GgaINT0019078 @ galGal4
Intron Retention
Gene
ENSGALG00000006708 | COL23A1
Description
collagen, type XXIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:22990]
Coordinates
chr13:13600437-13601012:+
Coord C1 exon
chr13:13600437-13600463
Coord A exon
chr13:13600464-13600958
Coord C2 exon
chr13:13600959-13601012
Length
495 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
CAAAAAAAAATCCATAACAGGGT
3' ss Score
2
Exon sequences
Seq C1 exon
GGAAAGCCAGGAGAGCCGGGATTAGAT
Seq A exon
GTGAGTATGGAGAAATTTGATGGTGATGTGTAGAAGTGTGAATCACACACATGTAGAGGCCATCAAGGTTGCTTGCTGTTCTCACAGATAGACGTAACTAACACTGCATAGGCTGTTCTCCCTTACTTAGGGCACCCATGTAACAGTGTCAGTAGGAAGAGGCTTAACTCAAGGCAGCTGTTGGATGGCTGCTCCCCCTGCACAGCAGTACCGTACCACACCGGGTACCACTGCTCAGCTGAAGGTGCTGTGGGGGCTTTCCCTCCCAACTGGGAATACTTCTATCAGATTCAGGAAAACCAAAATCTCTTATAGATGAAATACTAGTAGGATAGTTAAAGCAGTAGCTTTCCCAATAAATTTATGAGATACAAAGACAAGAGGGGAGAAATGTCGTATTCTTTGCTGGTTGCTTCTGTTAATTTGAGATACTGGGATGTGCACGAAGTAAGCTTACAACCCTTTTCTTTCCCACCAAAAAAAAATCCATAACAG
Seq C2 exon
GGTTTCCCAGGTCTCAGAGGAGAAAAGGGAGAGAAGAGTGAAAGAGGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006708:ENSGALT00000010851:20
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=FE(11.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(24.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]