BtaINT0040843 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14934672-14935471:-
Coord C1 exon
chr9:14935332-14935471
Coord A exon
chr9:14934802-14935331
Coord C2 exon
chr9:14934672-14934801
Length
530 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
TTGTAAATTTTCATCCCTAGTTT
3' ss Score
8.32
Exon sequences
Seq C1 exon
GTGACTTGGAAGCACCTTCCAACCTAGTTCTTTCTGAGCGGACCCATCGTTCTATGAGAGTGAGCTGGACACCTCCTTCTGACAGCGTGGACAGGTACAAGGTGGAATACTACCCAGTGTCAGGAGGGAAACGGCAAGAA
Seq A exon
GTGAGTAGACCTCACAACCCGCTCCTTCCTGTCCCGAGATTGGGTCCTCCTCCTTAGGGCTCTGGGAGGAATGCCGGGGGGGAAGTAGGGGGCAGAACTGGGTCCATGGTGGTGTTCTCCATTTCTTGCAGGGCAAGCACTTCCATTTGGGCTTAATTAGAGGGAAGAGCTTTTAATTTCTTATGCTTTCCAAGAATTGCACATATCAATACAATTTTTAATTAGGGATTAAGAGGGTGTTTAATTTGTTCATGAGTTTATACGAGAATCATCGAGTAGGAAGGAAACATTGAGGATGTTCTAGTTTTATGCACTCATCTTACAAATAAGGAAACAACAGCTGGGAGCATAAACTGTATGGATTATCCAAGATCTCACTGTAATCTGATAGTTTTCAAAAACAAAAGACAATGACCTCATTAAAGAATATTTCTTAAACTCATTGAAGTTAACTCCTTCACAATTAACAGTAGAAAAGAGGGAACTGATTCTAACAGAAGTTGTTATTTTTTGTAAATTTTCATCCCTAG
Seq C2 exon
TTTTATGTGAGCCGATTGGAAAGGAGCACGGTCCTGAAAGATCTGAAGCCTGAAACTGAATATGTTGTCAATGTGTATTCTGTAGTGGAAGATGAATACAGTGAGCCTCTGAAGGGCACAGAAAAAACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.234 A=NA C2=0.091
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
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:
AGCACCTTCCAACCTAGTTCT
R:
TTTTCTGTGCCCTTCAGAGGC
Band lengths:
255-785
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]