BtaINT0040712 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021217 | COL11A1
Description
Bos taurus collagen, type XI, alpha 1 (COL11A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166509]
Coordinates
chr3:40550744-40555253:+
Coord C1 exon
chr3:40550744-40550788
Coord A exon
chr3:40550789-40555199
Coord C2 exon
chr3:40555200-40555253
Length
4411 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGC
5' ss Score
4.47
3' ss Seq
TGTTTCTTTTTTACTCCTAGGGT
3' ss Score
10.04
Exon sequences
Seq C1 exon
GGAGAAGATGGAGAAATAGGACCAAGGGGTCTTCCAGGTGAAGCT
Seq A exon
GTAAGCAACTTTCTTTTTTTTTTTCTTTTTAAATAATACCCTATTTAGGAGGAATAGTGCTTGGTGTTACAAATATAAAGTCACTAATAATTGCAATCTTACCTAACCTAACCAGGTAATTTGTTATGTGAAAAAACATTTTAAAAGGATACTTACAGCTCTTCTGTCATTAAATTTTAGGAAATTGAGAGGAAAAAAATGTGGGATATAACATCTTAACTACAAAGAGAGATAATAAAGCCTTTTTAAGTGAATAATGCAAATAAATAGAGGAAAACAATAGAACAGGAAGGACTATAGATCTCTTCAAGAAAATTGGAGATACCAAAGGAACACTTCATGCAGAGATGGGCACAATAAATGACAGAAATGGCAAGGACGTAACAGACACAGAAGAGGTGGCAAGAATACACAGAAGAACTACATAAAGAAGGTCCTAATTACACAGTTAACCACGATGGTATGATCACTCATATAAGGCCCAGATATTCTGGAATGTGAAGTCAAGTGGGCCTTAAGAAACATTACTTTGAATAAAGCTTGTGGTGGTGATGGAATTCTAGCTGAGCTATTTCAAATCCTAAAAGATGATGCTGTTAAAGTGCTGCCCTCAATATGCCAGCAAAATTGGAAAACTCAGCAGTGGCCACAGGACTGGGAAAGGTCAGTTTTCATTTTAGTCCTGTTGCTGCTGCTGCTGCTAAGTAGCTTCAGTTGTGTCCGATTCTGTGCGACCCCATAGACGGCAGCCCACCAGGCTCCCCCATCCCTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTTCTTCTCCAATGCATGAAATTGAAAAATGAAAGTGAAGTCGCTCAGTCGTGTCCGACTCTTCGCAACCACATGGACTGCAGCCTACCAGGCTCCTCCATCCATGGGATTTTCTAGGCAAAAGTACTGGAGTGGGGTGCCATTGCCTTCTCCATTTCAGTCCTAAAGAAAGGCAAATGCCAAAGAATGTTCAAACTACCATACAATTGTGCTCATTTCACATGCTAGCAAGATAATGCTCAAAATCCTTCAAGCTAGGCTTCAATAGTATAAGAACCCAGAACTTCCAGATGAACAAGCTAGATTTAGAAAAGGCAGAGGAACCAGAGATCAAATGGCCAACATTTGTTGGATCATACAAAAAGCTAGAAAATTAAAAAAAAAAAATCTACTTCTGCTTCATTGACTATGCTAAATACTTTGAATGTGTAGATTACAACAAACTGGAAAATTCTTAGAGATGGGAATACCAGACCACCATACCTGTCTCCTGAAATCTATATGCAGGTCAAAAAGCAACAGTTAAATAACCAAACATGGAACAACAGACTGGTTCAAACTTGGGAAAGGAGTACAACAAGGCTCATGCTTTCACACTTTTATTTAATTTCTATGCAGAGTATATCTTGCAAAATACCAGGCTGGATGAATCATAAGCTGGAATCAAGATGCATGGGGAAATATCAACAACCTCAGATATGCAGATAATAACACTCTAATAGCAGAAATTGAAGAAGAACTAAAGAGCCTCTTGATGAAGATGAAAGAGGAGAGTGAAAAAAAAGCTGGCTAAAAACTCAACATTCAAAAATCTAAGATCATAGCTTTCATTCCCATCTCTTCATGGCAAGTAGATGGGGGGAAAGTGGAAACAGTGACAGATTTTATTTTCTTGGGCTCCAAAATCACTGCAAACAGTGACTGCAGCCATGAAATTAAAAGACTTTTACTTCTTGGAAGTAAAGCTATGAGAAACCTAGACAGTATAGGAAAAAGCAGAGACATCACTTTGCCAACAAAGGTTCCTATAGTCAAAACTGTGGTTTTTGCAGTAATTATGTACCGATGTTAGACTTGGACCATAAAGAAGGCTGAACACTGAGGAATTGATGCTTTCAAACTGTGGCACTGGTGAAGACTCTTGAGAGTCCCCTGGACAGCAAGATGAAATCAGTCAATCCTAAAGGAAATCAACCCTGAATATTCAGTGGTAGGACTGATAGTCGTGAAGCTCCAGTACCTTGGCCCCCTGATTCGAAGAGACAACTCATTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATCATAGCTTTCATTCCCATCTCTTCATGGCAAGTAGATGGGGGGAAAGTGGAAACAGTGACAGATTTTATTTTCTTGGGCTCCAAAATCACTGCAAACAGTGACTGCAGCCATGAAATTAAAAGACTTTTACTTCTTGGAAGTAAAGCTATGAGAAACCTAGACAGTATATTAAAAAGCAGAGACATCACTTTGCCAACAAAGGTTCCTATAGTCAAAACTGTGGTTTTTGCAGTAATTATGTACCGATGTTAGACTTGGACCATAAAGAAGGCTGAACACTGAGGAATTGATGCTTTCAAACTGTGGCACTGGAGAAGACTCTTGAGAGTCCCCTGGACAGCAAGATGAAATCAGTCAATCCTAAAGGAAATCAACCCTGAATATTCAGTGGTAGGACTGATGCTGAAGCTCCAGTACCTTGGCCCCCTGATTCGAAGAGACAACTCATTGGAAAAAATCCTGATGCTTGGAAAGATTGGGGGCAAGAGGAGAAGGGGACGACAGAGGATGAGATGGTTAGATGGCATCACCTACTCAATGGACATGAGTTTGAGCAAATTCCAGAAGATAGTGAAGGACAGGGAAGTCTGGTGTGCTGCAGTTCAAGTCACAAAGACTTGGTCATGACTGAGCGACTAAACAACAACTTGTCATCCAAAAAACCTTATCTAGTTTTTGTGGCTGTTTATTTTGTTTCAGTTTTTTATATCAATACCTCTAGAATTTTTTATTTGTTTAGGATAAACAATTATTACTAGAGGAAACAAAAAATGAGGTGCTTGCTACTGTTAGTACAAAAAATGAGGTGTTTAGTATATATCAAATATAACTATAAAATTTATTAAATTATATCCTTTTTTCCATTGAATTTTACAAATGAGGAAACTGAGTTGGAAAGGTTTACTCAAACCTAGTCAATCAAAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTAGATGGCATCACTACTCAATGGACATGAGTTTGAGCAAATTCCAGAAGATAGTGAAGGACAGGGAAATCTGGTGTGCTGCAGTTCAAGGGTCACAAAGACTTGGTCATGACTGAGCGACTAAACAACAACTTGTCATCCAAAAAACCTTATCTAGTTTTTGTGGCTGTTTATTTTGTTTCAATTTTTTATATCAATACCTCTATAATTTTTTATTTGTTTAGGATAAACAATTATTACTAGAGGAAACAAAAAATGAGGTGCTTGCTACTGTTAGTACAAAAAATGAGGTGTTTAGTATATATCAAATATAACTATAAAATTTATTAAATTATATCCTTTTTTCCATTGAATTTTACAAATGAGGAAACTGAGTTGGAAAGGTTTACTCAAACCTAGTCAATCAAAGATCCACACTAGAAGCAGACCTCTTAGTTTTACTGCTAGTTTGCCACATTATAGAACCTGTCAATTCAAAGGCAAAGCATGTTTGTATATGTTAGTTGCTCAGTTGTGTCCAACTCTTTGCAACTCCTTGGAGTATAGCCCACCAGGCTCCTCAGTCTCTCAAGTAAATATAACAGTAAACCATACTGTTGACTTTTTTGAAGAAGGAAAAGAAGGAGGAAAAAAATGGAGAAGGCGAAGAAGAGAAGAAAATGCTTGCTTAAATCATAATAATTTTAAAAATCATGAAAGTGGTTTCTATAACCTTCCTAATATAGTCCTCCAGCTGTTTGTTTCTTTCTCTCAGTAGAATATTCTCTCAAGATGGAATTTACCTAAATGTAAAATAAATGAGCATCAAGACTCTTTGTGTAGTCTGTTTGAATTATAAGATTTAATAAGATTCAGCGTTGCTATTCAAATTGGAAAATGGCACCAAAGTTACTTACTTAAAGCTTTAAAATATTTCCTATATTGAAAGTTTCACAAGTGATTCATATGTAATTCCATAGACTCAAAGATACAGTTCCTATATTAAAGACTCACTCATTCATTTTGGCTTTTGGCTCAATATAAACACTAGGTAATTGTGTCACACAAAATGCTATTTTAAATGCCCTTATTGGTGTGTTGAAAGAGGGTGAATAAATATTTTAATCAAAACATTACATTAAAATGTGTTTTTTTAAAAGACAAGACATGTTTTGAAGGCCTTTTTTTTTTTTGATAATCTGTTTCTTTTTTACTCCTAG
Seq C2 exon
GGTCCACGAGGTTTGCTAGGACCAAGAGGAACTCCAGGACCTATTGGACAGCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021217:ENSBTAT00000028276:20
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(15.9=73.3),PF0139113=Collagen=FE(16.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.5=100),PF0139113=Collagen=PU(2.2=11.1)
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]