GgaINT0079942 @ galGal4
Intron Retention
Gene
ENSGALG00000016292 | COL21A1
Description
collagen, type XXI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:17025]
Coordinates
chr3:86704876-86705454:+
Coord C1 exon
chr3:86704876-86704930
Coord A exon
chr3:86704931-86705253
Coord C2 exon
chr3:86705254-86705454
Length
323 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TTCTGTTTGAATTCTTCTAGCCC
3' ss Score
6.63
Exon sequences
Seq C1 exon
GCACGAGAATTTTCAGAAGAATTTATTCGACAGGTGTGTTCAGATGTACTGAGAA
Seq A exon
GTAAGTTTGAAAGACTCTTTACTGTTCTTGCCTTGTTTAAAGTGCTGAAGAAGTTTCCTTGTAATTATGAAGATGCTTTCTTGAAAACAACACCAATATTTTGATCTGATTTATCACTGGTTTTCATAGAGTTGTAGAAATACGCTTCCATGCCAGTGGCTCCATAACGTGCTAAAGGCGCCTTGTTTCCTAAAGATACCATAGCGCCTAAAGAAAGGAAGCTGGTTTTATTTTAGTGAAGAGGTAGAAATATTTTTATATTTCTATAAATATATAAATATATATATATATATAAAGCATTTTTTCTGTTTGAATTCTTCTAG
Seq C2 exon
CCCAGTTACCTGTGATCCTTCAGAGTGGAAGGCTACAAAACTGCAACCACTGTCAGTCCCAGAGCGCTTCCCCAGGACTTCCAGGACCACCAGGTCCAAGAGGCCCAGAAGGTCCAAGAGGGTTTCCTGGTTTGCCAGGGAATGACGGTGTTCCAGGTCTGACTGGCATCCCGGGTCGCCCTGGGGCTCGTGGGACAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016292:ENSGALT00000026273:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.842 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(6.5=21.1)
A:
NA
C2:
PF0139113=Collagen=PU(76.3=66.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACGAGAATTTTCAGAAGAATTTAT
R:
CTCTTGTCCCACGAGCCCC
Band lengths:
256-579
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]