BtaINT0125985 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002315 | RNF34
Description
Bos taurus ring finger protein 34 (RNF34), mRNA. [Source:RefSeq mRNA;Acc:NM_001014858]
Coordinates
chr17:56025064-56027065:-
Coord C1 exon
chr17:56026658-56027065
Coord A exon
chr17:56025166-56026657
Coord C2 exon
chr17:56025064-56025165
Length
1492 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
GATATCCATTATGTGTGTAGGAG
3' ss Score
4.69
Exon sequences
Seq C1 exon
CATGTATGTTGTGACTGCAAGAAAGATTTTTGCTCCGTGTGTTCAGTCTTACAAGAAAATCTCCGTAGATGTTCCACTTGTCACTTATTACAAGAGACAGCCTTTCAGCGCCCTCAGTTAATGCGACTGAAAGTGAAGGATCTCCGACAGTATCTCATCCTTCGAAACATACCGATTGATACCTGTCGGGAGAAAGAAGACTTGGTGGACCTGGTCCTGTGCCACCATCGGCTGGGCTCTGAGGATGACTTGGACACGAGCAGTCTCAATTCCTCAAGGTCCCAGACTTCTAGCTTTTTTACACACTCATTTTTTTCAAACTATACAGCCCCGTCTGCTACCGCATCTTCGTTTCAGGGAGAGCTTATGGGTGGAGACCGGACCTTAGGATCTGGAGCGCTGGCACAG
Seq A exon
GTACGAGGGTACAGTTACCCCAAGGGCCTGGCACATCATCCGCTCTTGGCCAGTGTGGTGGGGCCTTCAGGGCTGATGGCTCCTTGCTGAGGCAAGGTTCCACACTTTGCTGAACTCTGTGCCTGCTGGCTCCCCTAGTGTGAAGCTCTGCACTTGGGTGCTGTACAAAGGGTCTGAAAAGAGCTCATCAGTCTCTTGACCTTAGTTATCCCAGTTTCCTTAAATCCTATAGTTAAATACTAGCTGTCGAAATAATGGCCATGAAACGTAGCACATAAATGTTTACAGGATGTAAACATTTTTACTGTTTGTGTTTACTATTAAAACTAGTAAAAATGTTTACTATTTGTGTGTCAGTGACCATGGAAACTATAAGGTAACCTAATGCCCAGTTGTCTTGCTACAGTAAAGTTGTGCTCATCTAGATATTGGGAAAGAGCCATCTGAATTAGCAACACGATACGGTTATTTACTCATTTCAAAGAAATGCCAGTGCAGCATGTTGTCCCAGTGAGGTCCTTGGGCATTCTGATGGAATAACGTGCAAGGGCTTGTAATTAATACCCAATTTGTATATATGAATGATTCTAAAATGCTGAAAGAATTGTTTTGAACATTTATCTCCGAGTTTAATTTTCTCCTCTGAGGAAAAAGGTTAGAAGCAGAGGGAAATGTGGTCTAGTTGCTTTCTAAATAGTCATAAATTAAATAAGCCCAAGCTAGGCATTTTATTGTTTTGTCAAATGGCAGCTGGCACAATTATGATGCAAACAGAAGACGCATGTGTCTGACCTTCGTGTCACTTTGGGGTATATGACACCACTCAGGAGGTGTGGGTTTTGGGTATTACAATATGGTGCTTATGAACTACTAGGATAGAATACTTGAAATTGAAAATTGACATAGGCTTTCTGTTCTCCCTAAAGAAAAAAGTATCTGATGGTTGAGGAACTTCTAAAAACTAGAACTAGCATCCACCATCAGTGAATTATTCTAGAAAGCTTTGCTTGGAATTAGAATGGCTAAGTATGAGATAGTAAGACTGAGATCTTTGAAATCAAATAGCCCTGACACTAGGGCTGATCTTAGAGCTTTAGTTTCTACCTGTATCTTAGAGGCTCCAGTTAAACTAGCCATGTGCAGGTCCTTTATCAGGACACAGTGCAATTTCATACACTGTTGGCTTTGGTATCCTGTGATGGGCCCTTCTTAACTCCTTGGGGAGTTAATATTTCTGGTTAGACTTTTACAGATTCACACTCTTATAGGAATTTGACTTGTGAGATAACTATGGAAGGTTAGTTGTTTAGAGAATCATGTGGGGCCCAACTCTTTGGGAGGGGCAGCGGCTCTCAGGACCCTGGGAAGGTGTGGAGTATACCAGGTGTTGGGGTCATTCTTAGGGAGGATGGCTGGAAGGGTTTTCTCCAGTGATAAATACGGGTTGACATTGCTAGGAAAAGTCCTGGCCTGATATCCATTATGTGTGTAG
Seq C2 exon
GAGCCCAGTGAAATAGCTTCAGCAAACACAGAAGACGATGAAGATGATGATGACGACGACGACGATGACGACGACGATGACGAAGAAAACTTGGAGGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002315:ENSBTAT00000002986:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.169 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0306610=Nucleoplasmin=PU(59.8=47.1)
A:
NA
C2:
PF0306610=Nucleoplasmin=FE(30.8=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:
ACAAGAGACAGCCTTTCAGCG
R:
GCTGAAGCTATTTCACTGGGCT
Band lengths:
342-1834
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development