DreINT0049043 @ danRer10
Intron Retention
Gene
ENSDARG00000078322 | col12a1a
Description
collagen, type XII, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-090728-1]
Coordinates
chr17:49811396-49812008:-
Coord C1 exon
chr17:49811844-49812008
Coord A exon
chr17:49811543-49811843
Coord C2 exon
chr17:49811396-49811542
Length
301 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
ACATGTTCTGTGATCTGCAGGTG
3' ss Score
9.91
Exon sequences
Seq C1 exon
GCCTTGCTTTGAATTACATCCTTCAGAATAACTTCAAGCCTAACGTTGGCATGCGTCCAAACTCCAGAAAGATCGGCGTCCTGGTCACTGATGGCAAGTCCCAAGACGACATTGTGGCGAACTCACAGAACCTGCGGGACCAAGGGATTGAACTGTACGCCATTG
Seq A exon
GTAAGAACTAGTTTGCGTTTGTAGACTTTCTGTTTAGGCCTTTAAAGAGGCAGTTCACCCAGAAACGAAATTTCAGTCATCCTCAAACTTGTTCAAACATGTTTCTTTCTTCTGTTGAACACAAAGGAAGATATTCTGAAGAATGCAGCCATTGACTTTCATAGTATTTTTTTGTTCCTACTATGGATGTCAGTGGCTGCATTCTTCAGAATATCTTCCTTTGTGTTCAAGAGTTTTAAAACAACTGCAGGTGAGTAAACGAGGAAATGTTCATCTCTTTAACATGTTCTGTGATCTGCAG
Seq C2 exon
GTGTAAAGAACGCAGATGAGAATGAGTTGAGAACCATTGCTTCCGATCCCGATGACATTCACATGTACAACGTGGCTGATTTCTCCTTCCTGCTGGACATTGTGGATGACCTCACAAACAACCTGTGCAACAGCGTCAAAGGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078322:ENSDART00000154728:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.260
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(31.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.4=74.0)
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:
GCCTTGCTTTGAATTACATCCTTCA
R:
CTGGACCTTTGACGCTGTTGC
Band lengths:
312-613
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]