GgaINT0032136 @ galGal3
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
NA
Coordinates
chr9:10411619-10412428:-
Coord C1 exon
chr9:10412324-10412428
Coord A exon
chr9:10411784-10412323
Coord C2 exon
chr9:10411619-10411783
Length
540 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TCTGTATCACTGCTTTACAGGTC
3' ss Score
8.55
Exon sequences
Seq C1 exon
GCCCACCAGGAGATCCTGGATTTCCAGGTCCTGCGGGTGACATGGGGTCAGTTGGACCTTCTGGCCCTGTGGGTATGCTAGGAAGACCAGGAGACGATGGAACAA
Seq A exon
GTAAGAGATTTTGGGAACAAAATAATAACTCTATACCAGTAAGAGAGAACTAAAAGAAAACTCTTTGTTCTGGTTTCATGCAAGTCACCAACAATAAGGATTTGGGGTCCACAGAAAATGAAAAAAAAATATATATTATCCCAGTACTTACTCATACTAAAAAAAGAACCAAAATGTTCCAAATAGAGCATTAGGAGTTGCTAGAAAATGAACAGAAGGCAGAGCAGAAAATGCTGCCATGTACTGTATATCCATGGTGTACCTGTATCTGTAGCATTGTGCTCAAAAATCCTGTTCACAACTTCAAAAAGTTGTAAAGGAGATGATATAGATGACTTGGCTCTATATAAGGACCAACTGAATAAACTGATGTCTGGACAGATAACGAGGAGAAGGAGAAGAGGCATTTGAAGGTACAAAGCAGAAGCCACTTGTGTTTCCTGGGGAAAGAAAACATAAGTATTTAGATTTAAGTCTTATTTATCGAACAGAGTCTCTTCTGCATGACAGTTCTGAATTGTCTGTATCACTGCTTTACAG
Seq C2 exon
GTCTGCCTGGCCTGCCAGGAATAAGTGGGGCACCAGGACCTCAAGGTTTTCAGGGTGACCCTGGTTTGCCTGGAACAGGTGAAGCAATTCCAGGAAGACCTGGATTTCCTGGACCACCTGGACTACCAGGACAGCCAGGAAGACAAGGCTTACCTGGACTACCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:19
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=FE(42.2=100),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PD(28.9=42.9),PF0139113=Collagen=PU(91.7=98.2),PF0139113=Collagen=PU(32.0=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATTTCCAGGTCCTGCGG
R:
TAGGTAGTCCAGGTAAGCCTTGT
Band lengths:
254-794
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]