGTTCCCCTTAATCTCCCTTCTCCACTTCTGAGTCCTCCCAGCTGCCTGTCAGAGGAAATGGGAAGCGGGAAGATGAGCCGCTTGGATGAGTTCTCTGTGTACATCGCACGCACAAATATTTCTCCTCAGCGCATCTGTGTAAACATGGCGCACGGCTTCCCAGAGACCAGGAGACCTCATAGGCAGTGTGGATAAGGCTTCTGTGTGGGGGTGCTTTGCAACCCCTGCTCAGCTGCACCCCACCCCCTACTCATTCGCCATGGTGACCAGATTTCCAGGGCTTCCCACCTACACTTGAGTAGATCTTTTCACTTGTCAAGACCAAGCCCAACTTTGACAAGAGAGTTGTGTGCTTTCAAAGACGTATATCTGAGGCATTCTGCCATCCACTATCCCAGGAGAAGAGTCATTCCTCGGTTCCTTTGGCTGGGAGACTAGAAAGGGACCTGGCCCAGGGCCAAGACCTCCAGTCATTCACCTCATTATTCCTGCAGTCTTGGGAGCGAATAGGGAGACGCTACACCTGTCTCACATGTGGCTACCCTCACACATGCAAGTGTCCCGACAGGGTCGGGCAGCCATCTACCCAAAGCCTGCCGCAGACTCTTGAGTACCAGCCTTGCAGGCCTCTTGTGCTGATTTGACCCCTCCCCTTGTGCCCCAAGTGCAGATCCTCTCTCCTAAAGTGTATGTGGGACTCAGAACATTGAGAATGTTCTGGGTGGGTGGTGGTAGGGAGACCAGGAGAAATCTGGGGTACGTTTTGAAAGAGGACATCCAGAAATACAGATCCCAGAGCAGAGAAGCTCTCCTTTCAAGCCAATAGACAATAGGAGGCTTTGTTCTCCTTTGGGGGTTGGACACAGCAAGGGCTAGTGGCAGGATGAGGGCCCAGGAGTGATAGGAAGAAGATGGTTGTGGGTCAGGTGATTTCAGCAGGGTGCTGGGCATGGAGGAGGGGCTGAGTGTTCTGCTGGCTGGGGCAGGAGGCCGGGCTACCCTCGGCCCTCCCAGCTTTTTCCCTTAGCCTTCATTGGTCCACTTGGATGCCTGGGCCTGGGGTCCATTTTGCCCCTGGGGAAGCCGGATACTCTTCAGGTAGATGGGAAAGAGGAGTTGTGTTTGGGGTCTATTCTCTCATTCTGGCAAGTTGTGCTTTTGTCAAAGTTGTGTTTGAGGGGTGCCTGTGGGCCCCTGATCACTGGCTGGAGTCCACAATGATTTGGAATGCAAAGAGAGTAGTCCGAGTGCGCCCCCGGCACAGGGAGCCCTAGCAGGACTGACCCGGCTTCTTGACTGACTGTTGTCAACCCAGTTTGGAAGCTGGGCTGGGCCCCTGATCTCAGATGTTCCCTTTCTCTTCCTCTCTGCAG
Seq C2 exon
GGAATGCTGATAGAGGGGCCCCCTGGCCCTGAAGGCCCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(18.9=71.4)
Main Inclusion Isoform:
NA
Other Inclusion 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]