GgaINT1010119 @ galGal4
Intron Retention
Gene
ENSGALG00000008266 | COL4A6
Description
collagen, type IV, alpha 6 [Source:HGNC Symbol;Acc:HGNC:2208]
Coordinates
chr4:14027693-14028951:+
Coord C1 exon
chr4:14027693-14027809
Coord A exon
chr4:14027810-14028882
Coord C2 exon
chr4:14028883-14028951
Length
1073 bp
Sequences
Splice sites
5' ss Seq
CCGGTACGT
5' ss Score
10.49
3' ss Seq
TGTCATTTATTTTTTATCAGGGT
3' ss Score
8.92
Exon sequences
Seq C1 exon
GGTCACCCTGGCCAGTCTGGACCCAGGGGTCCACCTGGCCTCGATGGCTGCAATGGAACCATCGGGAGTCCTGGTGTTTCTGGGCCAGATGGATTTCCTGGCATACCCGGGCTGCCG
Seq A exon
GTACGTCCCAAGGCAATTGAAGTGTTTTGTTGTCACTAAGCCAGGATTTGCTTTTCTTGCCAGTGGTGGAAAAATAGCTCTGAAGTTCTTAGGAAGAACCCTATAACCCCGAGTTCCTTAGTATCCTTAGAGCTCAGTGTCATTTTCTTATTGAAATTCCACTCTTATTTACTGTGTAAATGTTAACTTCTGAGGCTAAAATGAAGATCCTGTGACAATATGCTCCTGCACCACCCTATCCCTTTGTCACTGGCAACATTCAAGCTGGCTCAAAAGAGACTGTGATAAAGTTTTTAAGAACTATAATGTGTCAAACATCTTCCAGTTGAAATGTTTCAAGTTAGGGAATGCTGATTCAAAAAAGGAACTGATTGTGTGTCTCTTTTACATGTCATCCAGACTTGAAGTTTATGTAATGTTGAAAATAACAAAGCAGCAGAAAAAAAAGTTAAAGTATGACTTTCTAAAATAACTGATTTACTCATACCTCCTGCTCAAATTTCTATTTTGTAATGCGTGTGGGATTTTATTTTTGGCAAGGAAAGCTGCTTGGATCAGCTAGCTTCTCTCAAATTAAGGTGACAATTACATGAAATCACCTTGGATAAACTGAATGGAATGATGAAGATTAAAATAAATGGGGTAAATCTAGAATTATAACAGCTGCTTTTTCAGAAGATCAATGCAATCTGTTGTTTCTGGTTTTGGTTTTTTTTTTTTTGTCTCACTGTTTCTAAGTAAATATGGTAATTTACAGTGCTACGGAAGAGATACATACATGTACAGGAGAGTTACAGCGTGTCATACAGATTCAGGGAGAATCTTCGATGTTTTTTAAGGCCTAAAATAAAAGGAAAATCTAATATAAGCAGGAAAATACCAGAGAAAATGTTTGCAGAATGTTGTTTTTCTAAAGCTCCAGGAAGTCTTAAATTCTCCTAATACCACTGCAGTGCTACTTTTGTAGGTTACTGGAGCAAGAAGTTCCTTATACCGAATATAATTTCTTTCAAAACCAAATCAGTGTATTTCTTTTTCTAGAAATTTACTTTTTGTCATTTATTTTTTATCAG
Seq C2 exon
GGTCGTCCTGGTCCAAAAGGTCTTAAAGGAGAACCTGTTTATGCTCAAGGCAGCCTTAAAGGAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008266:ENSGALT00000013447:6
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=0.974
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(16.2=46.2),PF0139113=Collagen=FE(58.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(25.8=73.9),PF0139113=Collagen=PU(13.3=34.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCACCCTGGCCAGTCT
R:
ATTCCTTTAAGGCTGCCTTGAGC
Band lengths:
182-1255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]