BtaINT0042257 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012837 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:HGNC:27023]
Coordinates
chr1:153429856-153432384:-
Coord C1 exon
chr1:153431824-153432384
Coord A exon
chr1:153430414-153431823
Coord C2 exon
chr1:153429856-153430413
Length
1410 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
ATCTCCTTTCTCCCGTGCAGCCT
3' ss Score
9.96
Exon sequences
Seq C1 exon
GTTGTGTGGACACGGAGGAAGCAGACATCTACCTGCTCATCGATGGCTCCGGGAGCACCCAGGCCACAGACTTCCAGGAGATGAAGACCTTCCTGTCAGAGGTCGCAGGGATGTTCAACATCGCTCCCCAGAAGGTGCGGGTTGGGGCTGTCCAGTACGCCGACCGCTGGGACTTGGAATTTGAGATCAGTAAATACACGAACAAGCACGACGTCAGAAAGGCCATCGAGAACATCAGGCAGATGGGCGGGAACAGGAACACGGGCGCCGCCTTGAACTTCACCCTGGGGCTGCTGCAGAGGGCAAAGCAGCAGCGGGGAGGCAGAGTGCCCTGCCACCTCGTCGTGCTGACCAACGGTGCGTCCCGGGACAGCGTCTCGGGGCCCGCAAACAGACTGAGCGAGGAGCTCATCCACGTCTATGCCATCGGGGTCAGGGAGGCTAACCAGACTCAGCTGCGCGAAATCGCCGGCGAGGAGAAACGGGTCTACTACGTGCATGACTTCGATGCCTTGAAAGACATAAGAAACCAGGTTGTTCAAGAAATCTGTGCTGAAGAAG
Seq A exon
GTAGGACTCCTTACCTTTGGACTTCAGCTCCCAAGCTGCCTCCCTGCAGTATTTTCTTAAATGTTTTGTTGCTGTTGTTGAAGTATAGTTGATTTACAATGTTCTGTTAACTTCTGCTCTGCAGTGCCACATGTAGAAACATTCTTTTCCATATGCTTTTCCATTTATGGGATAGATCCCTGTGCTATGCAGTAGGACCTTGTTGTTTCTCCATTCTATATAGTTGGCTTCTGCACCCTTCAGTATTTGACATTTCAGGTGTGGAGAAAGGGCATAAATATCCCAGCTGAAATTTCTTGACTTTGTAGAGCTGTTTATTCCCCAGAACAAAATGGAGGACCCATTAGAGTGTTGCTCTATTACCTGATGCATAAAAAGAGTGTTTTATGTTTATTTAAATTGCTTTTTAACAAACCCTGTATAAAATCTTCTAGAGCTAGGTAAGTGATTTTCAACCAGGGGTGACTTCCCCCCACCAGGGGATAGTTAGCAATGTCTAAAGACTTGGTGGTCATAACTGGGGGAAGTGCTAGTTAATTGGCTTCTGCTGCTGCTGCTGCTGCTGCTGCTAAGTCGCATCAGTCGTGTCCGACTCTGTGCAACCCCATAGACAGCAGCCCACCAGGCTCCACCATTCCTGGGATTCTCCAGGCACTGGAGAACACTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAAGTGAAAGTGAAGTCGCTCAGTCGTGTCCGACTCTTAGCGACCCCATGGACTGCAGCCTTCCAGGCTCCTCCATCCGTAGGATTTTCCAGGCAAGAGTACTGGAGTGGGGTGCCATTGCCTTCTCCGAATTGGCTTCTAAGAAGTATTATTTAGTATCTCCCCACAAATTCCTATGAGGATAGATCTATGATTAGACCATTGCATGTGTAATATGATCAAATGATTTCTGGTTTTAAGGAGTATTGGGGGTTTATTTAATAACTTTGTAATAAAACTTGTATGAAATCTTCTAGAGTTAGATCAGTAGTTTTAAACCAGGGGTGATTTTGTCCCTAAGGGGATGGTTAGAAATGTCTAGAGACATTTACTTTTGGGGGTCATCATTGGGGGGCATCTAACAGGTAGAGTACAGGGATCCTGCTAAACATTCTTCAGCATCCTGCAGTGCCTGGATTGCCGTCCACAGTACAAACTTTCCAACCACAATGTTAGTTGTGCTGAGGTTGAGAAGCCCTGGGTTATACGTTAAATAATAAAGAGAATAGGTTCCCCTTCATCATCTTCAACGCTTCATTTACCTGCTAACAACCCTTAGCAAGCACACACTTAACTTCGTATAGAATTGTTTGTGTTTTAGATTTTCCTGTTCACTCTTCATCTTTTCACATGAAGCCAACTTGAATATACATCTCCTTTCTCCCGTGCAG
Seq C2 exon
CCTGCAAAGAGATGAAGGCCGACATCATGTTCCTGGTGGACAGTTCTGGCAGTATAGGACTAGAGAACTTCATCAAAATGAAAACATTTATGAAGAACCTGGTGAGCAAATCTCAGATCAGGGCAGATCGAGTGCAAATCGGTGTGGTCCAGTTCAGCGACGTCAATAAGGAAGAGTTTCAGCTCAACAGATACACATCCCAGGAGGAAATTTCAGATGCAATAGACCGAATGGCTCACATTGGAGAAACCACCTTGATGGGTAGTGCCCTGACCTTTGTGTCTCAGTACTTCAGCCCTGCCAAGGGAGCCCGGCCCAATGTCAGGAAATTCCTCATCCTCATCACGGACGGTGAGGCTCAGGACATAGTCAAGGACCCAGCGGTGGCACTTCGGGAAGAAGGCATCATTATCTACTCTGTAGGGGTGTTTGGCTCCAACGTCACCCAGCTGGAAGAGATCAGCGGGAGGCCAGAGATGGTTTTTTATGTTGAGAATTTTGACATTCTGAAGCACATTGAGGATGACCTTGTGTTTGGAATATGCAGCCCCCATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012837:ENSBTAT00000017057:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=92.0)
A:
NA
C2:
PF0009223=VWA=WD(100=90.9)
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:
TACGTGCATGACTTCGATGCC
R:
CACAAAGGTCAGGGCACTACC
Band lengths:
351-1761
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development