BtaINT0040727 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40583740-40586658:+
Coord C1 exon
chr3:40583740-40583784
Coord A exon
chr3:40583785-40586604
Coord C2 exon
chr3:40586605-40586658
Length
2820 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
CTACTGCTTTTTCTTTTCAGGGT
3' ss Score
11.6
Exon sequences
Seq C1 exon
GGCACTTCAGGTGGTGATGGCCCTCCTGGCCCTCCTGGTGAAAGA
Seq A exon
GTAAGTATAATAGTTACATCATATAAATGTTTGTATTTCACAAGTGTTTAAATTTCTGGGAAAAGACATGTGTTTGCAAATCCACAAAACATCAGAGTTTAAAAGTTCCTATTCTTTAATATGTGTGTGTGTGCTAAGTCGTGTTGGTCATGTCTGACTCTTTGCGACCCTATGGACTGTAGCCCACCAGGCTCCTCTGTCCATGGGATTCTTCAGGCAAGAAGACTGGAGTGGATTGCCATGTCTTTCTCCAGGAGATTTTCTTGATCCAGGGATCGTGTCTCACGAGTCTCCTGCATTGGCAACTAGATACACGTGGGAAGCCCACTCTTTAATTTACTTCCTTAAAAAAATCTTCATCATTTATGTGCTACTAATTTTGTTATAGAAGTGAGAGAAATTATATGTGTAACTGGCGTATGTTATTAACTCTTAAACCGAAATCTTGTTTTTCTTTTAAATATGTGCTGCTAAGTTGCTTCAGTCGTGTCCGACTCTGTGCGACCCCATAGACGGCAGCCCATCAGGCTCCCCCGTCCCTGGTATTCTCCAGGCAGGAACACTGGAGGGNNNNNNNNNNNNNNNNTTTGTTTGGCAAACTATAGCATTTTTGTAGCCAGATTTTAAAAGCTATCCTCTTGAAAGAATTTAAAATATTCTACATTACTATCAATGAAATTAGGCTAATGACTTAATATTCTATACTTTAATTATACATTTTATATTATAAAATTGATATTATAAAATATAAAATTGATATTATATATTTATAGAATTATACATTTTATATTATTGAAATTTATAATAGGTATTTCACAAAAAGTAAAACAGAAATACCCTCTGATGTATAACTTAAAACTGAGAATAGGTCATTTTTTAAAAAATAAACTTTCTATTTGTGACAGAAATGTCAGTATATAAGACCCAAGTATAAACTTTAAATTACAGTTGTTTCAGGGCTTTGGGTCAAGTTTAATTAAGTTTCTATTAAATATTTCTTACTGTTGATGAGCTATTTCCAAATTAAGTTCATCCTGTACATTTTGACTTCATAAACAATATACACATTTAAAATATTTTATATCAGTCATCTTAATTGGAATATACAGTTAAATTAATTAAAATGGCTGAATCATTAACTGGAATAGAACCAGTAGAACCATTTAACAAATTGTAGCATAACTAAGAGTTTTGTCTTTAAAGCACAAACTATTCTATTTACATATTTTATTATACATTCCAAAATCTCAGTATCAGCTATAAATCTTCATGATTTTATTTTGGAACACAACAGTGTAACCCAAGAACATGATCACTTGTGACTGTGAAGAAATTTTGAGAATGAGAAAAGTATATTTTGAGGATCAAAGTAAAGTGAGTGTTAGTCGCTCTGTTGTATCTGACTCTTTGTGACCGCATGGACTGTAGCCTGTCATGCTCCTCTGTCTGTGGGATTCTCCAGGCAAGAATACTGGAGTGGGTTGCCATTCCCTTCTCCAGGGTATTTTCCAAACCAAGGGATTGAACCTGGGTCTCTCACATTGCAGGCAGATTCTTTACCATCTGAGCTGCCAGGGAAGCTCAAAGGTTGATTTTAAAAAGCAAAAAAATTTTTAAGTGTGCTTGAAACCATTTCCAAGAAACATTTATACTTGTTTTAAATATACAAAATGTATTTCTTGCATTCTGTGTAGTTTATCATACATTTTCTCTATAATATAGCATTTTCTCAAAGAATTTTAAGTATCATGAACTATTTGCTATGTCTTAGGCACACAGTTGAAGAACAATAAAAGTAATATCACAGAAATGTTCTCTTCTGTATATATGACTTGGGAAGTTCAAGGAGAGAGTTTTGTAGTACCATTGAATTAGAAATTAAAAATACCTATATTTGCCCATTTTAATGACCTTCTTTAACAATATATTTATGTATGTATATATATATAAATAGCATTATATGTACAAACAATATATATTATATATGTATATATACATATATATTTATATGCACTCATTAGGATATTCTACAAGTTAAATATGATCCCTCATACTCATGATTTGCAGAGCATGAATGCCTACCAATAAGGACTTAGTTAATATAGTTTTTACTTAGGTCTAAAATGAGAAATTTTAGCAAAAATAAAACAGAATAAAAACAAAAAATGAACATACTGAAATAAATTGAATTTTGCATAAACAATGGATAATTTGTGGCATAAATATTTCTTTTTCAATATTTGGGACATAGTATTTTCATCTTATCTACAAAAGAAGCTTATGCATGAATAAAATGAGATAGCAATATCCTCAAAAACAAATACATTTTAAATATAGAGATTAGTTAAAGGTGTCCTCTATGGTCTTTTTGAGATAGTCACATTTTTTTCTTTTAATTTTGTATGACTGTAGTGTCAAAATATGTATAGAGTCAATTTTAAAAATAATTTGGGGGAGTCTATTGAATTGAAATATTTCCATTTATAGATGTTTTTAGCTAATATTGAAAATAGATTATCTACAAGGTTTCCTGATACACCCATGTTCTATTTACTTTTAATATGAATTCTGAATATTTTCAGTGTTCTTAAGCTAATGCCACTTATGTGATGTGCAGTTTTGAGTACTGAATTTTGTGGAAAATCATCCATTTCCTAATAGATTAGCATAGATTACCTCATTGTATTGCCCATTGTTCTGCCATTATGGTAAATAAGCTGTGGTCTGTATTGTTCTTTATCTGTAGAAATAAACTTCAGAGTGTAAAGATGTTCCTTTTAAAGTATATGCTTAGATTACCCTACTGCTTTTTCTTTTCAG
Seq C2 exon
GGTCCTCAAGGACCTCAAGGTCCAGTTGGATTCCCTGGACCAAAAGGCCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(23.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=100),PF0139113=Collagen=PU(15.1=61.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
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]