RnoINT0040002 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6562211-6562534:+
Coord C1 exon
chr3:6562211-6562318
Coord A exon
chr3:6562319-6562480
Coord C2 exon
chr3:6562481-6562534
Length
162 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAC
5' ss Score
7.48
3' ss Seq
CATTTTCTGCTCCTTTCCAGGGC
3' ss Score
10.55
Exon sequences
Seq C1 exon
GGCCATCCGGGCCTGATTGGACTCATCGGACCTCCGGGCGAACAAGGTGAAAAAGGTGACCGAGGACTCCCAGGCCCCCAGGGCTCATCTGGTCCTAAAGGAGAACAG
Seq A exon
GTATACACAGTCACACATCCTTGGAGAAACTTCTAGTTTCTCAGGGAGGCTGGGAAAAGGGACTATGAGGGAATCTGGGATCATGGCAGGGTCACGGGGGTCACCTCCCTCATTCTACCCTCATCTAGAAGCTGGTAACCTGCATTTTCTGCTCCTTTCCAG
Seq C2 exon
GGCATTACAGGTCCTTCTGGCCCGCTTGGGCCTCCTGGTCCCCCAGGCTTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:58
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=PD(4.8=11.1),PF0139113=Collagen=FE(53.8=100),PF0139113=Collagen=PU(3.3=5.6)
A:
NA
C2:
PF0139113=Collagen=PD(15.2=55.6),PF0139113=Collagen=FE(28.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCGGGCCTGATTGGACTC
R:
GGGACCAGGAGGCCCAAG
Band lengths:
146-308
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]