RnoINT0039966 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6520212-6524350:+
Coord C1 exon
chr3:6520212-6520265
Coord A exon
chr3:6520266-6524305
Coord C2 exon
chr3:6524306-6524350
Length
4040 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
GACTTTCTCTTTTGTGACAGGGG
3' ss Score
8.38
Exon sequences
Seq C1 exon
GGTCCTTTGGGGAAACCAGGTCTCCCAGGAATGCCCGGAGCTGATGGACCCCCG
Seq A exon
GTGAGTAGTGTCCCCCACCCTGTTCCTCTCTCTCCAGGAAGCTCATCTCCTCTCCAGAGGGGCCCTGGGAGCATGGTTGCCCAGAGCCACTGTGGATGAAGATCATGTGCTCTGGTCTCTGTGCTGAGTGATGACTGGATTCTGGACAATCTTTCATACCATGTTCCTGTCCCGGAGGGGATGTGACTACAGAGGGGGCATTACTTACTTGTTAGGGTGTGCAAATTAGTCCCCGAACTCAGCATCATGTTTGAAACTGCAAGGCGTACTGGGCTGGGCTCCAAGCCATCACACCTGTCACCGGTGGGGGAAGTGAAGGGCGGGGTGTGCCAGAGGTATTTTTAGTGTTCACACATTTGAGTTTGGGGTGGGAGAGGCTGCTGGGTGGGGGGCAATGAGTCTGCAGTGAGCACAGCTGGGAGCCAGATTAGACAGTGCCTGGAAATAGCAAGTGAAGGACAGGTCCAACCTGGGGGGTGCGAGTGGGGGGCTGTGCAGAAAAAGGGGAGCGGGGAAGAGGAAGCAGTTAGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGCACGCACACACATGCCTATCAACACCTGCCATTCTGCCTGAAGATGCCCTCTGGTTTGAGAGTTTTTTTTTTAATTTTATATTTAAGTATTTTTAAAGTAAATTATTAAACTCGTCCCTCCAATTTCTCCCCTCCCCCTCTCACTTCGTGTGCTCTTTTGTGTTTAGGGAAACCCAAAGAATGTATCTCAGAAGGCAAGATGAGATACATTAATTATTTACGACAGTTTCGTTTATTATTTTAATAACACCATTAAAGTGTAAATGCAGGGGGTAGATGGGGGGGGTGCTGAGGAAATGCCTCAGGGGCATGAAGGGATTGCTGCACAAATGGGAGGACCAATGCTCAGATCTACAGACCCCCTGTAAATGCTGGGTGGTCATGGTGTACAATTCCAGCCTTGGGAAGCAGAGACGGGACTCACCACAGCAAGCTGGCTGCCAGTCTCTAGGTCTGTGCATGAGCCGGAGCAGTGACCAAGGATGACTCCTGACATCAGCCTCAAGCCTCCATGTGCTCATGCACACATGCATGTGTTTACATGTAAATATACACTATACACACATATACACATATGTACACCATACACTCACATGCAAATGTATAAAGAAAGACTAAAGTGGGATGTCTCGTGTGCTAATGTGCTAGGGTTGGTTCACTATCAGCTGCCAACTCCACTCCACACTAAGGTCACATGGGCCAGTGAATCCCAGACCCCAGATTGTCTTCGGTTGGCCTGAGCAAATAAGTGTAGTCACTCCCATTTCTGTGTGAACATCCAGGGAGTTTGGGAGCTGAGTGACTGGTATTTCCCAGTGTGCCACTTCTGTCTTTTTAATTGTCATGTATTTTGTGTTACGCATGCATGCGCACGCGCGAACACACACACACACACACACACACACACACACACACACACACGGTGTCAATGACACATTTTCTAGTAGACATGGAGGTCTGGGAACTGGCCTGTAGATGGCTTCATCCATCCCCATTGGCCATTCTTGGTCACAGGACCATAGTTCCCGAGTGTCCGGTTTCCTGTAGGTGATGCCCACAAATGGAGGTCTACTGCACAATATGTCACATAGCTCCTGCAGGGAGGAGAGAGCAGCTACACCCTTTCTGTAACCATACATGTCTCAGGCCTCCACAGACCTAGCTGGTTCTGGCCTGTAATTCCTCTCACCACCCCGAACGCCTCCTTCCCTTTAGGGTCAGGTCCCTGAGTATGGTCTCCTTTTACATCTTGTGTGTGCACCAGAACCTCCTGGCCTGGAGACTCTCTTCTCTGTTCCTGGCTTTATCAGTTACTTTTCCTACTATTGTGACAAAATACCAAACAAAAACAGCTTAAGGTAGGAGGGGCTCACGGTTTGAGGGTGTACGTCCATCAGAACAGGGAAGTCATGGCAGGCAGCTGCAGACCGGGCAGCTGGTAACATTGTATCAGCAGGAAGCAGAGAGCATGGTGCTCTGCTCGCTTTGATCTTTTCATTCAGTCCAGAACCTCAGCCCATGGGATGGTGCTCCCCACAGTTAGGAAGGGTCTTTACCTCAGTTAGCCTAATCTAGAAGCTCCCTCAAAGGCGTACCCTAGGGTTGGCTCCTAGGTGATTCCACATTCTGTCAGGGTCCAATACTGAAGCTTTAAAATGTGCAGTGGGAGAGGCCTGGTTTCTGCCTGTGCCCAAAGACAGCAGGTGGGCCAGAAAGACATGGGGGGCCCTAAACAGATCCAGCTGTCCGTGTTTGGAAGGGAGGGAAGATGAATGGCTTCCCTTACAAAAGCAGCTTACTGTTGATAAACCTTGAAGAGGTAGGCTTGTGCTGAGGCTGTTTTGCTCCAGCATTCCTTTAGTTTTGGTTGTGAAGAAAGAGTGATTGACAGGCCAGGAAGATGGCACTGTTAGGAAAGTGCTTAGCCCAGCATGCATCGAGGCTGGGCATGGCAGTGCAGGCCTGTGAAAGAGAAGACGGACAGATCCCTGGGCCTTCACAGCCAGCCCATCTATAGAGTTTTAGGTTCAGTGAGATCCCATCTTAATGGTTACAATGGGGAACAGTCTAGAAAGACACCCAATACCAGGCTCTGGCCCCTACATGCACTCACATACATGTATACACATGCCTATAAACAACATGCACGCACATGGATGGGCAGGGGGACGGGGGAGAGAGGAGATGAGAGGAGAGGAGGAGGAGGGGAAAGAAAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAACAGAGAGAGAGACAGAGAGAGAGAGGAGGGAGAGACAGAGAGACACACAAACAGAGACAGAGAGAGACAGAGAGACAGAGAGACACAGAGAGAGAGAAGGTTTTAAGTCATACCTAGTACTCTGAAATGTGATTAATTCCCCACAGCACACAGCGGAATGATGGGTAAATGGAGCCAGTAAAAATAAAATGTGACTGTCTATCCAAGGTTTGGAGAAAGTGCTCATGATCCAATATTAAATCCAGATCATATTATACCTGCCCACTTTGTATGCACACACACAGAAAATATGGATTGGAAGCCTGTGCCCCCGACCAGCCTCGTGGCTCTGCATGGTGGGCTGTGGAGGAGTTTAATTTCCTTTTCCGCTCTCCTAATTGTCTACAATGAACATATATTACTTTTTTAATCAGAAAAATATCAAATACAAATAATTTAAGCTTTATTATTTTTCCATTATGAAAGTAACTGTAAAATATTGGAAAAATGTACAGTGGGAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCAGTGAACAGCAAGAACAGCAGCCTAGCCTTGCACAGCAAGAAGATTTGTCAGTGTTAAATTTTCTTCTATTCTCCCCAGCCTCATGGTTACAAAATGAGCCCTGTGCCTCCCCACTGCTGTTGCTTCCTTCTAGCACACAGCTGAGACCCATCTAAGGCATCTGGGCAGCCATGGCACTGGTGTGCCCCAGCTCCTGTCTGTCACACTCTGCTTGGTGTTTGCTGAGGCGAGGGCATCTGGTTTCCTAGTGCCCACCCACCCTGATGCTGGAGCAGACCCATGTTGTGGGTGGGCACTGAGAAGAGCACAGGCAGCCCTATGGTGGGACACTCTCTCCTGGGTGTCCTACATTCATCCTTGCAACCAAGAACCTCTGGTACCTTAGGCATGTGTAGGGCACATGGACCGACCACAAGCATGATTGTTATTTCTGAAAGGCAGGGGTTGGTCCAGCTTGTCCTCAGGGCCAGAACAGCAGCCACAATCCACCAGTGGGTGCCTCAGTCTCCCTCCAAGGTTACTGGATTCCCCCATTGGAACTTTGAGTCCTAATTCACTTGCTAGGCTCTTTATAAAATCTGGGGAGGGCAGAGACACAAATACTGTAAAGGCAGGAGGCCTCTTTCTGAGCAGGCGGCTAACTAATGAAGACTTTCTCTTTTGTGACAG
Seq C2 exon
GGGCACCCTGGCAAAGAAGGTCCTCCAGGAGAGAAAGGAGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:25
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:
PF0139113=Collagen=PU(18.5=94.4)
A:
NA
C2:
PF0139113=Collagen=FE(18.2=100),PF0139113=Collagen=PU(13.3=53.3)
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]