BtaINT0042249 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012837 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:HGNC:27023]
Coordinates
chr1:153352924-153354172:-
Coord C1 exon
chr1:153354110-153354172
Coord A exon
chr1:153352960-153354109
Coord C2 exon
chr1:153352924-153352959
Length
1150 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
CATTCTTTTTGTTTCCCCAGGGT
3' ss Score
10.9
Exon sequences
Seq C1 exon
GTATCTGCTGGGCTTCCCGGAGAACCAGGATCCCCTGGGGAGCTGGGACCTCCTGGACGCAAG
Seq A exon
GTAAATCAAAAACCCATAAATCACATCAGCTCCTTTTCCAGATAAAAAGTCAGTGCCCGAAGTCTTCATTATCCAAATGCATATGCTTTCTGTGTTTGCAGCTTGTCAATGATTTCCACCACTTTTCCACCTTCAATGTCCTCAGGGAGAGGAGGAAAAAAAATGCTGATTAAATATTAGTTGCTATTTCTCGGGTGGTGGGGGGAACCGAGGAAGGAAGCAAAAAGACATTTCTTATTTCATCTAGAATGAGGTTTCTCAATGATCAGTGAATTTTATTTATCTGACCAATCCTTGCCTTTTTTCTCAGAGTCAGTGATCAGTGAATGAAAGAAAGGGAGAGGAAATTAACAAATAGTGAATAAGCTCCCAACAGTGCATTCACATGGAACTTATTTTCTTGAGGAGTTTGGGTGGGGCGCCGTCACATTTTTCCCCGTCTCTTTGAGCTCAGCCAGACTCTTCCTGTTCCAACTTGAGACTGAACAGACGAAATACAAAATAATTCCACTTTGTTCTTTCTATCCCCTACCCAGATAGATAGAAATGTACATATATATATATGTGTGTATATATATATATATGATCATATATGTATATATGGTCATATACATATATATATATATATATATATACTCATTTTTGGAAGACAGTGCGGATTGCCTTTCCAGATATTTGGCCTGTCTAGGCCCTTTGTCATCCAGCTGATGATGGGCACAGATTCAGGCTCTGCTCAGCGGCTGCCCAGTGACCAAGGCAAAGTGTTGGGGAACTCGATACCTCTGCATTAAGGAGGGCCCGGCACAGGGGATGGCTCAGCCTTGTCTAGTTCTAGCCCCAGGGTCTGCTGCAAAGCTCTCCCGGCCGGTGTCTCATTGCCAGCTCCGTCTTTATCTTCTGGACAACCCTTATCGTCCAGAGACACAGCAGGAGGACAGTGGCCGCTGGAGGCTCACTACGTACAGTTCCCTCCCCTTAGAACGTTATTGTTAATCTAATGATGAGTATCCTACAGGGAGTTTTTTTCTCCCTCTTAGTGAGAATAAAAAGGTTAAGAAGCTATCTTTTTCTTAGAGTAATGTTGATGCATATTCTGGCTCCTGCGATGTGCTTCCAAAACCCTGAAACCACATTCTTTTTGTTTCCCCAG
Seq C2 exon
GGTGTGAAAGGGGCCAAAGGATTGGCTTCGTTTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012837:ENSBTAT00000017057:28
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=0.417
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(33.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(16.9=83.3)
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