DreINT0049791 @ danRer10
Intron Retention
Gene
ENSDARG00000002831 | col4a4
Description
collagen, type IV, alpha 4 [Source:ZFIN;Acc:ZDB-GENE-101001-1]
Coordinates
chr15:36117024-36118730:-
Coord C1 exon
chr15:36118563-36118730
Coord A exon
chr15:36117168-36118562
Coord C2 exon
chr15:36117024-36117167
Length
1395 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAG
5' ss Score
5.2
3' ss Seq
CTTTGAAACTCTTTGTCCAGGTT
3' ss Score
6.11
Exon sequences
Seq C1 exon
GCTACCCTGGAGAGAAGGGGTCACTTGGGGAGCTGGGATGTCCTGGCATTGGAGCCAAAGGAGCCCGGGGTAAACCTGGTACTCCTGGACCCCAAGGATGCATAGGCCTTCAGGGACCCGCAGGAGTCAACGGTGACGGTGGAAATCCTGGATATCCTGGACCAAAGG
Seq A exon
GTAAAGAGTCTTTCGAAGAGAGCTTAATGTGTTTTAGGAAGTTAATTTTAATGTTAAATGTAACTCAATTACAACAAATGCCTTTAACTGCCATCTGTAACAATACATTTGGCTTGGATTTGTATGGAAGTTAGATAGATGTGGTCATCAAGGCTTATTTTAAATACACAATAGATTTACACCGCTAAGAGATTTTGTCTTGTTTCTAGTCCAAATATCTAAACAATCTTAAATCAACAAGCATATTCTAGACATGTAAAAATGTTGCTTTATTTTTAGAAATAATGAGTCAAAATTAAGTGAGATTTTTCCTAAAACAAGCACAATAATCAATTTGTGGGGCAAGTAAAATAATATTGTTTTCAGTTTGAACTTTGAAATAAGATTATTTTAATTTCATATTTTTAATGTTGACATATTATTCTGAAACCAAAACATACATTTTTTTTACTTAAATGCTTCATGGTTTAAAATGTTGAAAAACTGAAATAAAAATAAAAAGTAAGAAAACCATTTTTGCATTGTAAAATTTTGGGGTTGAACATGTTTTAAAAGTAGTTGTCAGCAACATTGCATTTTTACAAAAAAAAAAATACAGCTATTTTCTGAAATGTGATTGCAATTTATAAATTCTTTATTGTGTTTTAATATATTTTTAAATGTAAAAAAATATATATTTCTTTGCTGGCAAAGCAGCCTTGAAAAGCTGTCACTCAATCCTTCAGAAATCATTCTAATATGTAGTTTTGGTGTTCAGTAAACATTTCTTATTAATATCATCAATGTTGAAAGCCGTTGTGCTGCTTTTTGGTAGAAACAGTGATGATTATTTTAATAAATAGAATATTTTGTAATGTTACTGTCGCTTTTGATCTTTTGGTATTTCCAATACATATTATGTGAAATATTATGAATTAAATGGGGAGAATAGACCTAAAGCACAGTATTGTATGTTTCCTTTCTGCACACTATTACAGCAAAATACCAAAATAAAATCAAAAAATTCACAAAGAAACGAAAGAAAGCCTGAAAAGAGCTCTTGTCATAGATATTCTTGTTATATAAGCTCACATTAAAACACCGAGCCTGTTGTTTTCCTGAGATCTAAAATCCAAGAACTGTAAAGAGATGATGCCAACCATCAAAGACTTCAAGAACAACACATACACTTAATACACAAATACACTTCATTAAACATGTACACATGGATATAACTTTACTAATAAAAACTAACCTATAACTAACCTATAACTAACCTATAACTAATAAAGTTAACTAATTACCTAAACTTTTTTTATTTGATTGTAATGCAGTCATGTGCACCTTTTGTAAAGCTGCTTGGAAACAGTAATTATGATTCTCAGCTGTCTTGTGTCTTTGAAACTCTTTGTCCAG
Seq C2 exon
GTTTGCCTGGACCATGTGGACAAAACGGCTGTCCTGGAAACATCGGGCAGACGGGCTGTTTAGGGCCTCCTGGACCGAAAGGCTTAAAGGGCCTCAATGGATGTTCAGGCTTCCCTGGATTTAACGGAACCAAGGGCCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002831:ENSDART00000154476:31
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=0.653
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(27.9=33.3),PF0139113=Collagen=PU(67.2=71.9),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PD(29.7=38.8),PF0139113=Collagen=PU(79.3=93.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGAGAGAAGGGGTCACTT
R:
CTGGCCCTTGGTTCCGTTAAA
Band lengths:
303-1698
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]