GgaINT0068167 @ galGal4
Intron Retention
Gene
ENSGALG00000008141 | COL4A5
Description
collagen, type IV, alpha 5 [Source:HGNC Symbol;Acc:HGNC:2207]
Coordinates
chr4:13883542-13884660:-
Coord C1 exon
chr4:13884493-13884660
Coord A exon
chr4:13883632-13884492
Coord C2 exon
chr4:13883542-13883631
Length
861 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TGGTGATTCAATATTTTTAGGTG
3' ss Score
6.45
Exon sequences
Seq C1 exon
GGTTGCAGGGCGTACCAGGGGAGAAAGGGGATCCAGGTCCTCCAGGCTTCGATGTTCCTGGTCCTCCAGGTGACCAAGGAACCCCAGGATATCCAGGACCCCCTGGCCTCCCAGGCCCTCAGGGTTCACCCGGACCACCTGGCCGGGATGGAATACCTGGATTTCCAG
Seq A exon
GTAAGTTCACATTTTTTACCTGTGGACAAAGGCCAAACTGTAGTTACAGGTGGATATTTCTTATGCTTGGCTTAGAGAGCCTCAATGTTTATCCTATTTGTTTAAGGATGGATACACATTAACAATTGCATTTCATAGCACTGTTGCATTAAACTCCTTCTCACCTCTCCACTCTTCCCTTTAATTTGATACAATATTGTTATTGTTTCATAGCTTTCAAAAGTGAAATCAATCATTTTCATTACAAGACTTTCTAGTTTATTTTCCTATTTCTTTTCCTGTCATCGCTACAATTTAGGCTTGTTTTTGTTTTTTGTTTGTTTGTTTGTTTGTTTTTAAAGGAAGTAATTACAAATGCTGTCAACTGGATCCAGCACATAGTTTTAAATGTTAATTTCTTTATTCCGTTTGTTATTCAACCATGACAGTCTTTTTCTCTCTCTGGACAAGAAATCTAAGGTTTTGAGGGTTTCTGTTTATGCATGTAAAAGGGGGCATGTAAAAGTTTTTTAAAGTAGTGTATTTGTAGTGGTCTTCTTGGCTTTCAATAAATATGAGTTTACTTTCAAGCAAGTATTTGGAGAATTGAAGTTACTGGAGTTCTAAATATGCTTTCTACTGAACAGTGCACTGCAAATTTTCTTTCTAGGACTTAACTGAAAAAATTGATAATGTTTTCAAGTGTTCTTCTATCTAATTTAGATCAGTGAAGAATCAAGTGTTTGTGATTTCCTTAAAACAAAGTTCAGGCTTTATATGCATTTGCTCATTAATATCATAAAGATACAGACAAGTTAATGTTAGGTACCGATGGGTTTTGGCTTCTTATTTGGAATGACAATGGTGATTCAATATTTTTAG
Seq C2 exon
GTGCCAAAGGTGAGATGGGCGTCATGGGAGCCCCTGGGCCTCCAGGGCCTCCTGGGACTCCTGGAAGAAGTGGCCTTCCTGGCTTGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008141:ENSGALT00000013221:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.909 A=NA C2=0.564
Domain overlap (PFAM):
C1:
PF0139113=Collagen=WD(100=84.8),PF0139113=Collagen=PU(43.1=37.9)
A:
NA
C2:
PF0139113=Collagen=PD(55.2=58.2)
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:
GGGCGTACCAGGGGAGAAAG
R:
AAGGCCACTTCTTCCAGGAGT
Band lengths:
238-1099
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]