BtaINT0161504 @ bosTau6
Intron Retention
Gene
ENSBTAG00000039223 | WDR38
Description
Bos taurus WD repeat domain 38 (WDR38), mRNA. [Source:RefSeq mRNA;Acc:NM_001163946]
Coordinates
chr11:95846743-95848532:+
Coord C1 exon
chr11:95846743-95846863
Coord A exon
chr11:95846864-95848415
Coord C2 exon
chr11:95848416-95848532
Length
1552 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ACCATGGCCACCCGCCCCAGGCC
3' ss Score
4.16
Exon sequences
Seq C1 exon
GTCAACTCTTCAGCCTTCTCTCCCGATGGCCAGAGGCTGCTCACGGCCTCTGAGGACGGCTGTGTATATGGCTGGGAGACCCAGAGCGGGAGGCTACTGTGGAGACTGCGTGGCCACAAAG
Seq A exon
GTGAGGCTCTTCAGCCCAGATGGGGAGACTGAGGCCCATTGACCTGTTCTGCATTCCACAGAGTCTACCAGCATTTGAGCTGGGCATTCCAGCAAGATAGCACCGGTAGGGCTGGGGTAAGAGGGCAAGGAGATGGGACCTGGTCCCTTGGGTCCTGAGCCTGACTCTTGACAGACCTGGACTCAAATCCTACCACTTAAAACTCGGTAATACCACATTCAGTTCAGTTGCTCAGTCGTGTCCGACTCTTTGTGACCCCATGAATCGCAGCATGCCAGGCCTCCCTGTCCATCACTAACTCTCGGAGTCCACCCAAACCCATGTCCATTGAGTCGGTGATGCCATCCAACCATCTCATCCTCTGTCGTCCCCTTCTGCTCCTGCCCTCAATCTTTCCCAGCATCAGGGTCTTTTCCAGTGAGTCGGCTCTTCGCATCAGGTGGCCAAAGTATTGGAGTTTCAGCTTCAACATCAGTCCATACAATGAATACCCAGGACTGATCTCCTTTAGGATGGACTGGTTCGATCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTCTGCGCTCAGCTTTCTTCACAGTCCAACTCTCACATCCACACATGACCACTGGAAAAACCATAGCCTTGACTTGGCAAAGTAATGTCTCTGCTTTTTAATATGCTGTCTAGGTTGGTCATAACTTTCCTTCCAAGGAGTAAGCATCTTTTAATTTCATGGCTGCAGTCACCATCTGCAGTGATTTTGGAGCCCCAAAAATAAAGTCAGCCAGTTTCAGTCATTTTTAAATGTACAGTTCAATGGCGTTGTTTACTTTGTTGTGCAGCTGGTCTCCAGAACTCTCATTTTGCAGAACTGCAACTCTGTACCCCTTGAACTCATATCTCCCTTCCTCAGCCCCTGGCAACCCCTGTTCTGCCTTCTGTCTCCAGTTTAACTAAATACCTGGTGTAAGTGGAATCTTTCAATATTTCTTTTGCTGACTGACTTCACTTGGCACAACGTCCTTTATATTCATCTCTTTACCCACTTTTTTGACTGTGATTGAAATCAAGTCTTGTCACTTTCTCTGTGCCTCATTTCTTTAGAATGGGGATAATAGTTGCTATCCTATAGAATGACATTAATGCAAGCAAAGCGCCTGGCTCCCAGTAAGAACTCAGTAAATTATAATTAAAAAGACAAGGGAAATCTGATAATTATAGGGCAAATTGGTTCATGTTATACTAGGCAAAGTCCAGGGGCTGGGGAGTCAAAGAGGATAATGTAGAACCTAGGCTGGGCTGAAAGGAGGTGTTTTATTTGATTTATTCATCTTCCAGATGGGCAAACCAAGTTTGCCATTTCAGACCAAAGGCATGGAAGCCCAGGAATTTTCCAGCTGGTTGGAGGATAAGGGTTAGAAGGGAGTGAGAAGGGAGACAGGCAATGCAACTGAAGAAATCAGCAGGGGTTTAGACTGCAAGGGCTGGAGGTGGAGGGTAGCTCCCCATTGCTTGACCATGGCCACCCGCCCCAG
Seq C2 exon
GCCCCGTGAGGTTCTGCCGCTTCTCCCCTGATGGCCGCCTCTTTGCCAGCACCTCCTGTGACCGCACCATCCGCCTGTGGGATGCCACAGATGCCAAGTGTCTGCAGGTCCTGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039223:ENSBTAT00000053781:2
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=0.000
Domain overlap (PFAM):
C1:
PF0040027=WD40=PD(67.6=61.0),PF0040027=WD40=PU(28.2=26.8)
A:
NA
C2:
PF0040027=WD40=PD(69.2=67.5),PF0040027=WD40=PU(20.5=20.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCAACTCTTCAGCCTTCTCTCC
R:
CCTTCAGGACCTGCAGACACT
Band lengths:
238-1790
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development