BtaINT0042248 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012837 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:HGNC:27023]
Coordinates
chr1:153354110-153360788:-
Coord C1 exon
chr1:153360726-153360788
Coord A exon
chr1:153354173-153360725
Coord C2 exon
chr1:153354110-153354172
Length
6553 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
TAAATAAATTCTGCTTTAAGGTA
3' ss Score
6.75
Exon sequences
Seq C1 exon
GGTGAGGTCGGGGACCCTGGTGGCCCAGGACAAACTGGACCCAAGGGCGCTAGAGGCAAGACG
Seq A exon
GTGAGTTTCGTCGGTCATAAAAGCCTTACAACCTCAACTACCGTGGGAAGTCCTTTCTCAGGCTCTTACAGTCGTTTGAGTTGGCACTCGGTCCCAAAAGCTTGTAAAACGTGTAGGTTTTGTTAAGGCAAACTTGGGGCAGGGAGATGGATATTTGGCTCCTTCTTTGCCAGCAATAAGGCAACGAACCATTGGCTCTTAGTGACCGGGTTCACCTGATCTGACTGATAAGGTACCAATCTTAACACTGGAAATAAATTGTGCATTTTTTTTTTTAAGGAACCCTTGTGGTCCAAAACAGTGTTTGCATTTAATCCTAGCCCCTCAGCAGACCTCATGTAACTTACTGCCCACTGGCGTCTTATCTCCCTTGTTAAGGTCTCGTCTAACTACTTTAAGGAGATGATCTTCTCCCAATTTAGCTCAGGAAAGTGCCTCTTGAGCTCTCTGAGAAAGTTTCCATTTATCATGTAAGACGGTGCCTAAAGCTTTGGGCCACTCAGAATAACATCCCATCTCCCGTACCCTAGAAGCATCCGCACTCGTAACTTGAGCTTGCCTCGGGTTCTCGTGGGCTAACAATGGCTTTTGCCTTTGCTGACTCTATTTACCATACATTGCAAAAGTGAGATGGTCACTTTATAAAAGACACAATCTTATGACAGTCATCTCCTGAGACTTTATCTCTTTTCATCAGAACAACTCCGATCAGGTAAATAGATCTTGATACCATGTCAATTTCTGGATAAGAAAAACACAAAGTCTGATGAAAAAAAAAGCTGTTACTTGAGGCGGCTTTTCAGTTTTGTCACCATAGTTAGTTTGACCCTAATCTGTTTTCTCCTACAAAGTATAGCGACAACTGTATGCGAAGGGACTATTCATGAGGGCTTTAGGGGTACGAAGTAAAGAAACTTCTTTCCCTCCATCCTGCTTTTCCCAAGAGGCCTGTTTCCTGGCTGTAATTCTTTTCCTTATACATGTTTTTGGTTGACTGTCCCTTAACATTTTTGGTCTCAAAGGAAAAAAAAAAAAGACTGATAAAGATAATTGGAAAAGACCTTCAGATTAATCTAGATGTCATCTGCATTGAAATACATCTGGATCTTTTCCCTCAACGTGTTAATGAGGTAGTTTACCCTTGAACACTGGAGGCCCGTAAACACGGCCAGCAGTTTCTTGGGTTCTCTTAGTACCCAGTGACATATTCATCATTAAAAAAAAAAAAAAATATATATATATATATATATAGCTAATGGGGAATATATAATCTTTTTCTCTTGGCCTTTGGTTACTTCATTTTTTTTTTTTCCCACATTGGACAATTTATCACTATCTTCAACTTGTTTATTTCACCTGCCAATCTGCCTTTTTCTACAACTTGTATTTTTGAGTTTGAAGTTTAGACACTGAAAAACTTCCAAGTTTTCGTTGGAGGGTTTTGGTAATAAAGCTTTGAGTATCTCTTTAGTTCTCTTGGAATGATTACATTCCTAGTTTGCTGCTGCTGCTGCTGCTGCTGCTAAGTCGATTCAGTTGTGTCCGACTCTGTGCGACCCCATAGATGGCAGCCCATCAAGCTCCCCCATCCGTGGGATTCTCCAGGCAAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGTGAAGTCACTCAGTCGTGTCCGACTCTTAGGGACCCCACAGACGGCAGCCCACCAGGCTCCTCCGTCCATGGGATTTTCCAGGCAAGAGTACTGGAGTGGGGTGCCATTGCCTTCTCCGACATTCCTAGTTTAAGTTTTCTAAATCTTTACCTTTTTTCACCCCAACTGAAGCATTTGTTTTTTCGTTTTTTGTTTTTTTGAAAATGCCATAATTTTTAACCTGCCTTGTTTGGGGTATAAAGGTATGTTTGTATTTATACTTTTTATCAACTTTACACGTGCACACCCTTCAAGGCAGGGCTCCTCAGCCACAGTACCACTGGCATTTTCAGCTGGGTAATCGCTGTGGGGGCTGTTCCTTGCTTTGCAGGATGTTTAGCAGTGCCCCTGGCCTCTACCCATGAGGCTCAGTGCCACCCACCCCCCTCTCCCCATCATGACAGCCAAAAATACCTCCAGTCATTGTCAAATGTCCCCACAGGAGTCAGGGTTGAGGGACACAGACTTGCCCCCAGTTTTTTTTTTTTTTTTTTCGTGCCTGAAATTCTTTTTTAAACTATCCTATCCAGTCCCACCACTTCATGGGAAATAGATGGGGAAACAGTGTCAGACTTTATTTTTCTGGGCTCCAAAATCACTACAGATGGTGACTGCAGCCATGAAATTAAAAGACGCTTACTCCTTGGAAGGAAAGTTATGACCAACCTAGATAGCATATTCAAAAGCAGAGACATTACTTTGCCAACAAAGGTTCGTCTAGTCAAGGCTATGGTTTTTCCTGTGGTCATGTATGGATGTGAGAGTTGGACCGTGAAGAAGGCTGAGCACCAAAGAATTGATGCTTTTGACTGTGGTGTTGGAGAAGACTCTTGAGAGTCCCTTGGACTGCAAGGAGATCCAACCAGTCCATTCTGAAGGAGATCAGCCCTGGGATTTCTTTGGAAGGAATGATGCTAAAGCTGAAACTCCAGTATTTTGGCCACCTGATGCGAAGAGTTGACTCATTGGAAAAGACTCTGATGCTGGGAGGGATTGTGGGCAGGAGGAGAAGGGGATGACAGAGGATGAGATGGCTGGATGGCATCACTGACTCGATGGATGTGAGTCTGAGTGAACTTCGGGAGTTGGTGATGGACAGGGAGGCCTGGCGTGCTGTGATTCATGGGGTCGAAAAGAGTCGGACATGACTGAGTGACTGATCTGATCTGATCTGATTTTTGTTTCATGGCTGAAACATCTCATCTCTCTAAGGATATAAATTAGTACTTTTGAAGTCTCCTTTGCCCAACATAGCCTGTTCCTGGCAGTGTTTTTTTCTGCCCTGCTCTTTGTCTCTCTCTGCCCAGCTCACGAGTCTCTCTATTGAAGAGTTAAGGACACAAAATCTAACTGGAAGCCCCAAGGAAATGAATGGGGCTCGTCAACTACAAGTTTCACTGAGGAGTGATCTGACTGAGTTGCTACTTAGCAAACATCTGAGATCAGCATCCTGGGGTCTTTCTTCTCTGTCTAGTCAGATTCCCCTGAAAAGATTGTTTCAGTCTTCCACCTAAGGGTGAAGGTCTGGCTGCCAGCTTTCTGGGACCCCCCGCTTTCTAGGGGTCTCACATCTATTCCTCAGCTTCAGATTGCCTTGTATTCTGGACCGTACCACCAACCTTCAGCTCTGCCTGGGTTTCCTGGTGTGTAGCCACCTCAGTTTCACCTTTGCCATCAAGGAGAAAGAAGGGACATTCGACTCAACTGTTGAGAATGGGGAGGAAGCCCGGGAATTCCCCAACCAAGCTGCCTTATTTGCCCTCTCTCCTACACCCGCACTTCTAGAGGTACTTTCTGAGAATGCATCATAAAACACTCAACCTCCTAGCTTTCCCTGCTGCTGGCCTAGGATTCAGCTTTTTCAGCTCTAAGTCATTTAATGCTTTCCAGTTTGAAAGCTATTGTCTCATTTCTCATTCCCCCTATGTTTGTTATTTTTTGTCTTAAAAAAAAAAAAAGTCTGCTTAGTATTATTTTAGTAAAACACTGGAGGGAACAAAAGTAAGCACTTATGTCCAATATACATTTTTCCCCCCTGGAGGTTAATCTATATCTTCTAAATAAAATAGTAAGGTTGCATTTTGTCTTGCTTTGTCACTCAACCCAGCATGCTGTGCATATCATTGGAAGACACAAAGGTCATCTAGTAATTATTTGCTATTTAATAGGCAATGGTTTTACAGATTAAGTTGGTTTTAAACAACCTTGTTTTTCACTCTCATAAAGCTTGTACATCTCATGACATTACTAATGAACAAAGAAATACTGTCCTAATTTTTAAACTAAATTCTTGCTTTCTTTATGATAAATTATGTTGTTGAATGCACACACGTAAACTAAGTAGTCAACAGCTGGTGTTTTTTTGCTGCTGCTATTCCCCATTTTACTACAGATATTTCCAGCCACGTGTTCTATGCTTTCTTGTGGTTCTTTCAAGGGTTTTTATATTTAAATTTTTGCTTTTCTGAGTTTTTTTTGTTGTTGTTGTTTTCATGTGTTTGTTAGTTTAGTCACCTACTAAATTCAGATAAATTGAGATAAAAATTCATTTAGATAGAAGTTTCTCCCTTGACCCAGCAATTCTAGTTCTAGCAATCTTTCTTAAGGAAATAATCAGAATTGCACATATGACTTTATAGTGGCATGCTTATTGCAACAACAGCAAACTTAAATGCCAACAATAAGGAACTGATTAAATAAATCAGTATATTCATTTGATAGAATACTATGGCAGCCATGATGGAGAAGGCAATGGCAACCCACTCCAGAGTTCTTGCCTGGAGAATCCCAGGGACAGAGGAGCCTGATGGGCTGCTGTCCATGGGGTTGCAGAGTCAGACACGACTGAAGAGAAGTAGCAGCAGCAGCAGCATGGTGGCCATGAAAGGCAATTTTTGTGAAAGAATATTTAGTTACATGAAAATGTCCAGAAATACATGTTTAGTTTAAAAGGCAGCAATAAAAAGTATATAAATATATTAAGATGGAATGTAAAATACCAGATATGAACTCTAATGTAAACTATGAACTTTGGGCGATTATGATGTCAATGTAGGTTCATCAGTTGTAACAAATGTACCACTCCAGTTGGGGATGCTAGTAACCGGGGCATCTAGGAGTGTGAAGGATCAGGATACATATCGGAAACGTATGTAACTTCTTAATTTGTTTTCTGAACCTAAAATTGCTTTTAAAAAATACTCGTTAGAATTAAAAATAAAGACCATGATTTTAATCTAAATATATATATATAGATAGATAGATAGATAGATATAGATATAGATATAGATACAGATATATATAGAGTAACACCAAAAGGATAAATAAGTAAAATACTAGAAGAAGAAACAACAAAATGTCAGCAAGTATTATCTGGGGGAGAAGAGGCTGCTGAGGATGTTTTTCCTTCTGTGTGCTTTTTGGGAATCGCTCAGTTTTCTAAAGTGAAAGTGTGCTGGGGTCCAGCCCCAGCTGATCCAGGGTATTTGAAGGGGAGATAGCGTCGCAACTATTTAAATATTCATCAAAGATATAAAGAGTAGTAGAATGAGGATAGCTCAGTAGGAAAATTCAGTGGAGAAAAGAGGCTGAGTAGCTTGGTTTACGCGGAAAAGCAATATAACCTGTGACACCAGGTTAGCTCTGACCATGGACGCCGCAGGCGCCCTCTCGAATAGCAGAAGGTGCCCCACCTTAGACACCTTCTCAAGTGGGTCTTAGAAGCCCAGGCAAATAAATGGTCGAAGAGGACCTCCACACTCCAGATGGAAACTTCAGCCGGAATGTGAAAAGAATGACATGGGGAGACCAAGCTTTGCTGAGCAAGGCCCGTAGCTTTATTTTCAACAGGGGCTTTTATACCGTAAGTTGCACATAGAGGATAATAGGGGATGTGAAATCATACAAAGTCAGCAGTCTTTGATCCTTATCAAAAACCAGAGTTTCTTTCCTGCAAATTTATCGTATTCAAATGGTTTAGGTGATTTACATCATCTTCTGGCCAGAAGGCCTATTAACATTTTATGACTCTTGGCAAAGGTTTGTCAACTGTAAGACTTATTTTCTCTAAGAGTAATTATTTTAAGGTTTGGCGCCATCCTCCGAAGGCGTTAGATAAAATTGCATTCCTATAGGGCAGAGGTGCAGTGGGTTTACAACAAAGGAAAGAATTTATTACCTTAAGGGTCTAAAGTTGCTAACACCAAGGCCACTACTTATTTTTTCGACATACCAACTATATTAATTAATACACATTCAAGGATACAATACAGGGGATGTGGAAACTTGGCAGCAAGCATTGTCTCATCAATGAAATCTTTTACTAGTTTTATTCTGACAGTTTCTAACTCTCTGAGAGGCTCTAAGCTAATTGAATATCTTAAGCTTCCCGTGCCTCTCGAGGCTGGGAGACTGTAAACAATCATATGCATAGCTGTAGGAGTCCAGGTAAACTTGTCAGGCGAGTTAGAGAGCTATCTGAGGGGTTTGGATTTAAACACTCCTAATGCCCAGGAGCTTTATTAACTGGAGCTGTCAGTTAACTCTTTATCAGAGAGAGCGAGATGGTGGTGGGGGACAGCCCCCAGTAAAGTCGGAGGTGAGAGCACAAAGCAGTAAAGTAGGCAGACTCTGGTTTTTGGGGGTAGATGCTCGAGAATATCCAGCGGGACTCCTGAGGCTCGATCCCACCTTTACGTATGCCGAGCCTCCTTCCTCATGACCTTTGTCATGAGTGGAGTGCCTCTCGCCGGCTCCCGGCAAAAGTGTATTGCTTTTGAAATGTAAAACACCCACATAGCACACAAACATATATGTATAATTTTAAGGTAAATAAATTCTGCTTTAAG
Seq C2 exon
GTATCTGCTGGGCTTCCCGGAGAACCAGGATCCCCTGGGGAGCTGGGACCTCCTGGACGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012837:ENSBTAT00000017057:27
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(33.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(33.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
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]
SPECIAL DATASETS
- Pre-implantation embryo development