GgaINT0068161 @ galGal4
Intron Retention
Gene
ENSGALG00000008141 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chr4:13892021-13892926:-
Coord C1 exon
chr4:13892758-13892926
Coord A exon
chr4:13892114-13892757
Coord C2 exon
chr4:13892021-13892113
Length
644 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTTCCTCTTTTCTGTCTCAGGTC
3' ss Score
12.5
Exon sequences
Seq C1 exon
GGCAGTGTTGCATTCAAAGGAGAAATGGGAATTCCAGGTGACCCAGGAGCACCAGGTCTTCCTGGAGACAAAGGACTTCCTGGACCTCCTGGTTTTGGTCCACAAGGTTCACCTGGTGAAAAGGGCATCCAAGGTGTATCAGGTCGTCCAGGGCCTCCTGGAGTTCCTG
Seq A exon
GTGAGTTAGTCTCTGTGTGTTCTTGAAAAAAAGCTGTAAGTTTTTATCCATGGGCTCTGGATAGTTCTCAGAACATAATGCTGCATTTAAACTTTTCTCAAAGGCATTGTAAGACCTAGCATTTGTATACTCCCTTACTGAAGGTCACCACAGAATTGCAAAGTGAGCTGAAATTTTATATTACTATAGGAGTTTGACTTTCCCTTCTATTCTGGCCTCTAGAGAGAAGCTTCTAATTTTTAATTTACTTCAGTAGAAATGCACTGTATCTTCCATCTGGCTTATGCTTAATTATGGTGTGACCACAACTGCTTTTAGAAACAAGGGTTTGCTTTTGTTACTTCTTTGTCAGCTGCACAGATCCTAAGCAAGTTGTACTGAAGTTAGCTATGGAAAATACTATTCACATCATGGTACCTTGGAGGAAGCTGAAAAATGATCTTACAGAAAACTGTAACATAAACAATGCTAAGCCCATAAGGACTGTATGCGGCTCAGGGCCAGATAGTCCAGTGGGTAAAGTCTTTGTGATGTTTATGTTCTTTGTAAGCTTGGGATATGGCTAGCAACATTTCTTTCTACTCAAATAAATACAGAGAAGAAAATTCTGTTGATTGATATAAACTTCCTCTTTTCTGTCTCAG
Seq C2 exon
GTCCAAAAGGTGACCCTGGTCAGACTATTACAGAACCAGGAGTTCCTGGTCCTCCTGGTCCTCCAGGAAGAAATGGTGACCCAGGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008141:ENSGALT00000013221:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(33.3=36.2),PF0139113=Collagen=PU(94.6=91.4)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping 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:
TGTTGCATTCAAAGGAGAAATGGG
R:
CTGGAAGACCTGGGTCACCA
Band lengths:
257-901
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]