GgaINT0032161 @ galGal4
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
collagen, type IV, alpha 4 [Source:HGNC Symbol;Acc:HGNC:2206]
Coordinates
chr9:8792233-8793459:-
Coord C1 exon
chr9:8793343-8793459
Coord A exon
chr9:8792422-8793342
Coord C2 exon
chr9:8792233-8792421
Length
921 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTCTTCTGTGTGCAAAAAGGTC
3' ss Score
7.58
Exon sequences
Seq C1 exon
GAAGGAAAGGTGAAGAAGGGTCATGTGGCCTGCCAGGTCAAGATGGCTTACCAGGAGCACCTGGACCACCAGGTGACCAAGGGCATGTGGGAGAACAAGGATATGCTGGACCACAAG
Seq A exon
GTAAGAACAGTTTCTTTTTTTTTTTTGTCCATTTACTGCCATGAAATGGGATAAGCAGATACTGCAACTTCATTTTGAAAAGAACTTTGCTGATATTCTTGGATAGTGGTGGCTCCAATTCCAAAAACTTCTAAAGACTCAGCAGGAGTTGCAGCTCAAGAAGTATTGGATTTCCTATCTGTGCTATTGCTGCAGCTACCCAGACACATGACTTCTTGGACGGAGATGTGCAGGATGCACAGACTAAGTTTTCCTTACTCCCCTAGTTCACACGTGGATACATCAAACTCTAATCCAAGAAACTATGACACTTCTTTCTATCTTAGTTCAAGCACTGATAGTGACATTTCTGGTTACCTCCACAACACAAGAAATGCCTCTTGAAAGAAAATTCATCTATGATCAATCAGGCAATAAACCACACATACTTAAACGTCATTTATCAATAGGTATGCAACTCTGAGACAGGGCTACTAGTGCAATTGTCCAAGTAAATGAAATTGTATTTCAGCTCTGACAACTGTTTAATAAATTACCAGTTTAACATGTGAGGAAAATGCATCGACTGTTACAGCAAGGATTTAAATTCAGTCCAAAGTAATCCATGTGACTGAGTCTGGAAGATCATTGCCCACCTCAGATCATTTCTTCATAGGCAAATATCTATGCAGCACAGGACAGAGGCACAGTAGAAATGCCAGCTGTGAAACATTCTGTACAATTTAGTTCTTTTCTCTCTGATAACAAGGATAGCAAGAGTCTACTGGTGTATCTATTGACCATGACAACCTCTGAAGTTTGTATTAGATTCAGCCAGAAACCCCTTGTTGAACACTAAAATACAGTAAAAGAGAAACGTTCCCACTAGCTACGTGTTCCTGCAAGCAAATTCACCTTACCTTTTCTTCTGTGTGCAAAAAG
Seq C2 exon
GTCCACCTGGCCAGACTGGTATCCCAGGACCACCAGGGCCCCATGTTAGATCTTCAAGTGGATTCTTGCTCGTCCTTCATAGTCAGTCAGACAGAGAACCACTTTGTCCACAGGGGATGCCAAAATTATGGACTGGCTATAGTCTGCTGTACCTGGAAGGACAAGAGAAAGCTCATAATCAAGATCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:44
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=0.562
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(43.5=67.5),PF0139113=Collagen=FE(67.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(29.3=26.6),PF0141314=C4=PU(63.2=67.2)
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:
AGGAAAGGTGAAGAAGGGTCA
R:
AGATCTTGATTATGAGCTTTCTCTTG
Band lengths:
302-1223
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]