DreINT0049040 @ danRer10
Intron Retention
Gene
ENSDARG00000078322 | col12a1a
Description
collagen, type XII, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-090728-1]
Coordinates
chr17:49815588-49816828:-
Coord C1 exon
chr17:49816679-49816828
Coord A exon
chr17:49815708-49816678
Coord C2 exon
chr17:49815588-49815707
Length
971 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
ATATGTTTGGGGTTTTTTAGGTC
3' ss Score
8.9
Exon sequences
Seq C1 exon
ATGCCCAGTGTAAAACCACGGCCCAAGCGGATATCGTCCTGCTTGTTGATGGATCTTGGAGCATTGGTCGCCTGAACTTCAAGACCATACGCAATTTCATTGCTCGCATGGTGGGAGTCTTCGACATCGGCCCCGATCGTGTCCAGATTG
Seq A exon
GTAAGAGAAGCACCTTACTGAGAAAATCGATCCGTGAAAGAGAAAAAACAACTAAACAGGTCTCATTGCAAGTTAGCAGGCAACAAAGAGAGATGTTTACTTAAGATTTCCATTACTTAGATGCTACTCTTGAGTTTGAAGATCACATTTGGGTTATGTTTTTACTTTAAACTGATGTTATCGCTACAGGAAGTACTGAATAATATTAATTAAATACTCTGTACTAATTACTAATTAACTAATGAGTATTTTTAGGGTTGGTTGCTTATAGTTAGGCATAATTGAGAAGTATTACTATTGATATTCTAATTATTATATGGTTAGTGTACAGCAGGGTCACCAATCTTGGTCCTGGAGGGCCGGTGTCCCTGCAGGGTTTAGCTCCAACTTGCCTCAACACTCCTGCCTGGGTGTTTCAAGAATACCTAGTAAGAGCTTGATTAGCTTGTTCAGGTGTGTTTGATTAGGGTTGGAGCTAAAATCTGCTGGACACCGGCCCTCCAGGAACAAGTTTGGTGACCCCTGGTGTACAGTTTAAACGTTTTTTGTATCCATTTAGCCTGTCTGGCTGGATCACTTTTAGCTTAGCTTAGCATAAATCATTGAATTGGATTAGACCATTAGCATCTCAGTCAAAAAATGTCAAAAAAGAGTTTTGATCATTTTCCTATTTAAAGCTTGACTCTTCTGTACCTATGAGAGGATAGGAACTATACTCTCAATCAGGCGTAATAATCAAGGAACTTTACTGCTGTACCATGGAGCAACGAAATATGACACAATTCTGTAGTAAACAAGACTTAATATCTAATGTCATTCAGAACGTCAAGTAAATGTATCCTAATTTCAGAATTTTTAGTTATTTACACTAAAGATTGACAAATCAATATGTAAACAATTAGATTTGTAGTATAAAATCTGAGCATTAAAATCTTCACTACATCTGATGCTATATGTTTGGGGTTTTTTAG
Seq C2 exon
GTCTGGCACAGTACAGCGGAGACCCGAAGACTGAGTGGCATCTCAATGCTCACAGAACCAGGACTCAGCTGCTGGATGCGGTGGCCAATCTACCCTACAAAGGAGGAAACACTCTCACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078322:ENSDART00000154728:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.098
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.1=78.4)
A:
NA
C2:
PF0009223=VWA=FE(23.1=100)
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:
ATGCCCAGTGTAAAACCACGG
R:
CGGTGAGAGTGTTTCCTCCTT
Band lengths:
270-1241
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]