BtaINT0040836 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14941387-14943006:-
Coord C1 exon
chr9:14942814-14943006
Coord A exon
chr9:14941509-14942813
Coord C2 exon
chr9:14941387-14941508
Length
1305 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
TGTATATTTTAACATTTCAGGGC
3' ss Score
8.24
Exon sequences
Seq C1 exon
CTTCTCGATTTAAATCACCCAGAAACCTCAAAACATCTGATCCAACCATGTCAAGCTTCCGGGTGACTTGGGAGCCTGCACCTGGTGAGGTCAAGGGTTACAAGGTCACGTTTCATCCCACGGGAGATGACAGAAGACTGGGGGAGTTAGTGGTTGGACCGTATGACAACACAGTTGTTCTAGAGGAACTTAG
Seq A exon
GTAGGAGTGAACTCTATTTCATTTTTGTTAACAGATTGCATAACCGATGTAAATTTGTAGGCCTTCCACACACGAACACTTATGTGTCTGTCGCTGGCAGAGTATTTAAAATCAGCCCAAGTTGCTTTCTCACTCTTGTTGAGGCTGAAGTTGAGATTTGGGTTCAGACGTTCAAATTTAGGCCTGAACAAGTGTACGATTTTAATGATGTTTGTTACTAAGAGATCAGGAATGGTGTTTTTTCCCACAGCACCCCTCTTTTAAAAAACTGACATCCACATCGCACCATTTCACCAAGAGCAGCTTGTCCCCAACCAGCCCCATGGAAATGTGGGTGTTCCTGTGCTTCAGGAAAGGCCCAGGGGCTGACCCAGAGATGCCTGCGTACATCCCCTCCCAGGAGTGAGGGAGGGAGTGGGCCTTTGTGCTTGGGGTCAGCTGAGAGGCTTGGGGAAGTGGGGGCTGATGGAAGGTCTTGCTGTAGGCTCCGCAGTGGAAAAGAAGGAGGTTTGAGTTTGAACAGCAGCCTACATCCTTTATAGTGAAAAAAAACAGAGTGCTCTGCATTCATTGCCAGGTGGAAAGTTGAGTTGTTTTGACTATTCATTCAACAACACTGATATCTGTTTGCACAATACTTATTTTTATCAGAATAGGGAGGATAAAATTGATTGAGCCTACTATGTGCCAGGGGGCTTCCCTGGTGGCTCAAATGGTAAAGTATACACCTGCAATGCAGAAGACCCAGATTCGATCCCTGGGTGGGGAAGATCTTCTGGAGAAGGGAATGGCTACCCACTCGAGTACTCTTGCCTGGAGAACCCCATACACAGAGGAGCCTGGTGGGGCTGCTGTCCATGGGGTCACAAAGAGTCCGACATGACTGAGCAACTTTCACACACTATGTGCTGGGCACTGTGCCAGGGCTTTATGTTTCCTTGCAAGTACAACATTTTAAATTGTTTTCTTAAAGCCCATTACTTAGCAGTAGTAAAAGTGAGAGCTTGACCCTTTCCTAACTTGCTCAGTGGGAAGGTGGGAATTCTACATTTGATGAAAGGCAAGGTGGAAACTGGTGCCCTGAACCCCCAGTGTTCTCTAGGATGCTAGTTTCCCTCGATACCTCACAGTGTGAGCTTAAACTGGAATGTGATGGAAATTATTCTTCTTCTCTTGCAATATTATGTGTTATAACTTCCTCTGAATGAAAGTTTGTACATCAAGATGAGTATTTATAACAAAACAAAAAAAAATGCTACCACTTGAGCCTATTATACATACAGACTGTATATTTTAACATTTCAG
Seq C2 exon
GGCAGGTACCACCTATAAAGTAAACGTTTTTGGAATGTTTGATGGAGGAGAAAGTTCACCACTTGTTGGACAAGAAATGACAACTCTTTCTGACACAACTGTAATGCCAATTTTATCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.415 A=NA C2=0.143
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(74.1=92.3)
A:
NA
C2:
PF0004116=fn3=PD(24.7=47.6)
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:
TCGATTTAAATCACCCAGAAACCTCA
R:
CAGAGGATAAAATTGGCATTACAGT
Band lengths:
311-1616
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]