DreINT0049896 @ danRer10
Intron Retention
Gene
ENSDARG00000052061 | col4a6
Description
collagen, type IV, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-101001-2]
Coordinates
chr7:50650358-50651094:-
Coord C1 exon
chr7:50650903-50651094
Coord A exon
chr7:50650645-50650902
Coord C2 exon
chr7:50650358-50650644
Length
258 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGA
5' ss Score
6.04
3' ss Seq
GATTGTTCTCATTTCCACAGGAT
3' ss Score
10.53
Exon sequences
Seq C1 exon
GACCTCGTGGTAAACCAGGGTTGCCAGGTATTCCTGCTCCACCGACGCGCAGCACTGGCATTGGTTATACTTTGGTGAAGCACAGTCAATCCACACGGGTGCCCATGTGTCCTGAGGGAATGACCAGGCTCTGGGAGGGGTACAGTTTGCTCTATGTGGAGGGACAAGAGAAAGCGCACAACCAGGACCTGG
Seq A exon
GTGAGACATTAGGCTTGGAATAAGCAAGTCCACAAACTGTAGCTTACACTAAGATCGTATAAAAGACTAGCTTTAATGTGTGATATTGAGATTGTATGTGTTTTATGAGTTTAATTGAGTTTTCCTAATTCTATTGAGTAGAGGCTGATTCAACTTATCATTGAATCAGTTGATTATAAATACAGTTTAACATGAATATGCAGATGAGTAAGTTTCTCCTCAAGATGGCGCTGTGAAAGATTGTTCTCATTTCCACAG
Seq C2 exon
GATTGCCCGGCTCCTGCCTGCCTCATTTCAGCACAATCCCCTTCCTCTACTGCACCGCCAATGAAATTTGCTACTATGCAAGCCGCAATGACAAGTCCTATTGGCTGTCCACCACAGCGGCTATTCCCATGATGCCTGTGGCAAATCAGGAGATTTCCCCATACATTAGCCGCTGCTCAGTGTGTGAAGTTCCATCTCAACCAATCGCTGTCCATAGCCAAGATCTGACCATACCAACATGCCCTCAGGGCTGGAGAAGTCTGTGGATCGGTTACTCCTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052061:ENSDART00000121574:45
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.385 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(29.8=26.2),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
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:
ACAAGAGAAAGCGCACAACCA
R:
ACAGACTTCTCCAGCCCTGAG
Band lengths:
293-551
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]