BtaINT0107942 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004561 | PAX6
Description
Bos taurus paired box 6 (PAX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001040645]
Coordinates
chr15:63360607-63361069:-
Coord C1 exon
chr15:63360987-63361069
Coord A exon
chr15:63360758-63360986
Coord C2 exon
chr15:63360607-63360757
Length
229 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
CTGTTCTGTCTGATTTCCAGGTA
3' ss Score
10.68
Exon sequences
Seq C1 exon
AGTTTGAGAGAACCCATTATCCAGATGTGTTTGCCCGAGAAAGACTAGCGGCCAAAATAGATCTACCTGAAGCGAGAATACAG
Seq A exon
GTACCTGGGGACTGTGTGTTCATGTGTTCATGTGACTCATACCATTTGCCTTTTTTAGAGACCCAGCTGCTTCTAAGGAATGTCATTTGTTTGTATCAATAGAAACAGATTTAGTTTGCTAAATGCTTTGCCGTCACTCGGGGACTGGGGGAGGAGGACAGTGGACCTGTCAGGGATGGGGCAGAGCTGGGAGCAGGCACAGGGCTCACCTGTTCTGTCTGATTTCCAG
Seq C2 exon
GTATGGTTTTCTAATCGAAGGGCCAAATGGAGAAGAGAAGAAAAGCTGAGGAATCAGAGAAGACAAGCCAGCAACACACCTAGTCATATTCCCATCAGCAGCAGTTTCAGCACCAGCGTCTACCAACCCATCCCACAACCCACCACGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004561:ENSBTAT00000005994:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.982 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(47.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=21.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTTGAGAGAACCCATTATCCAGA
R:
CGTGGTGGGTTGTGGGATG
Band lengths:
230-459
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development