BtaINT0041315 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54753162-54755358:-
Coord C1 exon
chr13:54755267-54755358
Coord A exon
chr13:54753273-54755266
Coord C2 exon
chr13:54753162-54753272
Length
1994 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CGCCTGTCCTGCTTCCTCAGCGA
3' ss Score
7.78
Exon sequences
Seq C1 exon
GCTGCGCACCATGAGCGTCCGCGTGCGCCCTCACCTCGGAGTCGGCCTCTGTCTGTATCTGAGTGTCACCCTGGGGCTCAGCCAGGGACAAG
Seq A exon
GTGAGGACACGGGTGAGGGTTCCTGGAACTGTTCCTGCTCCCGCCTGGCCCCCCCCAGGCCATACCTGCCCAGGGCACAGGCCCCCCTGCGGGACCAATCTCCCTCTGGCCCTGAGCAGCTGCTGCTTCCAGGGGCTCGGGTGCTCAGGGGACAGAGACGGGAAGACAGGACAGCTCTGCCCCCAGCATCACCCTCAACTGTGTGGCTTGACCTTTGGTACTGTGGTTTTTCCTTTTAGTTGGGCTTTTTTTGTCTTATCCATTTGTTAACACAAATGTGCATTAATGCACTGTGCATTTGATTCACTCTTGCATTAGTGATTTTTTTTTCATCATTCTCTGGACACGTTTTTAATTGTGAAATTTTCAAACAACAGAATCTAGAGTGAAAAGTGACCCCCCCGCAACACCCCCGAGGAGAGCCCAAGACGCCGCCTCCAGCAGGTCCCTGATCCTTTCAGCTCATTTATGGCCACGGGCAGCACCTTGGTCAGCTGTCCCCCGTCCAATGAGGGGATGCTCAGCTCCCTATGGGGCGTGTCCCTTTCAGGGTGATGCTCAAACCCGTCAGGGAAGGCTGGGGAGACCAACCTTGAGAGGTGGTGTTTGAGTCACGTAGCGAGCCTCCTCCACACTGCCCCCCAGCCACATCCCTGGCATTTGTCCAGCTCCCACGGGTGCCAAGAGGGTAGGAGACCTCTGAGCTAGTCCTCACGGGGGCGCGGCAGGGACCTGTCACACAGCCACCCAGCCTGGAGTCCTGGCTTCTCTAACTACCTTCTTACTAGCGGCACATCCTCCTGGCTATGATTTTGCTCACAGATGATTGGGGCCTCCATCCCTGGGGCTCTGACAAGATCCCCCAAGGGGACCAAGTCAGTAAGAAACCCCAGACACTCAAGGTAGACAGCACAAGGCACCTGCAGACTCTGGGTGGACTGCGTCGGGGGGTGGTTGGAAGATGGGGGTGGGACCCATAAGTCCAGGCTGCCCTTCTCCGAGAATGGCCCTGTGTGGGGGTGCCCCTGGTTGGGTGCTGTCTCCCCAGTGCCTGCCAAGGCTCCGACCTGCAGACCCAGAAGGCAGCTCGGGATGCCCCCCCAACAACATGTCAGGGGTGCCGGGAGACAGAGGCTCTTCATGAGCTGGGCCCCCCACTCACAAGCGTCTTTTCAAGGCCCCCACTGCTGAGACATTCCTGCCTTTCAGCTCACGCTCCAGGGAGCAGGGGGCCCATCCGGAGGCCCAGCTCAGCTGCTACCCGCTCTGAAGCGGCCATTGTGTCTGCCACGGGCTCCCCCCAGCCCTGCCCTTCCCCTGTGCCCCTGCTCTGAGGGGGGCAGCCAGAAGAAGTCCATCTCTGTCCCCACTTTCCAAAAATAGTCACCCACACCAAGGAGCTGCCGGAAGCTTGGAAGTCAGGCTGTGCTGGAGGGCTCAGGCCTCCATGGCCCCTTCCTCCTCCCAGGACGGCCAGGGCACCCTCCCCAGGGAGCCCCCGCCCCCAGGCACCCCCACCTCCTGGGATGTGTGACCATGGCAGCAGGGAGTCTGCAGCTGTGTCTCCACTGCACTTCGGGGACTCAGGCGGGGAATCGGGAGGGGTGGCTGGCTGCAGCTGGCTCAGAGCCTGTCTCCACTGGGTGGGTGGGCAGTTAGGGCCACTCTGGGATGCTGGCCTGAGCCTAAGTCCACAGTGCGGGGCACCCCTTATAGAGCCAGGAGGGCCTCTCTGGACAGAAGTCTCCCCCACCCAGATCTGCCCGGCAGCCTTGGACTGCAAGGGGGACCAGTCCTCCTCCAACCCTGGCTCGGGGGAGGTGGGCTCCTCTTCTCAAAGTTCCCCCCAGTGGCACTGGAGTCCCCTCTGAACCTCGGAGGGGCTGAGCCCCAGAAGGGCCACAGCCTCCTCGGAACCTCAGGATGGGGTCCCACAGCTGGTTGGGGAGGTCACCAAGGAGGATCAGTCCTGACCGCCTGTCCTGCTTCCTCAG
Seq C2 exon
CGAGTGGCCGCCTGAGGCTGGCGGTGCTGCCTGAGGACCGGCTGCAGATGAAGTGGAGAGAGTCAGAAGGGAGCAGCCTCGGCTACCTGGTGCAGGTGAAGCCCAGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.132
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(0.1=0.0)
A:
NA
C2:
PF0004116=fn3=PU(48.1=97.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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