BtaINT0040721 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40573150-40574935:+
Coord C1 exon
chr3:40573150-40573203
Coord A exon
chr3:40573204-40574827
Coord C2 exon
chr3:40574828-40574935
Length
1624 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TGCTCTTACTTTGTTATCAGGGA
3' ss Score
8.37
Exon sequences
Seq C1 exon
GGTGAAGATGGTTTTCCAGGATTCAAAGGTGACATGGGTCTCAAAGGTGATAGA
Seq A exon
GTAAGTAAAAAGAAAATCTGCACTAGTACATGCATTTATGGATGTGTGTGCTTATTTCTATATAGTTAAATACTGCAAACATAGAATAAGTCAAATGTTTGTACTACCTGAGACATTTTTCACTTCCACTTTTATCTGAAGATTAGGTGTCTTAATTTCTGTGGAAATAAAATATTATTAGTTATTTTTTGGATGCTATGCTAAATATATGTCCCATAGCATATCTACAAATGCATAGTTATATATTTATATATATATATATGTATAAATACACAAAATATATATTGTATCATATATGGTGTTACTCTTCACAGACATTTTATAAATTGATGATCAAATTGCTTTATATAATTAATTCAATAGATTTGTTTTAAATCTTGTTCATATATAATGAGCTATGCTTCCTGGAGACTATATCTGCAACTTTCATGAATTTTCACTTTATAGTTGTCTTGAATTTTTGAGTCTGAATATAGTACACCGTTTTTCTGTTAGCGAGTATCTTGAAAATAAAAGTTTGTCACCTAAAGTAAATTAAATGTTTTATTGGGAAAATTTGTTTTATAACTAGCATAATAGTATCTAATAAATGGAATAAAAAAACATGGTATAGAATATTGATTTTCCTAAAATGCATATAAAGCCTATGTCTGGGATGGGAGCAATAGCATACACATTCTAGAACCTAATACCTTAAATGTGAAAATAAAGTTTAAAGTCAGGTGAGATATTTTTCTTATGTTCCAATCAGTGATTTCCAAAGTTGCTATCATCTGGGAGGAAAAATTATTTTCCCTCCTACCCTGATAGAGTCTCAGACTGGAGCCGTCTAAAATTACAGAATGACAGAAGACAGATTAATAAGAGATAAGCAAACAGAAGTTTATCTTGTGTATCATGATTATACATGGGAACGCTAAATGATGAGTAATTCAAGCGTATATCATTTTAGCAAAGGAACAATAAATTTTAAAGAAGAAAGGACTTTGAGTTTCTAGTGCTATAAACTGTGGGAAGGCAGATAAATGGAAACTATTAATGTTATATAAAGGCTAGTTGGAAAGTTTGCTGTATAGATATATTCCTCTGGTGCTTGCTTCTGGCTCCAGACTAGTAAGGGTCTAGTTACCTCTAGTGACTAATTTTTGTCTTTTCTGATGAAGAGGGTAGGAAAAACACCTTTGCAAATTTGTTCCCCGCTTTTAAGCAAGTACAGGGTGGGTAGATCACTTTTTCTGTATCTGCTCCTTCTCACTTGCCTTCAGTTCAAAATAATCCTTATGCCAAAGTGGCGTATTTTGGGGTAGCATATATTGTCAACCTATAGTATCTAATTTTGATTCTTATTTTCTCTTTCTCTTTCTGTGACTCAGTGAATTAAAATTAATTTAGTGTGATACATGGTAGCATAGGACTTCTGTAGCTTTTCAAATGTCAGACTGTATTGAGTCATTTATGTATTAATTGAAAGATTGATAAAGTCAAAGACTTTCAGTCCTCTTTGTCATATATATGAGTAAATAAACCAAGAATTGAAGAATATAACTTTTTGATGAACTATAATTTCTGCCGTTCAGTCTCAAAGATATTTTAAGTTGCAAGAATGCTCTTACTTTGTTATCAG
Seq C2 exon
GGAGAAGTTGGTCAAGTAGGTCCAAGAGGAGAGGATGGCCCTGAAGGCCCCAAAGGTCGAGCTGGTCCAACCGGAGACCCCGGTCCTCCTGGTCAAGCAGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.5=100),PF0139113=Collagen=FE(20.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(4.8=11.1),PF0139113=Collagen=FE(42.7=100),PF0139113=Collagen=PU(18.0=30.6)
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:
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]