GgaINT0014395 @ galGal3
Intron Retention
Gene
ENSGALG00000002134 | THUMPD1
Description
NA
Coordinates
chr14:15620552-15621884:-
Coord C1 exon
chr14:15621686-15621884
Coord A exon
chr14:15620801-15621685
Coord C2 exon
chr14:15620552-15620800
Length
885 bp
Sequences
Splice sites
5' ss Seq
TAGGTGGGT
5' ss Score
5.56
3' ss Seq
ACCTACCTATTTCCTTGTAGAAC
3' ss Score
9.46
Exon sequences
Seq C1 exon
CTCTCGGAGCCTGCGGAGCGGCTGTCGGGGAGCGAGAGAGAGGAGGAACGGGAGGAGGAGGACGACGACGACGACGCGGAGGCAGCGCTGAAGAAGGAGGTCGGACAGATCCGCGCCTCCACTGAGCGGCAGCTGCGGCGCTTCCAGTCGGTGGAGAGCGGCGCCAACAACGTCGTCTTCATCCGCACCCGCGGCATAG
Seq A exon
GTGGGTGCGCTGCGCCGTGCTGGGCTGCGCGGGGCGGCGGCGCGGGGCTCAGGTGCCACACAGGTCCGGGACTTCTCCTGTGGGGGCCCAGGCAGCCAAGAAGGCCGGCGGTATCCTGGGCGGTATCAGAGGTGGTCATCCCTCTGTACTCAGCCCTGGGGAGGCCGCACCTCGAGTGCTGTGTTCAGTGTTGGGCTCCTCACTGCAAGAAAGATACCGAGGCCCTGGAGCGTGTGCAGAGAAGGGTAACAGGATCTCTGAGGTGTCTGGAGCACAAGTCTCATAGGGAGCAGTTGAGGGAATGGGATGGTTCAGTCTCAAGAAGAGGAGTCTCAGGGGAGACCTGCGCTCTACAACTCCCGAAAGGAGGTTGTGGGGGGCTGGGGGTCGGTCTCTGTTCCCAGGTAACAGCGATAGGACGAGAGGGAAGGTTCAGGTTCAGTATTAGGAACAATCTCTTTTCCAAAAGAGTGGTCAGGCACTGGAATGGGCTGCCCAGCGAGATGGTTGAGTCACCATCCCTGCGGGTGTTCAAGAACGGGAGATGTGACAATGAGGAACATGGTTGGTGGGTAAATTTTGGTGGTAGGTGACTGTTGGATGAGATGATCTTAGAGGTCTTTTCTGACTGTAATGATTCTACAGTTTCCCTTTGTCCTTCCCACTGGGTATTGCAATTAGCAGAGTTGCTGAAAGCAGAGGAATTGGCCTTGACAGAGTGATCCACACCTACCTGATTTTGGTGCATGGAAAGAATTCTCAGAAAAGGGTTTGAGGCTGAGCACAGTGCAGCTAAGCATGTATTTCTCCAGCTTATACTTATATGGGGGAACAAGGGAGAAGATGCTTCCAAGTTGATTCTCACACCTACCTATTTCCTTGTAG
Seq C2 exon
AACCTGAGAACCTGGTGCACCATATATTAAAGGACATTCATACCACTAAAAAGAAGAAAACCAGAGTCATTCTGCGCATGCTCCCCATTTCTGGAACTTGCAAAGCTTTTCTGGAAGATATGAAAAAATACACAGAAACGTTTTTTGAGCCTTGGTTTAAAGCCCCCAATAAGAGTACTTTCCAGATCGTTTACAAAGCTCGTAATAACAGTCATATGAATAGAGAAGAAGTAATTAAGGAGCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002134:ENSGALT00000003334:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.522 A=NA C2=0.024
Domain overlap (PFAM):
C1:
PF087955=DUF1796=PU(63.0=76.1),PF0292612=THUMP=PU(16.8=35.8)
A:
NA
C2:
PF087955=DUF1796=PD(35.8=34.5),PF0292612=THUMP=FE(58.0=100)
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:
GTCGGGGAGCGAGAGAGAG
R:
GGGGCTTTAAACCAAGGCTCA
Band lengths:
342-1227
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]