GgaINT0068160 @ galGal4
Intron Retention
Gene
ENSGALG00000008141 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chr4:13892758-13893522:-
Coord C1 exon
chr4:13893331-13893522
Coord A exon
chr4:13892927-13893330
Coord C2 exon
chr4:13892758-13892926
Length
404 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ACTGCTGTTCCTATTTTCAGGGC
3' ss Score
11.26
Exon sequences
Seq C1 exon
GGATTCCCAGGGCCACCAGGTGCTCCTGGGAGACCTGGTCCTAAAGGAGACCCCGGGGATGTCTTGGCTTCACCAAGAATGAAAGGTGACAAAGGAGACCCTGGCTTCCCTGGACCTCCAGGTCTTCCTGGAATAGATGGCACTCCTGGACGAGATGGACTGCCAGGTCTGCCTGGCCCTAAAGGGGAACCT
Seq A exon
GTGAGTTTCATTTTATGATGTCTTGATTGGACCCATGTTTTGGATACATTTGGGATAGTGCAGATAAGAGGACTGACAAATGCAGATTTTTCTTAATGTGATTAACTCAATAATTCTCTTCGGTAGATGCTAATCTAGTGATGATATGCTGAGTAGTCCCTGCTACCAATGTCTCTTCTCATGGATCATATCAGTTGCTCCTTCCATTGTTCTCTGTATTTCACCTGTATAGCATGAAGAATTAATTAGACAGTTTTAAACCTTGCGTTTACCATGTTAATAAGATGCTGACAGCTAATGGCTGTGCAGGTTAGAAAGATGAAAATCATCAAATAGTTTCAAAACAGGAGAAATTAATTACTTCACACATACCTCTCTTTTTATACTGCTGTTCCTATTTTCAG
Seq C2 exon
GGCAGTGTTGCATTCAAAGGAGAAATGGGAATTCCAGGTGACCCAGGAGCACCAGGTCTTCCTGGAGACAAAGGACTTCCTGGACCTCCTGGTTTTGGTCCACAAGGTTCACCTGGTGAAAAGGGCATCCAAGGTGTATCAGGTCGTCCAGGGCCTCCTGGAGTTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008141:ENSGALT00000013221:24
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=PD(31.7=31.2),PF0139113=Collagen=PU(63.5=62.5)
A:
NA
C2:
PF0139113=Collagen=PD(33.3=36.2),PF0139113=Collagen=PU(94.6=91.4)
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:
GGATTCCCAGGGCCACCA
R:
CCTGGACGACCTGATACACCT
Band lengths:
344-748
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]