DreINT0007236 @ danRer10
Intron Retention
Gene
ENSDARG00000089078 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:22990]
Coordinates
chr21:32059193-32059493:-
Coord C1 exon
chr21:32059455-32059493
Coord A exon
chr21:32059321-32059454
Coord C2 exon
chr21:32059193-32059320
Length
134 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAA
5' ss Score
7.08
3' ss Seq
CTCCTATTGCTCTCTTGCAGTAA
3' ss Score
9.22
Exon sequences
Seq C1 exon
GGTCGAGATGGACTGCCCATACCAGAATGCTGGCATAAG
Seq A exon
GTATAATCATATATGAAAACTGAGATCGTTTTTTCCATCATATTTGTCATAACAGTGGTGATATTGCAGTATGACTGCAGTGACTGCTTTCTGTGCGTGTCTTCTAACAATTCCCTCCTATTGCTCTCTTGCAG
Seq C2 exon
TAATGACTAACCTGGAGCATGGAGTTTGTATATATTGATATATATATATATAAATATTTTTTTTTTGCAAGTAACATTTGCTTTTTCTTCCTGTTTTAGTCATCTCTTATTTAATAAATTGGTTTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000089078:ENSDART00000147387:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(7.0=38.5)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCGAGATGGACTGCCC
R:
AGAGATGACTAAAACAGGAAGAAAAA
Band lengths:
146-280
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]