GgaINT0143674 @ galGal3
Intron Retention
Gene
ENSGALG00000001109 | GTSF1
Description
NA
Coordinates
chr27:1016793-1018383:+
Coord C1 exon
chr27:1016793-1016884
Coord A exon
chr27:1016885-1018256
Coord C2 exon
chr27:1018257-1018383
Length
1372 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TTCTGTTTTCCCTTCTTTAGAGC
3' ss Score
10.4
Exon sequences
Seq C1 exon
ATGATCCAGAGAGATTAATACAGTGTCCATATGATAAACAGCATCAAATCAGAGCCTGTCGTTTTCCCTATCATCTTGTAAAGTGCAGGAAG
Seq A exon
GTAAGTTGAATTGCTGAACAAGGCACCAAATGGGGCTTGTGTGTGTGTAAATAGTGTGCATATTCTTACTCTTATTGTGTTGTCTGGATGACTTGACTAAGTTCTTGACAAATAATCCCATTTAGTGTTTATTTCATATACATATTTATATTTATGTATTTATTTATTACTTCTTTAGAAACAGCTTCAAGCACACTGACTCACCTAAAACCAGTGTGGCTCTTCATGGTTGGGTCCGGGAGGAATTTATGGTCTCTTTGAGATCAGATAAATCTTCCCTCTTTAAATTCAAGAGAAAATTCAGGCTCAGTTATGTGCACCTCATCTGTCTCAGAATAGAAGTGGTTGGATGTTGCAGTTTGTTAAGTGATAGAAATGCTGCTGCATAGCTTTTTTTTTTAAATGTTGCTAATAAGTATTTAATGTGCATAGGCATGGAAACTGGACATCCTGGCTTCAGCACATATGGGAGAGAGTTGTTTTGTTTTGTTTTAACCTCTCCATTTACTATCTAGAATTTGAATACAAATCATGCAATAGGAAGCATTCCATCTTCTATTCTTCTCTTTACCCTCCAGGTTTGTTTAATTTAACCTATCAAATGCTAGTATCTGAGTGTTGGCTTCTGATGAGAGTTGTTCCTCTTTCAGCTTACCAGTAAATTTTCCAAATATATTTTTTTTCAAAACAGCGTAGCAGTGCTATGCCCTCCAGTGATGATGCAGCTGTAGGGTGAACATTCTGTTCTTAGAACTTTGGGTAATTTTGTGTGGTTCCAGGAGCTGAACTTAATAATTCCTGTGGGTCCCTACCAACTGAGGATATTCTGTGATTCTATGAATACTTGTTTTGAAAGGATTAATTAATTTCTTTGGCTTTGTGCTGACTTGCTTTAAAATATCTGAATGATTTAGATTTACCTAACATCTCCTCCCTGTTTTTTTGTTGTTTTTTTTTTTAAATAGCTTCATTTGTGTGGCCATTTTGCCAGCATTGCAGCAAATTGTAGGGTGTGTAGCTGAGGGTGTGTTTCGTTTGAATCAACTGTTTGTTTTTTTTCTAATGAACTGTGTTTTAAATAACAAACATAGCTATATGTCTGTTAGATAGCTTCATCTTGCAGTTGTAGTAAGTATCTTGCCAATACTTTGCCATTCCTTGATTAGTCTTTTTTAAAGCAACGTCACCAGTTATTGTAGAATCATAAAATGGCTCAAGTTGGAAGGGACTGTAAGGATCATATAGTTCCAACCCACCTGCCAGGGGCAGAGTTGCCACCCACCAGATCACTATCTCTTGCTAATCAGTAGAAAGCACAAGGAAAAGTGAACTTGGTTCATCTGGCACATGATTTCTGTTTTCCCTTCTTTAG
Seq C2 exon
AGCCACCCTGAAGTTGCAAAGTTATTGGCCACGTGCCCCTTCAATGCTCGCCATCTAGTTCCACAAGCCGACCTCGGTGATCACATATCAAAGTGCAGGGACAAAGGGTTCATTGAGCATGATATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001109:ENSGALT00000001663:2
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=0.000
Domain overlap (PFAM):
C1:
PF052537=zf-U11-48K=WD(100=87.1)
A:
NA
C2:
PF052537=zf-U11-48K=WD(100=62.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGATCCAGAGAGATTAATACAGTGT
R:
TCATGCTCAATGAACCCTTTGT
Band lengths:
214-1586
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]