BtaINT0040840 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14938329-14939223:-
Coord C1 exon
chr9:14939059-14939223
Coord A exon
chr9:14938476-14939058
Coord C2 exon
chr9:14938329-14938475
Length
583 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
GTATATCCATTTTCCCCAAGGTA
3' ss Score
5.94
Exon sequences
Seq C1 exon
GGATGGCCTTGAATTTCATTCGCCAGCAGAGCTTCAAGACCCAAGCTGGCATGAGACCTCGAGCTCGAAAAATCGGTGTTCTTATCACTGATGGAAAATCCCAGGATGATGTTGAGGCACCTTCCAAAAAACTCAAGGATGAAGGCGTGGAACTGTTTGCCATTG
Seq A exon
GTAAGTATGGATGAGAATAGCCGTGCCTCCACGGGTGACAAATATTTTTGCCAAGGATAATTTTGTAGTTAAAAATATTTTCTGAAGCATGAAAAATACAGAAACACACTTTCCCGATCACATGATTTATTAAAATAATGTGCCAGGAAGTTCATCTATTTTCTTCTTTTCTCCTTACAATGGGACAAAATTACATGGCTTCTTGGAAGAGAGTAATAAATCAAGAGGACAACTGTACTATTAATAGGATTCAGGAAAATTCCTGTTTGGTTTTCCACAGCATCATGTTTGTTTTTGATATCCACTATTTTATAATACTTTCCAGAAAAAAAACACTAAACAAACTCTTTTTGGTGGGGAATTGGTGCTAGAAGCATTGAGAAGAAGCCAAACAAAATAACCTTCAGTTTGTATTATTTTTTGTTTCTATTTAATTTATGTAATCATTTTATTGTTGGGGAAAATCTTATATACATTCTAGTTAACACGGAATGTATAAGGGTAGCCTATGAAATATTTGCTTTGTTCCATGAATTTTTTTCTGAGACATGCTTTTAATTTGTGTATATCCATTTTCCCCAAG
Seq C2 exon
GTATTAAAAATGCTGATGAAGTTGAGTTAAAGATGATTGCAACAGATCCTGATGATATCCACGCGTACAACGTGGCGGATTTTGATTCACTTTCTAGGATCGTGGATGACCTCACCAACAACTTGTGTAACAGTGTCAAAGGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:19
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=0.060
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:
ATGGCCTTGAATTTCATTCGCC
R:
CTGGACCTTTGACACTGTTACACA
Band lengths:
310-893
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]