GgaINT0115187 @ galGal4
Intron Retention
Gene
ENSGALG00000015850 | SCAF4
Description
splicing factor, arginine/serine-rich 15 [Source:RefSeq peptide;Acc:NP_001012840]
Coordinates
chr1:104006656-104008831:-
Coord C1 exon
chr1:104008641-104008831
Coord A exon
chr1:104006757-104008640
Coord C2 exon
chr1:104006656-104006756
Length
1884 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TGTTAACTCTTTGATTGTAGTTT
3' ss Score
4.95
Exon sequences
Seq C1 exon
GTCACCTAAAAGGAGACGTTCAAGGTCCGGCTCTCGCTCTCGAAGGTCACGTCATCGTCGATCTCGGTCACGATCCAGGGATAGACGCCGCCACTCTCCGAAGTCTCGATCACAGGAAAGACGTGAACGTGAGAGGGAGAGAGAACGCAGGTCAAAAGGCCTTCCTCAGATCAAATCAGAAACTGTTAGTG
Seq A exon
GTAAGTTTGCCTATTCTGTTTGTTGTTGCTGTAACCTTGACAATTCAGTTAGTACCCTCTTTCAGATGCTCGAGATCTTCATGGTTCACTCATGGATTTTTTTTCATGTGTCTAGTATTTTCTTTACTGAATTTTAGAGCTCTTCAAAGTTGAAGATCCTGTAGTAGATACTATGCCTATGTAAAATGAAATACTAGCAGGACAAAGTTATTTTAGAAAAATGGCAAATGGCTGAAGAATCTACTCTACTTAGACTTGTTTATTTAACTTAATGTTGACCAATTCTTTTACCTTTATTATACATCTTCTCCAAAAACGCACCAGAGACAGCTCAACTAAGATGTGAAGAAACGTATCTTAGGTCCTCCCTCTTGGCTCCCTGGCCAGATGTAGGCAACAGATGGCTTATTGTCACTTGGAGTATTTTATCTGATTCCAATCCATCTTCTCCATCTTTTTTTCTTGTGTTTGATGCTATTTGATACGTTCTCCAAGATTCATCTGTACAAAAGAGAAATAAATTGCACTGAATTGTTTTTCTGAACTGTTTTGAAGCCAGTGAGAATTAAATGCATTGCGTGCCAGCACACCCTGACTGCTCATAAGGGGCATTTGGGCCTTCTTGGAATGTCTCCAAGTCAGAAATATTTTGTTTGTAGAATAGAAAAAGAAAAATCTTAAAGACTGTGTTCTTCTTTTCTTTCCTTCAAGACATACAAAGTAAAGCAAACTGAACAAGGCTGAGCACGTGATTATGATTTTTTTCTAATGATCCAGTGTTGTGCTTCTCTCAAATCTGAAGGGGAGCTTTGACCTGGAAAACACATGGGCTAATGTTATTCTTAAACAATCTTGGCTTTGGGGGAGTTCATAGACAGTATCTCGTAGCTGTCTTCTAAATATCCTTGAGAGCATCAAATAGAATTAAAGTGTTCTTTCTGATATAAAAGGGACACAAGATAAGCATCTGTAACTAGTCAAAACCTGAGTATGACAGTAACATTAATTTTAAAGTACCACAGAGAGTTAATAGGTATTATTTTAAAGGATTTAACGGCAATGGTTTAAGATACTGTTTTGCCAACACCTCTCCCAGATTACTAATGTAAAAAGCATTATATGACAATTTTCTATCACATACAGGGAAAACATAGGTGAGTACTGAATGTTGCTATAGTACTCTTGAAAGGATGCGTTACTTTGTGCTTGTCTGCTGCATTATTACCCTGAAGAATGAAGCAAAATAAGCATGTTGCTTGCTTTCCTCCAGGGGGTGGGGAGGAAGCTTCTATTGATAATTTTTCACTTACCTGTTAAGAGATAGGACAATGAATTGGTTGCTAAAGAGGGTAAAACTGCTACTTGCGGTAGTTTGTCACAGCATTCTGGAGGAAAGCCTCCACAGCTGTGAGTGTATCACTGTAAATAACTATTGCTTTGCTAGTAAGTACCATCCATAACTTGGGATTCTGGCCCAAAGCTAGGGTTTCACGCCGAGCAGGCTAAGTTACCTTGTAAAATATTCACTGCAGGTGTGAGGATATTTCATGGAGCAGTCTTAGCAACAAAGCATATTTTTCCTTTCTGTAATTATTCGCAGAGCTTACGCTCATCAGGATTTGCAGGTCATCTTAACAGAGGTTAAGTGAACAGCTTCTGAGTTTGTGCATCCTGGCAATGGTTTTGGTGTCGTGGTTAATTTGTCTCTGGGCAGGCAGAAAAAGAGGCCTTTCAAAAACTCCTGAAGATAGTATCTTATACCAGCAGACTTTTCTCCGTTAGATGTCATAACTGACTATTGTAACATGACTGTTTTGACATTTTGGTTTGTGAAGTCTGTATTTACAAGCACTCTTACAGTCTTTGTTAACTCTTTGATTGTAG
Seq C2 exon
TTTGTAGTACTACGCTTTGGGTAGGACAACTTGACAAAAGGACTACACAGCAGGATGTTGGAAGTCTCTTGGAGGAGTTTGGCCCAATAGAATCAATAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015850:ENSGALT00000025555:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.923 A=NA C2=0.059
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0007617=RRM_1=PU(41.8=82.4)
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:
TCACCTAAAAGGAGACGTTCAAGG
R:
TTGATTCTATTGGGCCAAACTCCT
Band lengths:
286-2170
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]