GgaINT0032161 @ galGal3
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
NA
Coordinates
chr9:10385080-10386306:-
Coord C1 exon
chr9:10386190-10386306
Coord A exon
chr9:10385269-10386189
Coord C2 exon
chr9:10385080-10385268
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=1.000 A=NA C2=0.453
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(30.0=67.5),PF0139113=Collagen=PU(68.4=97.5)
A:
NA
C2:
PF0139113=Collagen=PD(29.8=26.6),PF0141314=C4=PU(39.8=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]