GgaINT0115178 @ galGal4
Intron Retention
Gene
ENSGALG00000015850 | SCAF4
Description
splicing factor, arginine/serine-rich 15 [Source:RefSeq peptide;Acc:NP_001012840]
Coordinates
chr1:104017704-104019110:-
Coord C1 exon
chr1:104018949-104019110
Coord A exon
chr1:104017840-104018948
Coord C2 exon
chr1:104017704-104017839
Length
1109 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGA
5' ss Score
9.78
3' ss Seq
ATCTGCTTTTGTTTCAACAGAGT
3' ss Score
9.55
Exon sequences
Seq C1 exon
TGCAAACCAGAATATAAGGTCCCTGGATTGTATGTTATTGACTCTATTGTTCGTCAGTCTCGTCACCAGTTTGGAACGGATAAAGATGTCTTTGGGCCAAGATTCTCTAAAAATATTACTGCCACATTCCAGTATTTGTATCTCTGTCCATCTGAAGACAAG
Seq A exon
GTACGACTGTGATTTCTTAAGTGTTGTCAGTTGGTAATGCTATTACTTTGAGATTTCCATATACAAGTGAGCTGATTTGGTGATATTCTTATGTCCTTGTAGTGAATATTATTGTATGAGATGGTAAAACATACTGAGAAAGGTTATCAGCAGTAACAGTTAAATAGAAGTTCTAGCTAAAAGAAATATTTTTGTCTGAATTCATCAGTTCTGTTCTGGTGTGAACAGTGTGTATGTGTGTGTGTGACTGTGCCAAAACTGATCTTCCTGAGACTTCCTCAGGACAGCTTACTAGTGAAGGTAGCGTCTCTCACAGAAAGAAAGTGTTAGAAGTGCCAGAGTTGTAATCAATGAAGGTTCGGTTCTTTTTTTGAGACTTTCAGAGTGATATTTGTCAAGGCCAAAGATGTTGCTGTCCTAGAATTGTTTTTCAGACCAAAATCTTGTTCAAAGATAATCATTGTAAGTTTCTATTGAGCAGATAGTATTGTAGAAAACGTTTTGTGAAATTGTTGTATCATTTAGCTTTAACTTCCTGCAGTGATCACAGATTCTTCTACCTGCTTTCCATTTGAGTAATGACGGAGAAGGATTTTCAAGCGTCAGTGCAGGAGTGGTTGGATTAGTAGAAAAAGATTTGAACAAACAGTGTTTGCTAACTTTAGAATTTTTTCTAGTATTCTAGTTTTGTGGCCCATCTCTCCATGGGTTTTTCTAGCTCATCTTCATTTTTCCTGTCTTTCCTATCACGTTTGTTGGTTTTTTTCCACCCCTTTATGACTGTCTGTGAAGAAATAGTGGGGCTGATGCGATTTCCTTTACTGTTTATTGAACCTGGATTTTCTGCCTGGCCAGAATAGCTTTAGAAAAATGGCGCAAGGAACTTTTTACTGAAGGGGATAATAAGTTGACAGATTCTATCTTTTGCATGTACAATATCTTGCTGACCTGTGTGACAGCAGTGGGTTATTTCAAAGGTCTCCCCAATTCTTTTGCACTGCTGTGTTGTTAGATCCATTCTTCTCAATGCTTAAAAAAATAGAATAAAATCGGGGTTTGTGTATTAGGAAAGCTATATTTAGTGTTGATATCTGCTTTTGTTTCAACAG
Seq C2 exon
AGTAAAATAGTCCGTGTCCTGAACCTTTGGCAGAAAAACGGTGTCTTTAAAATAGAAATCATTCAGCCTCTTCTGGATATGGCAGCAGGAACTAGTACAGCTGCTCCAATGACAGAAAACGCTACTAATAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015850:ENSGALT00000025555:5
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=0.326
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=PU(72.7=88.9)
A:
NA
C2:
PF048188=CTD_bind=PD(24.2=34.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAAACCAGAATATAAGGTCCCTG
R:
TTCATTATTAGTAGCGTTTTCTGTCA
Band lengths:
297-1406
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]