GgaINT0039358 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10282674-10283767:+
Coord C1 exon
chr8:10282674-10282727
Coord A exon
chr8:10282728-10283517
Coord C2 exon
chr8:10283518-10283767
Length
790 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
ATAATATTTTTCCCATTCAGGGT
3' ss Score
10.19
Exon sequences
Seq C1 exon
GGTCCTGCTGGCCAAAAGGGTGACAGTGGTTTACCTGGCCCACCTGGTCCTCCA
Seq A exon
GTAAGTAAGAACTCCTTCTTGATGCAAGCATATTCTACTGTTGTGATGACGCTGTTTTGGTGGAGATAGAAAATGGCACTTGTGGACTTGCAGAGAAGGAAAATAATAATGATTATTTGAAAACTAATTTGTCAGGAAACACAAATCTAACAGAGAAAAAAATACATTGTTTGCTCTGAAAAAAATCCATTAGACATTTTAAAAAAGAAAGAAAAAACTTCCAATTATTATTTAATGTGTCATATTGAAGCACAGAAAATGGAATGAATTTCTTTTCCCACTGTTAATTCTTTTCTGTTTCTACTATTTCTTTCTCATAGCATAATAATCCAGAGTGAAAACAGTGAAAATCTGAATGAAATATGTCAAATTGTGAAATAAAATACTGGTTTGTAGACCCTATGTGTAATTTTAAAGTTTCACCTATGGAAACACCTACAGTTTTTATTTGCTACAGGCTATGCCTCTTCTTCAGGGAACTGCTGGAGATATAAAGGAAATCACAAATAAGTTCTACACACTTATGTGAGGATAACACGCTTCCCCAGACTGCAATGTCTAGGGAAGAATTTAGAGCAAAACAATGGTTTAGCCTTCTACAATCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGCAAGCAAATTGGCATAAATCTGAAGGAAATAAGTTAAATAAATGAATTGAAAAAAGCCTATCCAAAGCATCTCCAAGCCGTGTTTTGTTGTCTCCATATTTATGCAGCTGGATAATCAACAGAAAAGATAATATTTTTCCCATTCAG
Seq C2 exon
GGTCCTCCAGGTGAAGTAATTCAGCCACTGCCAATCCAGTCACCCAAAAAGACTAGAAGATCTCCCGATTACATGGTATCTGATGCTGGTGATAATATTCTGGATTATTCTGATGGCATGGAAGAGATCTTTGGTTCACTGAATTCACTGAAGCAAGACATTGAGTATATGAAGTATCCAATGGGCACTCAGAACAACCCAGCCCGAACCTGCAAAGACTTGCAGCTCTGCCACCCAGACTTCCCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:62
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=0.655
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=9.5),PF0141013=COLFI=PU(38.0=32.1)
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:
GTCCTGCTGGCCAAAAGGG
R:
ATCTGGGAAGTCTGGGTGGC
Band lengths:
302-1092
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]