BtaINT0040757 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40667836-40670181:+
Coord C1 exon
chr3:40667836-40667889
Coord A exon
chr3:40667890-40669931
Coord C2 exon
chr3:40669932-40670181
Length
2042 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
GCAGATCATCTCTTTTACAGGGT
3' ss Score
6.5
Exon sequences
Seq C1 exon
GGACCTGCTGGCCAGAAGGGTGACAGTGGTCTTCCAGGGCCTCCTGGGCCTCCG
Seq A exon
GTAAGTGCATAGTAACAAGAGTAATATTTTGGCAATTAGCATCTTGAGACAGCCAGTGATTTCTCTGAATTTATAAGAATGAAAAAACACATTCTGTCAAAGTACTGATTTTCTAGGAAATAGCAACTACCTTAAATAAGTACTTAGGTCTGCATGCCAACACATGTCTCTTAATTGGGCTTCCCTAGTAGCTCAGATAATAAAGTGTCTGCCTGCAAATTGGCTTCACTCTTTGAATACACAGATACTATAACTATATATTATAATATCTTGCTTTATTTTTCAAGAAAATCATATATTTTTATATCACATTTTCATGAAAGCAACTGCTTGTATGCCACAAAGATATATTAATACCTAACTAGGAATAAAAAGTTCAGATACTTGGCATTTTTTTTTCCTACTGCATATAATGATAATAATAGCTTCTGCTGCTGCTGCTAAGTCACTTCAGTCATGTCCAACTCTGTGCGACCCCATAGACGGCAGTCCCCCAGGCTCCACTGTCCCTGGGATTCTCCAGGCAAGAACACTGGAGTTGGTTGCCATTTCCCTCTCCAGTGCATGAAAGTGAAAAGTGAAAGAGAAGTCGCTCAGTCGTGTCCAACTCTTAGCGACCCCATGGACTGCAACCCACCAGGCTCCTCAGTCCATGGGATTTTCCAGGCAAGAGTACTGGAGTGGGGTGCCATTGCCTTAGACGGCAGCCCACCAGGCTTCCCGTCCCTGGAATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCACTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGTGAAGTCACTCAGTCGTGTCTGACTCTTAGCGACCCCATGGACTGCAGCCTACCAGGCTCCTCTGTCCATGGGATTTTCTAGGCAAGAGGACTGGAGTGGGGTGCTATTGCCTTCTCCACCAGATAATAATAGCTGCTACTTATTAGATCTGACATTTACCAGGGTTCACACAACTACTGTGTTAGATCCATGTGACAAAATTTGAGACTTTCTTCTTGAACTTGTTTCTAAGCTATATGAGTACTAATTTGCTGCAATGACAGTAACAAAGAATCAAAAACTAGATGGTTCAAAGGATAGAAATGTTTTGTCTGACAAATTTAGAAGGCAGAAGTCCTAGACCAGAGTGTCAGAAACTTGTTTCTTTTTGAGGTGATGTGGCTGGGAAAGATCCTGTGGAGACTTCTCTCCTTTGGTTGTAGAAAGCTGTCTTCTTGTGTCTCTTCACATGGTCTTCTGACTATGCATGTCTCTGTGCCAGATTTTCCCATTTTAGAATGATACCAGTCATATCGGAATCAGAACTACCCTAATGCCCTCATGTTCACTTTAATAATTATATATACAGCCACCCCATTTCTAAATGAGATCTTCCTCTGAGTTATTGTGGCTTTGAAATTCTCCACATGGATTTTTATGGGATAGAATTCAGTCCATAAAAGTACAGATTAACTATTTGATGTAGTTCTACTCTTATAGATATGTAAATTCAAGTCTAATTGCACTTCTTTATTTATATATACAGCTATAAATGTTTGGAACCAGCTAATGTGTATTTTTAAATGTGATATAAATTGTTATCAAGTACCATAGACATCTCATTATATAATACAAGAACCTAAAAATGTTTTTTTAATCTTCAGAGACTAAAGTCTTGTTGCAGGGATAGGACATGGAAATGAGGACTAGTTAGTAAATAGAAAAGTAACAGATATAACATATCTCCACACAAATCTGTACTATGTTACTTGTATAGAAAAAGCCCAGAAGTCATCTGATTTTTGTGCCTACCTTGATACCTCCACTAGATTCTTTTTAAAGAATTCACAAAGTTTATATATAAAGATATATATGTATGATAAATATATATAAGCAATTAGAGAAAACTTTAAAAATAGGGAAAACATTAAAAGGCTAAATAAATTGTAATATCTTATGATATAACATAATCAGTAATAATTAATATTTGAAGAATATTTTACCCTAGGAAGCAGTTACATGCAGATCATCTCTTTTACAG
Seq C2 exon
GGTCCACCAGGTGAAGTCATACAGCCTTTACCAATCTTGTCACCCAAAAAAACAAGAAGACATGCTGAAAGCACGCAAGCAGATGCAGGTGATAATATTCTGGATTACAATGATGGAATGGAGGAAATATTTGGTTCCCTCAATTCCTTGAAACAAGACATCGAGCATATGAAGTTTCCAATGGGGACACAGACCAATCCAGCCCGAACTTGCAAAGATCTGCAACTCAGCCACCCTGACTTCCCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:63
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=0.869
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.1=9.5),PF0141013=COLFI=PU(12.7=32.1)
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]