BtaINT0148054 @ bosTau6
Intron Retention
Gene
ENSBTAG00000047673 | THUMPD1
Description
Bos taurus THUMP domain containing 1 (THUMPD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001046277]
Coordinates
chr25:18567606-18569003:-
Coord C1 exon
chr25:18568829-18569003
Coord A exon
chr25:18567855-18568828
Coord C2 exon
chr25:18567606-18567854
Length
974 bp
Sequences
Splice sites
5' ss Seq
TAGGTGTGT
5' ss Score
4.3
3' ss Seq
TGCTGATTTTTTTCTTTTAGAAC
3' ss Score
9.84
Exon sequences
Seq C1 exon
TTTGCAGACAAGGATCAACAACCCTCTGGAAGTGAGGGAGAAGACGATGATGTGGAAGCTGCCTTGAAGAAAGAAGTTGGTGACATTAAGGCATCCACTGAGATGAGGCTAAGAAGATTCCAGTCAGTGGAGAGTGGAGCAAATAATGTAGTCTTCATCAGGACACTTGGGATAG
Seq A exon
GTGTGTCTGACTAATACACTTTAAGATTATTGATCCTATAATATCAGGACATCACCCTGACTCTGAGAACACTGCCTACAAAATGGGTTCATGGGCATGGCTCAGTTAATCATTTGATTGCATCCTCTCTGTGTTAGCACTGTGTTGGCACTAGGCATATGGAAAGGTGAAATGGGGTGGTGGACTAGCATGGGCTTAGGAGTAGAAACCTGGGTTTGCCACTTCCTTTGTATTTAACTTTAGGCAAAACAAGAGTACATGGTTCTGTCTAAAAGGAGCAGATGCTACTCAGCTCTCCCAATTTGGAATGGCTCCAGACATTTGGGAATGTAGTCTCAGGATAGCCAGATCTTCCGATTTTTCAAAAGAAGTTGGAAATCTGGAGAAGTTTCTATGTTTTTAAATGTAGTTAACTAATTTAAAAATATTGAAAACACTGAACAGCCTCAAATAGAATTGTATGTGGTCAGGATGCTTCCTAAGGACTACATTATGATCTTGTGGCTAAGGGATGACTCTGAGGTCTGAAATCTAGACTTCAGTACAGACTTAGCTAATGGATTGATTAAATCTTGAGTGACTTGAAGATTTTTGTTTTGTTTTTGTAAAACATGTTCTATTTAATGTTTATTAGTTTGTTGCTGCTGTTACAGGAAAACAACAGTATGACGTTGTCATTAGATAAATCAGACATCATGAATAAATTAACTCCAGAGTCTTCATGAACAATTGCTTTTGATAAAAGTGGACTTAAAATATTAGATATAGTATTAATACAGAGTGCATCAAAGAAATATTAGTTGGAAGAAATGTTTGGTTAAACTTGCTTAAAATTCATTATGATAAGTTTTTCTAATCTACCGTCAGTTTATGTCACTGCCAATAAAAATTCTTTTTAGAGAGTCTGAAGAGTTTAAAATGTGTGAGGACTTTGAAACTTACCTGTTTGTTTTGTGCTGATTTTTTTCTTTTAG
Seq C2 exon
AACCTGAGAAATTGGTGCATCATATTCTCCAAGATATATACAAAACCAAGAAGAAGAAGACTCGGGTTATTCTACGAATGTTGCCCATCTCAGGCACATGCAAGGCTTTCTTAGAAGATATGAAAAAATATGCAGAAACATTTTTGGAACCATGGTTTAAAGCTCCAAACAAAGGAACATTTCAGATTGTATACAAATCTCGGAATAACAGTCATATGAATAGAGAAGAAGTTATCAAAGAATTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000047673:ENSBTAT00000064153:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.407 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF087955=DUF1796=PU(62.2=86.4),PF0292612=THUMP=PU(26.5=72.9)
A:
NA
C2:
PF087955=DUF1796=PD(36.6=35.7),PF0292612=THUMP=FE(51.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAGACAAGGATCAACAACCC
R:
TGTTTGGAGCTTTAAACCATGGT
Band lengths:
344-1318
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]