DreINT0049044 @ danRer10
Intron Retention
Gene
ENSDARG00000078322 | col12a1a
Description
collagen, type XII, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-090728-1]
Coordinates
chr17:49809250-49811542:-
Coord C1 exon
chr17:49811396-49811542
Coord A exon
chr17:49809396-49811395
Coord C2 exon
chr17:49809250-49809395
Length
2000 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
ACTGTCATTCTCCTTCCCAGGAG
3' ss Score
9.41
Exon sequences
Seq C1 exon
GTGTAAAGAACGCAGATGAGAATGAGTTGAGAACCATTGCTTCCGATCCCGATGACATTCACATGTACAACGTGGCTGATTTCTCCTTCCTGCTGGACATTGTGGATGACCTCACAAACAACCTGTGCAACAGCGTCAAAGGTCCAG
Seq A exon
GTCAGGGCCATGATATATTCATGCGTCTTTACCCAATAGGAGAGTTGCTTCTTATTATATTCATCTGTAGTATCTACAATATGGAAATAGTGGGTTGCCTGTTATGTTATTTAATTTGAAAACGTTCTACTACAAGGCTGTTGAACGGTTGATTCTGATTGGCTGATGAACCTTCTAAGGTGCCCAGTTGTTTTTAGATAAATGCACAGCTAAAGTAGTTCCGGCAGGTTTAGAGTGCATTGGAGTTTTGTATCACTACGCTGAATGATTTCAGTTATTTCACAGTTACATCAGTGCAAAATCACATTAAAATACATCAAGAAGGGTTTGGATGAGGTGTTTAAGAAACTAGTGCTACACACAGAAGTAGTTTGAGGACAAATGCCTGAAATACAACATCTGAACAGTGTCATTAAGTGTGGTAACCAGCCTGATCTCACGAGAAAACGTAAGTATTTTACGTTTTGCCAGTTTAGTGGCTAATTCGTACGAATTCGTACGAGTTCAGTCGTACGAAATGGTACGATTTTAAAAAGGAGGCGTGGGCCCTTGACCCCACCCCTAACCCCAACCGTCATTGGGGGATGAGCAAATCATACTAAATTGTACTAATTAGATCGTACGAATTCATACGAATTAGCCACTAAATGAAAAAGTTACGAATTGCTGTGAGATTGTGTTGGTGGTATGAGTAGTAAAAGTGGAATAATTGATTGTGCTCTATTGAGTTATTAGAAAAAAAAAGCACACCAGAGGTATATCGATCACTCTGCTTGACATTATGACCACATCACCACCTTATTATGTGCATTATTTTCTAATGATTCAACAGGCCTTTGTCAATTATTCCAGTTACAATTAACAAACTGATAAAAACAACAACATTTAAATACACTTGAACACATTCTAAAAGAGGAAAAAGAGCAAAGAAAGGAAAGGCAAACACTTGTGGATTAGCTGATGACAGCACTCATCAACACATTAAGATAACACGGCTGCAATTCAGACACTATTCACCATGTAATAACACAATTTAAGCCGCTTAGTTTTACTTTAATCTCATGGGTCCTTATTAGAATGCAAGAAAAAAGACAGTCCTGACAAATTTTTGTTCCTGTGTTACTAAAACAAGGGATAGGATTCATTTAATATTAGCATGAGATTATTTTCTTTCTGAGAAGTCATAATCAGATAGAGAGTGAACAGAAGTATCATATTTTGAAGTTAAATATATTATCATTCTGTTTCTGAATATCTTAAATGACCACTTATAAATGAATCTCATTTTTAATGAATATTAATATGAAATAATGAATATGTTTATTAAGTGTACTACTTAATAACTGTTCTGTTTAAATGCACAATATATATTGTCTATATTCCTTGAGAAATGGGTAAAATGTGTAACAATAAATAATTTTTACAAATTTATATATATATATATATAGCTGAATTCATAATTATTAGCCCTCATGTGAAGTATATTTGTATTATATTATGTTATTATATTTATATTATATATATTTTTTATTCAATTTTTATTATATTATATTATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATGTTATATTATATTATATTATATTATATTATATTATTATATTATATTATATTATATTATATTATATTATATTATATATATTATATTATATTATATTATGCTAATGAAAAGAAAAAATCTAAAAAGTACTAAAAATGCACTTATTTATTTTAACCTTTTTATCAAATGTGTAAAAGTGAATTATAAAATAACTATAATAATAATACTACTAAAACAAAAGGTTTAAACATTCTAGTTATTTACAGAAATAGTGATTTAGTTGTAGTGAGAAACAGCCATGATGACAGACACCATAAAACTGTTCATTCTGGAGTATGTGAGGGGTCAAAGGTTGAAGCCTAACTACTGTCATTCTCCTTCCCAG
Seq C2 exon
GAGGAGGACCAGAGCCACCCACTGATCTGACCACCTCAGAGGTCACACATTACTCTTTCCGTGCCACTTGGGTGGCTCCTGACGGGCCTGTGGAGAAGTACAGAGTGGAGTATGTGAGCACCGCTGGAGGAGAACCACAGCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078322:ENSDART00000154728:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.260 A=NA C2=0.469
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=74.0)
A:
NA
C2:
PF0004116=fn3=PU(54.3=89.8)
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:
AGAACGCAGATGAGAATGAGTTGA
R:
CTGTTGCTGTGGTTCTCCTCC
Band lengths:
287-2287
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]