BtaINT0128914 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018855 | SCAF4
Description
SR-related CTD-associated factor 4 [Source:HGNC Symbol;Acc:HGNC:19304]
Coordinates
chr1:3093916-3095591:+
Coord C1 exon
chr1:3093916-3094073
Coord A exon
chr1:3094074-3095425
Coord C2 exon
chr1:3095426-3095591
Length
1352 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTCCTTTCTTTCTTTCTAGGTC
3' ss Score
14.97
Exon sequences
Seq C1 exon
ATTGGAAGGGAATTCCCAAGAAGCATGAAAACGAAGTTGCTCAAAATGGAGGAGCTGAAACCTCACACACAGAGCCAGTGTCACCCACACCTAAGCCTCTGCCTGTGCCTGTGCCTCCTATTCCTGTTCCCGCACCGATAACAGTACCGCCTCCACAG
Seq A exon
GTAAGAGTACTTGGGGCATTGTTGAAGCTTTCAAGCATCTAAAAGATACCTTTCTAAATCTTACTGGTGATGTATGTCTAGATTCATAGCTAAAAGATGTGAGTACATACACGTGCGTATTAATTTCTTATATATTGGTATGTCAGACCTAATATTTATAAATGCTTTCAAAAACCAGAGTAAATTTCATTTTGCCTTACATCTGCCCAGATTATTCAGTATCTTATTACCTCATAAACTTTTTGACTTGAAATGTGATTTTCCTGCTACATGTTAAGAGCTAAGTAACTAATGTGTTGGTAAGAATTAGAAGTACTTGATCCATACTTTCATGTGTGATTCACTAGATTTTTCTCTTCTTTCAGTACCTTCTTTCCTCAGTTTCTCACATTAAAACTGAATAAGTAAATCTAAGCTATCTCAGGGCTGGGTTGCCTAGCTTCTTGATTTTCCTCAATGTTAAGAGAAAAGTACATGCTTTGGTACATTCTTAGCGGTGACATTTTATAAATGGATTCCCCAAATTGGCACTCCTTACGCAACCTTTTGGATATGACTTCCAGTGCAGGTTTCAGTGTATGTCAGCGCTCACTTAAAGAAACTTGACTTATCTGTTAAGATTGATACTTTTTTTTTTTTAAGCAATAACTAAAGTGTTGGGTATGTATTAAATGTCAGGCATTAGCACTCCACATTTATTTATTCTCTAATCTCCATAATTATGTGAGGTTGGCACTTTTTCATCTTACAGATGAGTAAACTGAGGTCTGCAGAGTGTAATGTAAGTCGCTTTCTCAGGGTCACAAAATGACTTAAAAGGGGGAACAGGCAGTTTGACCCCAGGAACTGTGATCTTAATCACAGTTAAGTGCAAATTACCTGGTAGCTTTTCTTAGAGTTGTATTCCTCAAACTTAATTGACCTGACCGTGAGACATTTTTTTAACAATATTCTGGCAGAACACCAGTGTAGGTGATGGTGAATCACAGTGTGGTATTTGCTTTGATAAGTATAGGGCAAACTGATTTCTGGAAATTCCTTGGTAGCTCAGTGGTTAGAACTCCATGCTCCCACTGCAGAGTTGCAGCTTCAATCCCTGGTGGGGGAACAAAGATCCTGCAAGCCACATGGAGCAAGCAGCCCAGAATTTTTAGAAAAGGGGAAAAGTATGTAGTTTCCATTGTTTTGGAGTGGGTACAGATTACCACTGTTATCTAATAAATGTATTCACATAATAAGCACAATTTAGAGATACTGGTTTTTTTCAGCAAGGTATTTTCTTTGTCTCTACCCACTATATGAGTGAGAGGGTGGCTAGATACGCGGCTTCATTTTCCTTTCTTTCTTTCTAG
Seq C2 exon
GTCCCACCACATCAGCCAGGACCTCCTGTAGTTGGTGCTCTCCAGCCACCTGCTTTCACGCCTCCTTTGGGAATTCCACCTCCAGGCTTTGGGCCTGGTGTTCCTCCTCCTCCACCTCCGCCACCGTTTTTGCGCCCAGGATTCAACCCAATGCATCTGCCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018855:ENSBTAT00000025104:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ATTCCCAAGAAGCATGAAAACGA
R:
GTGGCAGATGCATTGGGTTGA
Band lengths:
310-1662
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development