GgaINT0032159 @ galGal3
Intron Retention
Gene
ENSGALG00000004946 | COL4A4
Description
NA
Coordinates
chr9:10388240-10389787:-
Coord C1 exon
chr9:10389685-10389787
Coord A exon
chr9:10388386-10389684
Coord C2 exon
chr9:10388240-10388385
Length
1299 bp
Sequences
Splice sites
5' ss Seq
TACTTATGA
5' ss Score
-6.36
3' ss Seq
TTAGTCTAATTTACTTTCATATT
3' ss Score
-0.56
Exon sequences
Seq C1 exon
GTCCAATGGGAATCCATGGCTTACAGGGTCCACCTGGTGCTGTAGGACAACCAGGAGACCAAGGTTTTCAAGGAAAACCTGGTCCTAAAGGTCCCACAGGTAC
Seq A exon
TTATGAACTTGTTCCTCATTGGCACTCAATTGTAACTGTGATCTTTGTATTCATACATAAAACAATCTTACTATTTTTCACTTGTATAGAAACAATTTAAGCAAACTCAAAAAAATCTAAATGATTTCTCATTTGAGCTATGTAAAGACTTCCGAATTATGTGTTTGTTACTCCATATAAGTGATTTCAGTTCTCATTCCATTCTTTATTTTTGAGCTGTGTAAAGATTTCTGAATCACGCATTTGTCACCTCATAGAAATGATTTCAGTTCTCATTCCATTCTGTACTCTATTTGCATGTCTGAAATTTGATTCCACTTGCACTGCAATGGCTGAAATCTGCATTCCATTTTTCACATCCTTCAGGGTTCATAGGTAAGTTGATGACTATTGGTTATTGTCTGTAAGGATTTCCTTCTGTATAGGTGTACTACGCACTTACAGGAAGGTATTTTTGGCTTGGCTGGAATAGTAGATAATGCCACAACAACACAGCGCTAATAGGTTTTTCACGTAAACAGTTTGTGCTTCCAAGTATATCATAATACTACTACACTGAGAAGAAGCCTTGTGCCATGATGTCAGACATGAAAAATAACTTCCTTCAAATTATTTAACACTTTTTTCGTTGGTTTTTTTTTTTTTTTTTTGGAGAGGGTATGTTGCACTAGATATTTTCTAACCAAAACCTTGAATCCTAGACTGAATTAGTACAGACAGAAACTGAGCTCTTAATCTGTCTAAACCAACACAACTCTGATTTTGTTCCAAAATACCAGGAGTTACAGCCAATAGCTATAGCCATATAGCATGTAGCTATAGCCAGTAGCTCCTTGTAACTTTCAATACATAAGTGTGTCAATTCTTTATTACTACTATGAATGGAGATTGTGGGTTAGAAGAGTTAGCTCTCTTTCTTTTGCCTGCTTGTTGAGGGTTTTACAGTCGCAGAATAAGCAAAGTACTGTAAATGTTTACATGTGCTAAGGTGTTTGAGCTGAAGTTAAAGTATCAAGTTTACTTAGATCAGTTTGGGTCACATTAAGACAGAAACTGCACACCAATTGTTTGAAACATATCAGTTAGCATACACCTGATAACACATGCTTGCCATGCTGCTAAATGCTGTTCTTTAAAGACTGAAATTAAAAGCAGCGAGCATAGCTCAATGTTTTAAAATATTAAAGCATGCACTTCAATACTAAAAACAACTAACAGGTGTGTTGATTTTTCACATGGGAGCTATTAGTCATTTTTTCTGTTGTCATTTTAATGTAATTTAGTCTAATTTACTTTCAT
Seq C2 exon
ATTGCATGCAACAGGTGAGCCTGGTGAACCAGGAAAAACAGATGACTCATGTCCTGCAATCCCAGGGCCTCCAGGGGAAGCAGGACATAGAGGAGATGATGGTTCTATAGGATTACCAGGGCCAATAGGTCACCCTGGACCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004946:ENSGALT00000007918:42
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(51.5=100),PF0139113=Collagen=PU(14.4=37.1)
A:
NA
C2:
PF0139113=Collagen=PD(28.8=38.0),PF0139113=Collagen=FE(54.4=100),PF0139113=Collagen=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGAATCCATGGCTTACAGG
R:
CTTGGGGTCCAGGGTGAC
Band lengths:
243-1542
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]