GgaINT0039309 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10212601-10213008:+
Coord C1 exon
chr8:10212601-10212684
Coord A exon
chr8:10212685-10212951
Coord C2 exon
chr8:10212952-10213008
Length
267 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TGTTCTGTTTGTTTTCTCAGATT
3' ss Score
10.53
Exon sequences
Seq C1 exon
TTCCGCTTTGGTGGAGATGGTGAGAAAGGCCCAACAATCTCAGCTCAGGAGGCTCAAGCACAAGCTATTCTTCAGCAAGCAAGG
Seq A exon
GTAAGAGCCTGCAAATAGAACTGCCACAAGAGTATAATTCCAAATGAATTTCCATTTTATGACATTCAGAAGTCATGTCATGTGAAGTAAAGAGCTGTAAGCAACATTTCATGATGGTAGATATCCCTACGACAGAATACACTCATAACTGAGTGAATTATGGGGCCATTTGATAGTGCATTATGACACTGTGTTAATACAGAATTTGTGTGCTGGGCTGTCAGCTTTTCCTTGGCACCTGATGACTTGTTCTGTTTGTTTTCTCAG
Seq C2 exon
ATTGCAATGAGAGGTCCACCTGGTCCTATGGGACTCACTGGAAGACCAGGTCCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:13
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(26.6=89.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCGCTTTGGTGGAGATGGT
R:
CACAGGACCTGGTCTTCCA
Band lengths:
140-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]