GgaINT0115188 @ galGal4
Intron Retention
Gene
ENSGALG00000015850 | SCAF4
Description
splicing factor, arginine/serine-rich 15 [Source:RefSeq peptide;Acc:NP_001012840]
Coordinates
chr1:104004867-104006756:-
Coord C1 exon
chr1:104006656-104006756
Coord A exon
chr1:104004981-104006655
Coord C2 exon
chr1:104004867-104004980
Length
1675 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TTTTCTTAAAATACAAACAGATG
3' ss Score
5.41
Exon sequences
Seq C1 exon
TTTGTAGTACTACGCTTTGGGTAGGACAACTTGACAAAAGGACTACACAGCAGGATGTTGGAAGTCTCTTGGAGGAGTTTGGCCCAATAGAATCAATAAAT
Seq A exon
GTAAGTATAAATGCTTCAGTGCAAGCATAGGCTTCAAAAATGCTTTTCAGACTGTTTCAAGTTAGCTTTATTTTTAATATATTACAGAGATTGAAGGGCTGTTGTTTCCTTTATGATTGTGTTTTCTAATGTGAAAACTCAAGTCATTTGTCCTCTGATGTGGAAAGAAAAAAAGGCAGTTGCTTGCTATTTTGGGTATTAAAAATGCCTTTGGGATAATGAAAACTCCCACTTTCATAAAACTCACCCTTTTTCTAGAGGGAATGGAATAAGAAAGGGTTATTGAGTTCCTTGTCTGTTCTCTTCTGTCATTTTAGACGTAAGCTAAAGTTTCAATATGGCCAAGTGTCGGGTCCTGCATTTTGGTCACAGCAACCCCAGGCAACCCTTCAGGCTTAGGGTAGAGTGGCTGGAAAGCTGCCTGATGGAAAGGGACCTTGGTGTACTGGTGGACAGTCAGCTGAATATGGGCCAGCAGTGTGCTCATGTGGCCAAGAAGGCCAATGGCATCCTGGCTTGTATCAGGAATGGTGCGGTGAGCAGGACTAGGGAAGTCATCACGCCCCTGTACTCAGCATTGGTGAGGCCTCACCTTGAGTACTGTGTTCAGTTTTGGGCACCTCAGCACATAAAGGGACATGGAGGTGCTGGAGCAGGTCCAAAGAAGGGCAACAAGGCTGGTGAAGGGCTTGAAGAATATGCTGTACGAGGAGAGACTGAAGGAACTGGGGCTATTTAGTCTGGGGAAAAGGAGGCTGAGGGGAGACCTTATTGCTCTCTTCCAATACTTGAATGGTGCTTACAGCGAGAGCGGGTTTGGTCTCTTCTCACTGGTGACAGGTGACAGGACAAGGGGAAATGGTTTTAAGTTGCCCCAGGGTAAGTTTAGGTTGGATATCAGGAAAACTTCTTTACATAAAGGATTATTAAGCACTGGAATGGGCTCCCCAGGGAGGTGGTTGAGTCACCATCCCTGGATGTGTTTAAAAACCGTTTGGATGTGGTGCTCAGGGACATGATTTAGCAGAGGGTTGTTAGAGTTAGGGTAGTATGGTTAGGTCGTGGTTGGACTCGATGATCTTTAAGGTCTTCTCCAACCTGAGTGATTCTATGATTCTAAGCACAGAAAACTAGTATTACATGACTGTATTAAGGATGAATATATATGAGTGTGTGTGAGTGTGGAATTTTATTTAAACTGAATATGTGACTAATTTTTTTTACTGTTCAAAAATTTTGTAAAACAGAATCAAAAATTTTCCTCAAATTCTTTGCACATAGTAAAAATGATTATAAAACTGCACATAAAACAGTGTGAAGATACAGATGGCAATCTGTGGTATTTGGAATAAAGCAGTATTTGGAATAAAGAGGTATTAGTGTTTCTTGTTTCTTCCAACAGATTAACTAATTCTGAGGCCGTAATGCTTCCGTGAATGCTGCTGGAAAATTTTAAGGATTAAATATGCTGTAGGAGTCCATGTCCTCATGTTTATTAGAAGCATTTATTTCTGGAAGAAGATGCTGGCTGTTTTAGCCTCTTAAACTAACATTCTCATTCATACCCAGTAATCTTTTTTGTAACACCAGTTAGTGTTCTAATTTTCTGTAGTTAACATTTGTATGTTGCTACCTGGTTACTGTTAACACATTTTTTTTCTTAAAATACAAACAG
Seq C2 exon
ATGATACCACCGAGAGGATGTGCCTACATTGTAATGGTTCACAGACAAGATGCTTATCGTGCCCTACAAAAATTGAGCAGAGGCAACTTCAAAGTCAATCAAAAATCTATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015850:ENSGALT00000025555:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.059 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(41.8=82.4)
A:
NA
C2:
PF0007617=RRM_1=FE(55.2=100)
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:
TTTGTAGTACTACGCTTTGGGT
R:
TTTTTGATTGACTTTGAAGTTGCCT
Band lengths:
206-1881
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]