GgaINT1028856 @ galGal4
Intron Retention
Gene
ENSGALG00000027242 | TTF1
Description
transcription termination factor, RNA polymerase I [Source:HGNC Symbol;Acc:HGNC:12397]
Coordinates
chr17:6525714-6526509:-
Coord C1 exon
chr17:6526265-6526509
Coord A exon
chr17:6525900-6526264
Coord C2 exon
chr17:6525714-6525899
Length
365 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
AATTAAAGTTTCTGTTTTAGGTA
3' ss Score
8.65
Exon sequences
Seq C1 exon
GACACCAGAAACCTCAACATCAGATAAAAAGGAGGACCAGAATAATTCGTTTACTGAAACCACAGCTACTGGTGAGCTCAGTGTGGATGATGAAGAGTTCCTGCACTTGTTTACAGTCTTGGATTTAGATACCGCAAAACAAGAACTGGGGGAGTTTATTCCTCATGTGGGTCAGTTGTCTGACCATTCAATCAGAAAAATGGCTGGAAGAGACCTGTTGAGATTTAAACAGTTTAAAAAACAAG
Seq A exon
GTGAGACCTCAAAAGAATGCTGCAGTGAAACAGTGTGGAGCTATGCTGATCTTTTGACAGGGGGGAAATAGCTTGCTTTTGTGTCCTCTCACAGCCATGCTCTTGTTTCAGTATATTTAATTCTAGTGAACATGTTTTTTGTTGCTGTTTTGTAGCATCTCCTCCTTCATCAGCAAATGACAGCTCAGAGTGCATGCTTAAATTACCTGCTCCCGCCTCTTGTTTTCTTTCTGTTCCACATGCCATTTTACTTTCTGAATTTGTCGATCTTCTCTTATATCTTTGCTAAAACATCTTTGTTATCTTGAAGTATTACGTACCTGGGGCTACTTTAGGTATTTTTTTAATTAAAGTTTCTGTTTTAG
Seq C2 exon
GTATTGCTATCAAGTTTGGCAGATTTTCCCAGAAGGAAAATAATCAAATCAGGAAAAATGTTGAAGATTTCTTATCAATTACTGGGATAGACAGTGCTGAAAAGCTCCTGTTTACTTCGAGGTATCCAGAAGAGAAAGGAGCTATCAATCGCCTAAAAGCAGAGCATCTTTTTTGTGAAAAACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027242:ENSGALT00000046072:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF088896=WbqC=PU(54.4=86.0)
A:
NA
C2:
PF088896=WbqC=PD(44.1=47.6)
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:
TGGTGAGCTCAGTGTGGATGA
R:
AGATGCTCTGCTTTTAGGCGA
Band lengths:
345-710
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]