BtaINT0042240 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012837 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:HGNC:27023]
Coordinates
chr1:153433479-153435959:-
Coord C1 exon
chr1:153435372-153435959
Coord A exon
chr1:153434100-153435371
Coord C2 exon
chr1:153433479-153434099
Length
1272 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TGTCCGTTCCTTGCCCACAGTTT
3' ss Score
11.6
Exon sequences
Seq C1 exon
GCCCTGAGTATGCTGATGTGGTGTTTCTGGTGGACAGCTCCGACCACCTGGGAATTAAGTCCTTCCCATTTGTGAAGGCCTTCATCAACAAGATGATCAGCAGCCTCCCCATAGAGGCTGACAAGTACCACGTGGGCCTGGCCCAGTACAGCGATGGGCTCCACAGAGAGTTCCTGCTCAGCACCTTCAAGAGCAGGGGCCCCATGCTGAACCACCTCAAGAAGAACTTCGGGTTCCTGGGGGGCTCCCTGCAGGTTGGGAAGGCTCTCCGGGAGGTGCACAGGGCCTACTTCTCAAGCGGGAGGGACAGGAAACAGTTTCCCCCGATCCTGGTGGTCCTGGCCTCCGGCGAGTCTGAAGATGCTGTGGAAGAGGCCGCCGAAGCGCTGCGCAAAGATGGGGTGAGGATCGTCTCCGTGGGGATGCAGGGCGTGTCCGAGAAGACCCTGAAGGCCATGGCCACGGGCCAGTTCCACTACAACCTCCGGACTGTCAGGGACCTCAGCTCGTTCTCCCAAAACATGACGCAGATTCTCAAGGATGCAGCTCAGTACAAGGACAGGGCAGTCAATGACATCCTTGTGGAAG
Seq A exon
GTGGGTCAGGGCACGTGTGTAGGGATGATGATGATAAAATACTTTCAGAAAATCAGCATGAGGAAAGGATGCAGACTCTGTGAGCATCTCTTTCCCCAAAAGCTGACCTGCGTTTTCAGATGGTAATTTCTGCATGCCCCACGATTGTGGCCTTTTTAATCCAATAAACATGGGAAGCCTTGGTTTTCCGTGTTTCACTTATCTTATTGCCTGTTGTTTATAGGCTACCTCCTCCCTGCCACCAGCTATCTGAGCTTTCTCCTTGGGGTTCAGCTACTATGTAGTTTCATTTCCGGTTCGTTTAAAAGGACAATTTGCTCCTAAAGAAATCCTTAATTCCTAAAACCATATAAAGTCACCACAGACTGTTACAGCTTGAAACAACTTCAGGGAGTCCAAAACCTCTGTTCCACAGAGAGGAAGCTGCAGGCGCTCTTGGAAGCGATATGACCTGGCCCTGGGCCAGGCTGTGGTCTGGAGTTAGAGCTACACCTGTGTGGGTTCAGCCCCGCACTTGCTCCTTCCTGCAGCTCTGTTCTAAATTAGCTTTCCCATGCTCTGCTCCAACTCCAACCTGCTCTCTTGGTCTGTCCCCTTGTACTATTCTATTAGCAAGGATGGCCAAGCGTTTATGAACACCACCCAAGACAGGGACAGGGGAGAGCTGGTAAAAACAAAAAAACAAAAAACTTTGCTTTAAGTGTACAAGTTCAGACAAGTGACATAATAATGTCTGGTTGTCAGAGTGAAGTGATGTATACTGACAACAGAGAATGCTTTCTTGTAGTAATCTAAGAAAATATGGAATCTTATTACTAGCATTTTCCCCAGATAAAGTATTAGAACATCAACTGCTATTACATTTCCATCCCTTAAGAATGTTTGGACTATAAACTGCTGATTTTAGTAGTGGGTTTTAATACGATAGCAGCAGCTTCTGTTAACTGAGTGACTTTTTATGTGCCAGGCCCCATGCTAAACTTGACATGATCTCATTTAATCGCTACAACAACTCTATGAGATCAATATTCTTGTTACCTGTATTTTACAGATGTAGGAATTGGAGCCTGGAGGTGAGCTAAGATCCAGCTTTTGTGCCCAGGACCCTTTGATCTCAGCTGCATCATCAGTTTCGATACCTCCTTACTTAAGTGCAAAACTGCTTGGTTATTCTATGTGTATTCTATCTATAATTGCTCATAAGTCTACGTGTCTTTAATGCTGAGCAGAGAAGCTGAATTAAAACTCTGCCTGTCCGTTCCTTGCCCACAG
Seq C2 exon
TTTGCCAAGGCCCTTCCGTGGCTGACGTTGTGTTCCTGTTGGATATGTCCACCAACAGCAGCTGGGAGGACTTTGACTATCTTAAAGAATTCCTGGAAGAAAGCATATCTGCTCTGGACATCAAGGAGCACTGCATGAGGGTTGGCCTCGTGGCCTACAGCAACGAGACGAAGGTGATTAGCACGCTGAGCAGGGGCGTAAACAAGTCGGAGGTTCTGCAGGACATCCAGAGCCTTGCTCCCCAGGCCGGGAAGGCCTACACTGGAGCCGCCTTGAGGAAGATCAGGAAGGAAGTCTTCAGCGCGCAGCACGGCAGTCGGAAGAACCAGGGGGTGCCACAGATCGCCGTGCTCGTGACCCACAGCCCGTCCCAGGACAATGTGACCAAGGCCGCCGTGAACCTCCGACGCCAGGGGGTGATCGTCTTCACCATCGGTGTAGAGGGGGCCAGCGACACCCAGCTGGAGAAGATCGCGTCTCACCCCGCTGAGCAGTACGTGTCCCAGCTGAGGTCCTTCTCTGACCTGGCTGCCCACAACCAGACGTTTCTGAAGAAGCTGCGGAATCAGATCACACACACGGTCTCCGTCATTTCCGAAAGGACCGAAACCCTCAAAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012837:ENSBTAT00000017057:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.029
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=88.3)
A:
NA
C2:
PF0009223=VWA=WD(100=86.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCCGAGAAGACCCTGAAGG
R:
CAGCGTGCTAATCACCTTCGT
Band lengths:
344-1616
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development