BtaINT0040729 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40592786-40598389:+
Coord C1 exon
chr3:40592786-40592839
Coord A exon
chr3:40592840-40598335
Coord C2 exon
chr3:40598336-40598389
Length
5496 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TTGTTGTTTTTTCTCCTTAGGGA
3' ss Score
11.95
Exon sequences
Seq C1 exon
GGACCACCTGGAAAAGATGGCCTGCCAGGACATCCTGGGCAACGTGGAGAGACT
Seq A exon
GTAAGTGATCCCACTCTTCTGATTAACATTTTCTATCTCTAGCATCTCATCATTTCACAGAAAGATACTTTATTATTAACAAGTCAAATATCAGGTTAGGGACAATACCAAAATTAAATCCATTTAATCTTTTTAAAATATATATAAAATACATACTGCTGCTGCTGCTGCTAAGTCGTTTCAGTCGTGTCTGACTCTGTGCGACCCCATGGATGGCAGCCCACCAGGTTCCCCCGTCCCTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCAGTTCCGTCTCCAATGCATGACAGTGAATAGTGAAAGGGAAGTCACTCAGTCGTGTTGCAGCCTACCAGGCTCCTCCATCCGTGGGATTCTCCAGGCAAGAGTCCTGGAGTGGGGTTTCATTGCCTTCTCCTAAAATCCATACAGAGACCCATTTTGTGGCTAAATACCTAAATGAATATGATTATTTGGGGACATGCATATTACTTGATTTTCCTTATTTTCAATAAGAGCATTTTGGGTATTTGCTGATGGAAAAGATGTCATTATCATTTGGATCCCTCCATAAGGTTGTCATCCTTGATCCTTTCACTGAAGTCTTTGCTTACAGATACATTTACAAGTCTTTCACCCTTCTAGTCTCTGAAGGAGACACATTACAATAAACCATTCAGATAATAGGTTCTTGTGTCCAAAATTAAGGGATGAAATATTTACTGAAGTTGGAACCATAAATCTGTAATTTGCCTAGAACTGTGTCAAATAAACCCTTTCCTATCAGGTAAGAAAATGGAAAAAAATGTAGCTTAAATTATGAGGAATATAACATTAAACAGATTGTCTGAACAACTTATGTAAGAGTGATTGGGGCAGAGGAAAAACTGGCATCTCAACTATGGCTTAAGAATCCTGATGGTTTTGTTTATTTATTCTGCCACTGTTACAAAACCTTGTATCTGGCTCTTTTGAGTGAGTGAAGTCGCTCAGTCGTGTCCGACTCTTTGCGACCCCATGGACTGTAGCCCCCCAGGCTCCCCTGTCCATGGGATTCTCCAGACAAGAATACTGGAGTGGGTTGCCATTTCCTTCTCCAATCTGGCTCTTTTAGTGGGATGATAATCTAATCAGAAATCATCACGGAGGATTAGTATCTTTCCTTGATTTCAATTCTTGGCTCTTAACATTGATTAATTTTATCCGGATTTATTAAACCACAAGACAGACTGCCTTTGACTATGTGTCTCAAAATTATCCTAGGGTATTCTGTCAGCATCAGTACATATTAGGAGTTCAATTGAAGTACAGAATAACAGATCTGAAAACACAATGCTTTTCTGCATAGGAAAAACAATCTGGAAGCAGCAGCCAATTCTTGTTTTGCTCACCAAATGACAATTCTTCCTGTAACGACTTCTTGGTTTTAGTGAGATTTAGTAAACCTCAAAGTTTTGGATTACACAGCAAAATCAAGAATGATTTAGTGAGGCCAAAGAGTATAATTGTTTGGGGGTCCTCTTGGGAATGACATTTGCATGGTGAACAAGAAATAAGCTCTCTAAAGGATAATACACACTCAAATTTGCAAATGCATTCTCATTCAAATATTGCAGTCATTTCTAAGTCATGGTGTAGCTTCTTGGGAATAACTTTAGAATATTTCAAAAATGTATTTTGAGGAAGGGGTACCTAGAGAATTATTATTACAAAATCCTTTTGTCTTCAGTTTAATCAAGAGCTTCTGCTTCTATAGAGAGCAACAATATTATTGTTGTTCAGTCGCTCAGTCATGTCTGACTCTTTGTGACCCCATGGACTGCAGCACACCAGGCTTCCCTGCCCTTCACCATCTCCCAGAGCTTGCTCACTCATCTCCACTGAGTTGGTGATGTTAATGTCTAAAGTTAAACAAAGTGGAAAACTAACATGTTAACTAATGATTCTAAGATAGGTATTCTCACCTCGTAGTTTCTTATAAATAAAGGCTAGCATTATTTCTGGAAAATTATATTTCTGTTTTCAAATTCACTTAAAGAACAACAATGAGTCATGTTTATACTCAGGAACCTTTCTTGCTCACCTTGTTCTGTATTGATTTTGATTCATAAGATTGTCTTGTACAAGGGTCAGAATCTAGGGCAGCTATATTTTGATATATATGTGTTTCCTTATTTTAAAGAAGTTATTTTGTTATATTTGAGACTTGTCCTCATTCAGAAATCCTTAAACTGAAAGTTCATTCTGATATCTTACAATTTAAAGCTTTTTAGGAGTAATTAGAGTCCAAAATCACTGAAGATGGTGACTGCAGCCATGAAATTAAAAGATGCTTACTTTTTGGAAGGAAAGTTGTGACCAACCTAGACAGCATATTAGAAAGCAGAGATATTACTTTGCCAACAAAGGTCCGTCTAGTCAAGGCTATGTTTTTTTCAGTAGTCATGTATGGATGAGAGAGTTGGACTATAAAAAAAGCTGAGAGCCAAAGAATTGATGCTTTGGAACTGTGGTGTTGGAGATGACTCTTGACAATCTCTTGGACTGCAAGGAGATCCAACCAGTCCATCCTAAGGGACATCAGTCCTGAGTGTTCATTGGAAGGACTGATGTTGAAACGGAAACTCCAGTATTTTGGCCACCTGATGTGAAGAGCTGACTCATTTGAAAAGACCCTGATGTTGGGAAAGATTGAAGGCAGGAGGAGAAGGGGACGACAGAGGATGAGATGGTTGGATGGCATCACCGACTCAATGGACATGAGTTTGGGTAAACTCCAGGAGTTGGTGATGGACAGGGAGGCCTGGTGTGCTGTAGTCCATGGGGTCACAAAGAGTCAGACATGATTGAGAGACTGAACTGAGAGACCGTTTTATTATACTGAAACAACCCACATTTTTCTTAGAAATGCAGTGCCAAATTGTGTGTTAATCATACAGGTGATCAGAATAGAAGTTATGTTTTTAATAGCCATTTATCAAATTCATTTCTGTTCTTAAGAATTTTGAAAAACATAATTTAACATACTAAAATAAATGGCTAGTCTTAGTACATGGCAATATTAAATAATCACACTTCATTTTGATCTATAAAAGCTTTTTTTGTATGTATTTTATATGTAAGATCTTTACTGTCAAATTTACTAGATACTTGCAAAATTCTGAATATTTTGAATGAGCTGGCATATGGTCAGAGCTGTTTTCCAGCTCCTTACAAATCTGTCTGTCACTCAGATGAGCTAGCACACTCTTAGGGTGTATGAGTACAAGTCTGGGTAACACATTTTTTCACAGAATTTCCTCAGTGAAAGCATGAGAGGGCATTGAAAATGTCAAGTAGGCACTTACTGAGAGGGTTTTAAGACTCAGCAGAGACTAGAGGGTGAGAAATAGTTTGTTGCAGAGGAGTTGATCAGAATCACAGATATTAATAGGATTTGTTTTCATGGAAATTATTGAGACCAGATATCTAAGGAGTAGATAGGATGTGGGATTAAATGATGTAAACAAATGGTAAAAATAACTGCTAAGAGCTGTTAGCTCTCAGTGGAAAAGTAAAACATAAAGTAATATGTATATAATATAACTATATATATGTGCTTACCTATGTGGGTACTAATTTCCAAACCATTAAGTTCCCGAGAAGTTAAAATTAAGCAATAAAGCTATTATTTTGTTTATAAAATGCTAAATAAATTATATAATGCATTTCCCTTGAATTTATTAATTTTGCTATTGTGATTGATAAGTAAAGTGGAAACCTGAGGGTTTTAAGAATTAATGTGTTTTAAAACTAGGATAAATTTGTTTTTTTTCTTTCCCTGGAACATCAATTAAATAATTACAAATAGAAATTTTTTTCTTTTACTGCTTTTAAGTTTCATTTTTATAAATAATGTAATAATAATCATCAGGAAGGTCATGATACAAGTGTGGAGCCAGTTTCTGTCCCTTGCTTTCTAACTTTCTTATTTCCAATCTCATGTTATAAAAGTGAATAAAACTTTTGCAAATATTATTTGCTTTAATTCAGTTCTTTGGCACATTTTTCTCTCAGCATTTTGAATCTTTCTCCAGCTGTTAAGTGTAAATTAACTCACATGAGAAGGAAATTTGCTATTCATAATACAGTCATGCAGAAAATAACCCAGGAGTCTAGAGAAATAGAGGTACCAGAATATATGCCAAAGGCCTTATTTAGTGAGTACATGAGCTCACATGTACTGGATTTTATTCTAATGACTACAATATATGTAAGATACATTTGTAAGTATATTCTTTTGGGTTTTAAGAAAGAAAACTGATAAAATATTGAAATGGTGACAAATCATGTAAAATATTCTTTTTTTTTTAATTTAATTTAATTTTTTAAACTTTACAATATTGTATTGGTTCTGCCATACATCGAAATGAATCCGCCACAGGTATACATGTGTTCTCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCGTACCATCCCTCTGGGTCATCCCAGTGCACCAGCCCCAAGCATCCAGTATCATGCATCGAACCTGGACTGGCGACTCGTTTCATATATGATATTATACATATTTCAATGCCATTCTCCCAAATCATCCCACCCTCGCCCTCTCCCACAGAGTCCAAAAGATTGTTCTATACATCTGTGTCTCTTTTGCTGTCTCGTATACAGGGTTATTGTTACCATCTTTCTAAATTCCATATATATGCGTTAGTATACTGTATTGGTGTTTTTCTTTCTGGCTTACTTCACTCTGTATAATAGGCTCCAGTTTCATCCACCTCATTAGAACTGATTCAAATGTATTCTTTTTAATGGCTGAGTAATACTCCATTGTATACATGTACCACAGCTTTTTTATCCATTCCTCTGCTGATGGACATCTAGGTTGCTTCCATGTCCTGGCTATTATAATCTTTTTATAAATTTATTTTTATATCTTATTTTACGAGATTGTTGGAATGGAGGAAAGAGAAATGCATTGATATCACAGACTGTAGATTTATCTCTGCATGAAGAACCAGTGGACTGTTACAAATAGTGTCTAAGTCATCACTTATTTCATCCATAAATGTTTCTAGATTAAAATTTCTGTGTTGTCTGACACAGGGAAAGAGGGCTAAGAGCACAGTTTTGCTCCAGCTTCATCACATTTTTTAATTTTCTTTTTTAAGCTTATTGAAGATAATCATAGAACTACAGTGTAAAATAGTGAAGACAATAACTTTTAAATGTAAAGAGAACTGTAATGTAATAATTTATAGGCATTTAGAAACAAGTGCTTGTGTGCACGCTTAGTCACTCAGTTGTGTCCAACTTTTTGCAACCCTATCAACTGTAGGATATTTGCAACAGGCTCCTCTGTCCATGGGATTTATGAGGCAAGACATTTTTAGCCAAAAGATGGCTTCCTTTTAGAGTGAATTAGTCGACTATCTCAGAGAATTATAATGTATGTTTTGTGCCCTGGATGGCTTTTATAGTTTTGTTGTTTTTTCTCCTTAG
Seq C2 exon
GGATTTCAAGGCAAGACCGGCCCTCCTGGGCCAGGGGGTGTTGTTGGACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:38
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=PD(8.3=27.8),PF0139113=Collagen=FE(23.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100),PF0139113=Collagen=PU(6.0=27.8)
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:
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]