BtaINT0040760 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40676093-40678597:+
Coord C1 exon
chr3:40676093-40676161
Coord A exon
chr3:40676162-40678363
Coord C2 exon
chr3:40678364-40678597
Length
2202 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
CTTTATTCTCTTATTTCCAGCTT
3' ss Score
8.2
Exon sequences
Seq C1 exon
GTAAGAATTTCATCATGGCCAAAGGAGAAACCAGGAAGCTGGTTTAGTGAATTTAAGAGAGGAAAACTG
Seq A exon
GTATGTTATTACCTTAGCATGCATGGTGTATCTTAAACATCATAACTCAAGTTCAAATTATATAATCTCTAGCCCCTTACTGTGAAAGTCTAAATCATACAAAGCAGGATTCCATGTACTCTCTAGTTTGCTTTATCTAAATCTCTTAGACCAATTTTGGGATTTTTAGAGAGAAGTCTAAAATTTTTACCAAAATAAATGGAAATATATTAAATTTATTAAAATAATAAAATCAAATAAAGTATACATTTCACTAAGTACTTGAGATAGCATAAAAATGGACTATATTAGAAATATGAGTTATAGAGAATATAATATCTATTTAGGAAGGATCTCTGACTATTTCATTTCCTTTATACTTGAAATCTAATTTATTCTTTGTTTTCAATTGCAATAAGAATTTTTGGAATGTGAAATGTTTTTTCCAATAGTTACATCTGGAAATAAAGTGAGCTGACTGACTGACCTTTTATATGGATTACAGCACATGTTTACTTAGATATTTCCATAGAATTACCAGTTCGTGGTTAGTCATTTTCTAGAGATATTTTAACATTGCATGCCAAAACTAAATTTGCATTTAAAAGCTGTTTAAGATATATTTGTTTTTGAAATGTTAATTATAATGTATTCTAATGAAAGTTTCTCATTTATTCAGATAATTATTCAAATTTTCAATGTTCTTTAAAAAAATTATGATTTTCCATTTATGACTATTTATACAATCGTTATCCTCTAAAAATCTACACATATTACTAATATTCTCCACATTATAAATCTCTAGTTCAGTTTTCAAGTTACATATTAAATATCCATGTTACAGTTTTATCTTTGTGTGAGATAAAAATACATACACAAATAGAGCTCTCTGGGTGTAGTTTTATTTTTTGCTGTTTTGTTTTCCTTAGAGTGGATTTCCCAGTTTTTTTTCTCTAACCTCTCAGGTATTCTCATCATCTGAACTGTTTATCAGAAAGAATTAAGTAAATCAATAATAAGGAGGAAAAGTGAAGCAAAAGTTGCTTGTGGACAGTTGTCCATGGAATTCTCCAGTCCAGAATACTGGAGTGGGTAGCATTTCCCTTCTCCAGCAGATCTTCCTGACCCAGGAATCAAACCAGGATCTCCTGCATTGCAGGCAGATTCTTTACCAACTGAGCTATCAGGGAAGCCCAATAAGAAGGAAAGTCACAGATAACTGCCTTTATATTGAATTAATCTATAACCTGGGCAAATTTCTTACTTAATTTTTAAAATATAAGTTTATATGTCTCAGCTAATCCCAGATAGTTTATTTATACCCAGTAAAACAAATTACAAGCTTGACAAGAGAGACAGTTTTTAATAATTTGAAATTAGGACTGTGTTCCTTCTCAAAACGCAAATTAAGTATTTCCTGATAACAAATATTTACTTGCATGTCTCAGGCAATATGCTTGGTGCTGATGATACAAAGATGAATATAATTACATCAACTAAGAACAGACAAACAGGAGGTCTGTGGTGAAAATTAGAAGACCAAAAACCTCTTGGAAGACTGTGGCCCCAAAATGAAAAATGCAGGAATGTGTCGAAAATTTTGAATCAAACAGATATACTAGGAAAATAGGGGAAAACAAACATAAAAATAGTCTGTCTTTGCATTTCACTGAGATTCCTTGATTTTCATTTTCACTGTTTTACCACTCTATTATTCAAAAGGGCTTCCTTGATAGCTCAGTTGGTAAAAAAAATCCACCTGCAATGCAGGAGACCCTGGTTCGATTCCTGGGTCAGGAAGATCCACTGGAGAACGGACAGGCTACCCACTCCAGTTTTCTGGCCTGGAGAATTCCCTGGACTATATCAAAAAGGTACAGGAGTATAATGAAATAATTCTTGGAAACAAATAAAACAATTACATTTTTTTGTGGTATTTACTGACTGACTAGGAAAATGAAGTGTAGAGGTAAAATGATTTTTTTTTCCAAGATAAGTATTGTTGATAGTAGCTAAGGTGAAAACCCATCTTCATTTCATAAATTCCTATATCTGGGTGATATAGGACTTCTGACTCTCAGTGCATACCTTCTTTCATTAAGTAAGAAATAGGTCTGTTGATACATCCACATGCTTCTGGAATCTCAATTCACTGTTGACAGTGATTTTATTCTTTATAATAGAAAAGAGTCTTTATGTGTCTCTTTATTCTCTTATTTCCAG
Seq C2 exon
CTTTCATATTTAGATATCGAAGGCAATTCCATTAATATGGTGCAAATGACATTTCTGAAACTGCTGACTGCCTCTGCTCGGCAAAATTTCACCTATTACTGTCATCAGTCAGTGGCCTGGTATGATATGTCATCAGGAAGCTATGACAAAGCACTTCGGTTCTTGGGATCAAATGATGAGGAGATGTCCTATGACAACAACCCTTACATCAAAGCCCTATTTGATGGCTGTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:66
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141013=COLFI=FE(10.4=100)
A:
NA
C2:
PF0141013=COLFI=FE(36.3=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]