DreINT0049944 @ danRer10
Intron Retention
Gene
ENSDARG00000012593 | col5a1
Description
procollagen, type V, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-041105-6]
Coordinates
chr21:6765279-6765525:+
Coord C1 exon
chr21:6765279-6765332
Coord A exon
chr21:6765333-6765417
Coord C2 exon
chr21:6765418-6765525
Length
85 bp
Sequences
Splice sites
5' ss Seq
CCGGTACGG
5' ss Score
9.77
3' ss Seq
ATTATTTGTTTGTGTTTTAGGGT
3' ss Score
11.07
Exon sequences
Seq C1 exon
GGAGACGCTGGTGAAGCAGGAGAACCAGGCCCTCAGGGAGACATCGGCCCTCCG
Seq A exon
GTACGGAAAATACACCCTCAGACTAATGCAGACATCTGATGAAAGCACCTTAACACTCACATCTCATTATTTGTTTGTGTTTTAG
Seq C2 exon
GGTCCAAGAGGAGAGCGAGGAGAAAAGGGAGAAGCTGGACCTGCTGGTTCTGGTGGTCCTCCTGGACCCAAAGGACCCCCTGGAGATGACGGTCCCAAAGGAAGTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012593:ENSDART00000139598:48
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(2.4=10.5)
A:
NA
C2:
PF0139113=Collagen=PU(39.2=80.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTGAAGCAGGAGAACCAG
R:
GGACTTCCTTTGGGACCGTCA
Band lengths:
154-239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]