GgaINT0068167 @ galGal3
Intron Retention
Gene
ENSGALG00000008141 | COL4A5
Description
NA
Coordinates
chr4:14028080-14029198:-
Coord C1 exon
chr4:14029031-14029198
Coord A exon
chr4:14028170-14029030
Coord C2 exon
chr4:14028080-14028169
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=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(30.0=31.6),PF0139113=Collagen=PU(66.1=68.4)
A:
NA
C2:
PF0139113=Collagen=PD(32.2=61.3),PF0139113=Collagen=PU(42.9=87.1)
Main Inclusion Isoform:
NA
Other Inclusion 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]