GgaINT0039325 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10232469-10233435:+
Coord C1 exon
chr8:10232469-10232522
Coord A exon
chr8:10232523-10233327
Coord C2 exon
chr8:10233328-10233435
Length
805 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
TATATAATGTTGTATTTTAGGGA
3' ss Score
9.75
Exon sequences
Seq C1 exon
GGTGAAGATGGTTTCCCAGGATTTAAGGGTGACATGGGCCTTAAAGGTGATCGG
Seq A exon
GTAAGCATTGGCTCATGGCCCATATAATCTTAAAATGTTTAAGTGCTATTATTTTGAAAGGATCAGTGAAGTGAACAAATACATTTACAGTGAAAACAGTTAAAAACTTTTAGCTTAAGTTGTTTTTATTCCCTGCACAAACACAGATTTGCGTCAGATCTCATGAATCAGCAAAGGCACAGTTATAAAGAAGAAGCAAGTGTCAGTCTTTGATATCCTTTTCACTAAACTTCTTCCTAGGGAGTCTCCTTTTCAAGATACCAAGATGTGGTACTGCCTGAAGAAGATTTATCCTGAACAGGGATATTCCCATTTCAACCTAATAGTAGCTTATAAATCTCTGCCAAAATGTACTTTATTATCAATGGATGCTTCTGTCACAGGAAATGTTGCAGAGACAATTTAAAAAAAAACTTATTACAAGAGGCTACTGGCCCATATCTGTTATCTGCATACATAAATAACTGTGATGATGGTATCTATTTAACTTCTTAGATACAAAAATTATTCTAATACCATGAGAGTGCTTTCACAAGAATTTGTGTAGTAATTACTGGAATTCATTAACATTCCTATGAAATTGGAAAGCAGTTTCAAAACCCAGCTCTCTTCAGACAAGGACAACAGCCTCTAACACTTGCACAAGTAAAATTCAGTTTTCATGTTTTTGTATTTATATAATGAACATGAGTAGTGGCATTTTCTTAATCTCCACTTATGTTTGCTGAAAAAATATTTTCAAGTATTTGTAGCTAATGCATGCACACAGTCAATTGCTGCACATTTATATAATGTTGTATTTTAG
Seq C2 exon
GGAGAAGTTGGTCAACCTGGCCCACGAGGAGAAGATGGTCCAGAAGGTCCAAAAGGTCGAGCAGGTCCATCTGGGGACCCAGGTGCTGCTGGTCCAGCTGGGGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:29
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(27.4=100),PF0139113=Collagen=PU(12.5=66.7)
A:
NA
C2:
PF0139113=Collagen=PD(16.1=27.8),PF0139113=Collagen=FE(36.5=100)
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:
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]