DreINT0049895 @ danRer10
Intron Retention
Gene
ENSDARG00000052061 | col4a6
Description
collagen, type IV, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-101001-2]
Coordinates
chr7:50650903-50651790:-
Coord C1 exon
chr7:50651674-50651790
Coord A exon
chr7:50651095-50651673
Coord C2 exon
chr7:50650903-50651094
Length
579 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
CTTTGCTATGTCCCCCACAGGAC
3' ss Score
11.33
Exon sequences
Seq C1 exon
GCCCCAAAGGATTCAGAGGCCAAGTGGGTAGACTTGGTCCAGTTGGATTAGCTGGATCTCCTGGATTTACTGGTGATCCTGGTCCTTCTGGAATCCAAGGACCCACAGGACTCCAAG
Seq A exon
GTACAGATTGCAGCTGTAAATGTTTGGAAGCAATACTTTGGAAAAGATGGTTCATGATCAACAGATTAACGAGAAAAACGAATAAAATGTTTAAAAGACTGTGTCTAATCGAACAAATCTTTAGGAAATTAATATTTTTATTTAGCACAGACTCATATAAATTATGGTTTAATAATGCATTTCAGGTCATTAAAACCAATATATTTCTGTTGATAATTTATATAGTGTTGGATATTGATTTTTCATCCCATGCAATATTTAAATCTTTAGGCAAAACTGGATGAGAACTGCAGTATCATCCAGTGTGTTACTTCAAGAAAAAAAATATCTTAATATTAAATTGTATCTAGTAATCCTAAGAGTAGTTTTTGCAATAAATATTGTGTACATTGAAAAGTAAATTCCTTAGCCATATCAGGTAGACATTTTACGTTTGATACTTGATTTTACTTAAGGTAATTGTAAATTTCACTAAAACATTCTGGTTTATATCTTTCCCCCTTCTTCTCTTGCCTTTTCTGTAACTTCTGCTCTAAATTTTTTACTTTAAAATTTTAAACTTTGCTATGTCCCCCACAG
Seq C2 exon
GACCTCGTGGTAAACCAGGGTTGCCAGGTATTCCTGCTCCACCGACGCGCAGCACTGGCATTGGTTATACTTTGGTGAAGCACAGTCAATCCACACGGGTGCCCATGTGTCCTGAGGGAATGACCAGGCTCTGGGAGGGGTACAGTTTGCTCTATGTGGAGGGACAAGAGAAAGCGCACAACCAGGACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052061:ENSDART00000121574:44
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=0.385
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(46.7=70.0),PF0139113=Collagen=PU(68.4=97.5)
A:
NA
C2:
PF0139113=Collagen=PD(29.8=26.2),PF0141314=C4=PU(39.8=66.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCCAAAGGATTCAGAGGC
R:
CCTGGTTGTGCGCTTTCTCTT
Band lengths:
303-882
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]