BtaINT0040890 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020056 | COL12A1
Description
collagen, type XII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr9:14869899-14872008:-
Coord C1 exon
chr9:14871838-14872008
Coord A exon
chr9:14869931-14871837
Coord C2 exon
chr9:14869899-14869930
Length
1907 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CTACCTGGGTTGGTTGACAGTTT
3' ss Score
5.18
Exon sequences
Seq C1 exon
GTCCACAAGGAGAATCGAGGACGGGTCCACCAGGGTCCACAGGTTCCAGAGGTCCTCCAGGTCCCCCTGGTCGTCCTGGAAACTCAGGTATCCGAGGCCCCCCGGGTCCTCCTGGATACTGTGACTCATCCCAGTGTGCCAGCATCCCATACAATGGACAAGGCTATCCAG
Seq A exon
GTATGTTGTTGCCATTATAAGGACCCAAATTCAACTGAATTAAAAAAACCTGTATGGAAATAAAGTTCCCTAGGATTGAAGGAAAGTTGATTTTAGGATTTCTTGAAGATAGAACCTCTTTCAGTTGTGTGTTTTGATTATATAGTAATAGTCTCTCTCAAAAGAATCAATGTTAATTTTAATGACATTATTTCACTGATAGAAGTTGAATATTTTCTCCTTCTTTCTATACTTCTGCATTTATCAAATCACAACATAAACTTTTCTGTTTCTCCTGATAGTTCAAAGAATGTTATTGAATTTTTTTTTTTTTTTTTTTGCCTAAAAAAACCCTGTAGAATGCTAAGAATATATATAAAATTTGTTTTGGGAATCTAATGTGTAGGCAGACTATTTGATAACATAGTGGAGGCAACTGAAAATATTTCACTATTTCGCTTTGTCCATGAATTAGTATTTTATAAACTCTGGAACCTAATTTTTCAAGAGTTGGTCACGAAATTCTAATATTTGACAATTTGACAATTACAGGAGGCAGAAGTCTCTTAAGCCTGAATTCGGGGACTATGGGGACAGAGGCAGTATGCTGATTTAGAGATTAAAAAATTAATGCTGTGGGCAGTGGTCAGCAGTGACCTTTTTCATCAGTGCACCCTCAAGCATCTTGCAAGTTTTAAAAATGATATGCTGTTTGATATGGTTGGCTACTAGCAAGTACTGCATGAGTAGTTGAATATCTAAATATCTATATATCTATATATTTATGTGCATACTTATATATGACCAAAAAGAATCATGAATCTTAAGTTTCTTATGCAAACCATTCACAAAATTGTAATTTCATTCTTTATCAAAGAAATTTTAATTACCTCTGCCTTCTGGTATGTATGAGTAACTTGAAATATATGGATATATACATATATAATTTAACCATTACATACTTAAATGAATGTGTATAGATATTTTTTTTTTGCATAGTAATTCAACTTTTAAAAACTATCATCTTTGACCTGTTTCAGGTTCCGGCTAACAAATTTTCTAAGTCGCCAGTGCTGCTTACAGTTTGAATACATGAAAATCCTGTTTCTGAGATGTTTGCGCACGTGCTTATTAGAAAATGAGTCTGTATGGAAATCTCACCACAGATCTGGTTAACGAACCGGGTGGACATCATAAAGGAGGGTGGAGACTCTTTATACTAACTTGAATGAGACAAAAGCAGTGGTGTTAGTTTATAAGCCTGATGCATTTCAGTAATAATGTAGAAAAATATTATTTAAAAAAAAAGTTCAAACACAGCTCATGAGGCGCCTCGGTTGTGAAAGAGGCGCATAATAAAACTACTAACCGCGGAGATGATGCCATTTCGGGAAAAACAATTAACCTGGTTAAAGAGAAGTACCTTATGTAAATAATAAACTAATTATGGCTTGTAAATGATTTGTATGTGATACTGTCCACTAAAATCACTTAACAATTCTACAATCAGCTTCTGCCTGCCGCTTGCTCTCTGCCAGAATAACATCGAATTAGAATCTCCTCATCTCTTGCTTGTTAGCGATGTCTGATTATCTTATGTACATGTACTCTCATTTGGGTTTTTGTAATCATCCTTTTCAAACCAAAATTTTAGAATCCCTTTTTTTCTTCCTGTTTTGCTGTCGTCACGGGTGATCCTCACCCACCAGTTGTAACTCAGGCTGTGGGCCAGACAGCCACAGAAAACGTCGTGTACTGTATATTACTTGGTGATAATTGATTTTCACCTCCAGAGTTCAGTTTTAAGGAGCTAATATAACTTCCCCATCACTTGCTCATCTTTCCCAGTGGTTCTCTGAACTGAGGAATTTGAAGTCATGAAGTTACTTGGGGATTTGCAAAAAAATCCTACCTGGGTTGGTTGACAG
Seq C2 exon
TTTTCTTTGGCCCAGTTGCTGACCCTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020056:ENSBTAT00000026725:64
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.983 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(75.0=72.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACAAGGAGAATCGAGGACGG
R:
CTGGAAAGGGTCAGCAACTGG
Band lengths:
200-2107
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]