BtaINT0040837 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14939522-14941508:-
Coord C1 exon
chr9:14941387-14941508
Coord A exon
chr9:14939672-14941386
Coord C2 exon
chr9:14939522-14939671
Length
1715 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCTCGTGATTGCTGCGTCAGGGA
3' ss Score
2.89
Exon sequences
Seq C1 exon
GGCAGGTACCACCTATAAAGTAAACGTTTTTGGAATGTTTGATGGAGGAGAAAGTTCACCACTTGTTGGACAAGAAATGACAACTCTTTCTGACACAACTGTAATGCCAATTTTATCCTCTG
Seq A exon
GTAAGAAATTGAATTGCATTCTCCTAAGAAAAGTCAGTACCACGCAACTTTTTCAAATGTAAAGTGTTAGATTAATTATACCATGAAAATCAACCATTAAATTTTATGTTAAAATTTATTTCAGTAATATATACTTTAAAAAATTCTACAGACATCCAGCTAAGCACACTTTGCCAACATTTTTTTTAAGGCTTTCTTGTCAGCATTACATTAGTTACAGAGTACTGTATTGTTTAAAGCTGAGTTTTTCAATGGGTAGATGATGTACATTTCTCTCTTTTTAATGATTCAAATGCAGTTTTATTTCGCTAAAGTAATTGTAGAAAGGATTTATTTGGGCTGAGCAAGTGGTATTTGGTTATTGATACGTTAATAGGTGGGCAGCTAAGACTTGGAAAGCAAAATGGTAACATAAACCCCTTAGCCTTTCTGCTGCTGCCACGACTACAGCTTTGATACACATGAAGCTAGATTTGAACATTCTTAGCAGTGAGGGTGGTGGGTAGAGTTTACTTCTAAATATTTTCATCATTTGCTTATAAAGAGTAGGTCTTGGAAGAGCAGGAGCAGACCTGTAAAGACATAGGTGCATGGATGGCGTTGGGGAATCCTCACTCCGATGGCCCGTCCAGTATGCCAGTGATGCCTTTGTAGTATAATGAGCATCACTGAGTTTGCCTCAGTTTTTTTTTTTTAATAATATAAAGATCAGATGCTAACGTGGCAAGTAGTTGAAAAATTCATAGCTGGTAACATAAGCTCTTGGAAAAGAAAGCATTTGAAAATATGGATGTGGATAAAATAAAGTCTCAACTCTTGCTGTTTTGCATTGATGTTCTATTTTTTCTCTTATGATGATATTAACTGACTTATATTTTTATTTTGTAGCTTGTGCACTGAGGATTTGGGATAATTCTCTCTTTCCAAAGCACCCTAGCTTTGTATCAGTGTTTGTCCTTGTGGTCTCTGTAGCTCTCGATTTGTATACTTCTTTGCATCCTTTTTTCTAGATTGTCTTCCTTCTCTCTTGATTTTTTAAATGTGCAGATTTCACCATTTGTATTTACCTGATTCTTATATGTAGTAGATGATTAAGTTATTTAAAACTAAATAATAGCCATCAGATTTTTAAACAATATATTTTTTACTTCAGAAGGGTTGAGAGTTCTGTGCCTAATCCTTAATAATGTATGTATTACTGAGAGTTTGCATTAATTCAAAAGATATTTTTGGCTCACTGAACCTTTTTCTGGCTTGCACATTTTAAAGTTCATCTCATACTTGTCTGCTAATGACCACTGAAAATTAAGGAAAATGCAAAGTTTTACTAAAATTATTATTTCCTTATAGTCAGAAGGCTGTACATTCCCTCTTCTATATTTCAGTGTTTGGGTTTGTGAGCCTATTCAAATTTATAATGGCAGTTTAAGTCTCCATGTTCTATGATTGTGGCCATAAATATAGTCAAAGATGAAGGAAAGATTTTCCACTGAAATGGTTATTAGAGGGATGGATAGTTCCTGTGATTCTTATTTGAAGCTCTAAGTCATATGGACGTGTTTTCAAAGTCTTGAACTCCCAATCACCTCACTGAGCCACAGAACTGAGATTGTTAGGTGACCCTGGCCCCCGGGGGTGGCAGAAGAGTGCGCTGGGAAGTAACGTGACAAAGAATGTCCCCCTGACTCCATGCTGTCTCGTGATTGCTGCGTCAG
Seq C2 exon
GGATGGAGTGTCTCACCCGGGCTGAAGCAGACATCGTGCTGCTGGTGGATGGATCGTGGAGCATCGGCCGGGCGAACTTTAGAACCGTCAGGAGCTTCATTTCTCGTATTGTGGAAGTCTTTGAGATTGGCCCCAAAAGAGTACAGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.143 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(24.7=47.6)
A:
NA
C2:
PF0009223=VWA=PU(23.1=78.4)
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:
ACCACCTATAAAGTAAACGTTTTTGG
R:
TCTGTACTCTTTTGGGGCCAA
Band lengths:
262-1977
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]