RnoINT0040009 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6570756-6574580:+
Coord C1 exon
chr3:6570756-6570824
Coord A exon
chr3:6570825-6574346
Coord C2 exon
chr3:6574347-6574580
Length
3522 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
ATTGCTATGCCTACCCCCAGCTC
3' ss Score
5.87
Exon sequences
Seq C1 exon
GCCAGAATCACTTCTTGGCCCAAAGAAAACCCAGGTTCCTGGTTCAGTGAATTCAAGCGTGGGAAACTG
Seq A exon
GTAAGGTGACACCACGTTCTTTGCAATTGTCACTTTAAACCCGCCGTCTCCTATCTTGCAGAGTAAAATGGCCCGCTGGCCCAAAGAGCAGCCTTCCACCTGGTATAGTCAGTACAAGCGGGGTTCCCTGGTAAGTGGCCGCCTCACGCTGCCTGCTTGCGGCTCGGCCTGGCTCTGGGTGCTGCATGGGCCTAATTGCAGCTGGGACCACACCTGCTATTGCCCTTTCGGCCAAAGTGCTCCACACGCCTGGCAGCAAGGCCCGGATGGGTGTGATTCCCCTTCCTCTTGCCTCTTCTTCCCCCCAGACCAGAGTTCCTTCCCTCCTGGAGGTAGGCAGGGAGCTTTCCACTGAGTTTCAGGGCATCTGCAGTTGGAAGCGGGCAGTCCAGTAAAGCCGCATTGCCGCTTATGGGTGGCACAGCTTGGCTGGCAAGCCACAGGTCAGAGACATGCACAGAGCAGGAGAACCTTCACAAGGTCCTGGGCGTGGCCCATTAGGAGGCTCACAGAGAGTATTCCAGACCCTGCGGTTCACACCCTCTTCCTGGGCTGTGCAAGGCCCACAGGCCCTGGCTGCTGTTGACCTTGTAGGCACCGGGTGTGTGCCACATGGCTGTATTAGTCTGTGCTTAGCTTATGAGAGGTGTATCTTAGAACATTACCCATCTTGGAGGTGAAGAGATTTTTAAAAACGTCAACCAGAAGGCTCTTATGGCCAACGTGGAGGTCGGAAACCTGTCTAGATTCACTGCTGTGAGACCAATGTTCTCCCACTCAAAATGGGACATTCTTTTCCCCAAACGCCCAGGGCCTTTAGTGAAGTCAGCTCGAAACTTTCTGAAACTTAGCTAGACATCAGGTTCCAGGTCCAGAGAAGAGCCCACACCTTCTTTTGACTCTTCATGGAGAGGGCCTCTCCCTCCGAGTCCTTGCTCACACAAACCCCACTGGGGCTTCCACTGCCTTTCAGCACTGCACCAGCCTTAGCTTCTTTATGATCACAGAGCCAACTGGCTTCCAGGACCATCCTGCCCCCGCCTCTCTGTCATCCCTCAGCCTGGCAGCACGCCTGGCTCTCTGTCAGGGTTCTGAGGAGCTCACCTCTGCACAGAAGCTGTGTCCTGGGCTTTCCGGGCTTCAGCCCCACAGCTTTCTCTTTCCCTGCTGGGAGCTGGGCATCTTTGTCTGTTGCTTCCTCTCCTCTGCTTCCGTTGCTTTCTTCAGAGGAGAACGGCTGTCACATAGAAGGACCTGTCAGGAGGAAGACCCACTAACAGTGACAGGAGGTCTGAGGGGTCAGGCAAGAAAGGAGGAGGATGAACCAGACAGGTTCATCGGGCCCTGTCTGCCTGAACTTGACCTGGCTTCTCCCCTCTGCAAATGGCTTCTACCTGGTGTAGTTCAGGTGCCCCAGGGGGAGCAGCCACCCAATTGCTATCCTTAGAATGCCAGTGTCTAGGCACACCCCTGTCTGACATTTATGCTGAGTTGGTTATCAGGGACAGAGGCACAGGGACCATACAAGACAAACCAGCCTGCCTTCAGGCTATAATGTCTGGCTCCCAGTTCCCAGTAAGAACCAGGAGCTGCCTAAGATAGAGGATGCAGGGAACTGATCCCCTGAGGCAGTGCCTCTTGAAGACTCCCACCTGGTATGGTACTAGGGCTCAGGTCCTTCTGTGCCCCGCCCCCTGCCTCTGCTGTGGCATGTGTCCTTTCTCAAGTCAGTCGTGTGTCCTCCCAGGAGCACCGGATGCCCGGACGGCCGGTTGGTATGCATTTTTCCTTCTCAGAGTCTCACTGGGGTTCTTTCTCAAGCTGTCTCCAAGGGAGTGGAGTGTCCTTGGTAGCTTGGGAACCCCTAGAATGTCCCACCATCATGGTGGAAAGGAACAAAGTCCTGGGTCTGCCTCCACCACCCTATTCTGTCCTCCTATTACCATTGAAAAGGTGGGTTCTGAAGTTGTCATGTCTTCTTGGTCGCCATGGCCTGTGTCACACCCAGCACTGCCCCATGTGTTCCTTCAGTGGCCACAGACCCTTTGGAGTGGCCGACACAGAACAGTGTTGGGGCGGTAGCTGCTTGGAGCTGGGTTTACCAGAATGAGACACTGACCTCTGCCAGTCTCTCTGCTGATACAAATGTCATTACAGGGCCTGCCCCGCTGAGCCCTGCTAGTCCTCTCCTGGAGAGAGGTCTTCAGTCACATCTAGGCTTGGGGAGGCCCTGCTTTCTCCCGTAGCTAAGAGTCTTGCACCCCTGACAATACTGATGCCTCAGAAAACTCTTTGCAAAAGAACTGTAGACAATGTGATTCTTCTCTTACGGTGTCCATGGCAGCCTGCACCGATTGGAGCAGAATGGCTTCAGATACTGGTGACACTCTGGAAGCCACTTACAGGGTGCCATTCTCTTTCCCTGAGTTTGTTGTGGGGAGTGGGGGAGCGTGGGGCCTTCCAGAGAGGGTCTTATCTCCAGAGCCCTGTGCTGCTTGCTTGATATGGGCAGTGGTCAGCAGGATAGCCTGTTTGCTGCCTCAGAAGTCTGTCCCTTGGCAGAACAGGATGCCTTGAACCTCCAGGGTACACCTGGTCACTCCAGTTCCCACACAGTCGAGAACTTTCTTAGACTGGTCCATCATCCATCCATGTGCCGTTTCTCAACAGTCCCCAAGGTCTCTTGGCCATTCTAGCCCTTGACGGGCCTTGTGCACCCTGAACACTCAGCAGTGGCCTTCCATCTGTTCACAAGAGCCCATGTGACACAGTGATGGGGACACCAGGCTGAGCTCCTGTCCTGTGCCATGTGTGGTCTGAGGAAGGTGACAGATAGGCACTAAGACACAGGACCTGAGCTGGTGCACCCAGCCTCAGGGCTGCAGTGAGAACAGGGACAGAGCTGCGACCAAAGGTGACAGTTGCAGCATCTCCTGTCTATGGGCCATGTGCCCTACTAGAACACTCAAGAAGTGACAGGGTAGGAAAGGTCGTGGTCACCAGACCCCAGGAGTCTTTTCTACTCTGCTCCAAGGAGTCAGACCATGCCTCTTGCTCCCAGCACAGACTCATCCATAGGAGTGTGGGGCCTTCTGTGTCCCATGGACGAGAAAGCAGGTCTTAATGGTACACTAGGCAGTGCAGCCAAGCCAGGCAGATCCTGCCGAGTGGGGAGGAGGTAACTGGCTCCTCAGGAGTGGCCTGGAAGCTGGAGGCGTAAAAGAGGGTCAAATGCAGGAAAACCTGACCTAGGCAGGCTTCCTGGAGGAAGCAGGGCAGGCACTGAATCTGGAGAGACAGGGCTGCTAGCTGTCAGTCTCTGAAGAGTACAAGGTGCGTTTCACTTGACTCCTCTTCTCCGGTCTCTCAGGAGATGCCCTGTGTGCTTGGGGCGAGGAACACAGAAGCTTCCAGGCAGCAGCCTCAGGGAGACAGGCTTGGGCGAAGCCCTGTGGGTGTGGGAAACTGTGGCCATTGCTGTGTCTCCATCCTGCTCACCCCCATTGCTATGCCTACCCCCAG
Seq C2 exon
CTCTCCTATGTGGATGCTGAAGGCAACCCTGTGGGCGTGGTACAAATGACCTTCCTGCGGCTGCTGAGTGCCTCTGCCCAGCAGAACATCACCTACAACTGCTACCAGTCCGTGGCCTGGCAGGATGCCGCCACAGGCAGCTACGATAAGGCTATCCGCTTCTTGGGCTCCAACGATGAGGAAATGTCTTATGATAACAACCCCTACATCCGTGCCCTGGTGGATGGCTGTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:64
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.193 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141013=COLFI=FE(10.4=100)
A:
NA
C2:
PF0141013=COLFI=FE(36.3=100)
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]