GgaINT0014396 @ galGal3
Intron Retention
Gene
ENSGALG00000002134 | THUMPD1
Description
NA
Coordinates
chr14:15619628-15620800:-
Coord C1 exon
chr14:15620552-15620800
Coord A exon
chr14:15619963-15620551
Coord C2 exon
chr14:15619628-15619962
Length
589 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
AACTATATCTTGTCTTACAGGAA
3' ss Score
10.05
Exon sequences
Seq C1 exon
AACCTGAGAACCTGGTGCACCATATATTAAAGGACATTCATACCACTAAAAAGAAGAAAACCAGAGTCATTCTGCGCATGCTCCCCATTTCTGGAACTTGCAAAGCTTTTCTGGAAGATATGAAAAAATACACAGAAACGTTTTTTGAGCCTTGGTTTAAAGCCCCCAATAAGAGTACTTTCCAGATCGTTTACAAAGCTCGTAATAACAGTCATATGAATAGAGAAGAAGTAATTAAGGAGCTGGCAG
Seq A exon
GTACGTATAGATCACATATAGTACTGAACCCAAGTATACAAGCAGATCATAGCTGCATGCATAACATAGGTTAGGCTATTTGAAGAAAAGTGCTGTAAACAAGGAGGTATATTTGTTGCTTAAAATCTGTATGTTGAGGTATAAAAATGTAAGGATGTGGAAAGAGCTTGACATCCTGTTGATGTTTCGAGATGACAAAGCAGAACAGCGTGCAGTAGTGAATTCAGTTTGGTGTGTCAGTTATGCATGCTTTGAAATGACTGCATCAAGTTGTTTTCTCTAAATGCTATACTGAAAAATACACGTTGCTAATTCTATTTAGTGTGGGACTTAAAAAACAGTTCTGCAACAAGTTGCATACTTTGGCATCTTGTTTCTTGCTAGTTGCAATGGGAAAATTCTTAGTTGCTGTAGTCCTCCTAGTAGTATTTCTTAAGAATCCTGTTCTGTTCTGCTGTTTTTACACAATTGCAGTAACTAATAATTGGTTACAAGTAGAGGGTTGTTGATCTCTATTCCCTTCAGGAGAGTATGCTGATGCTCTGAAACTGTTTTCCCAACATCTTTTAAACTATATCTTGTCTTACAG
Seq C2 exon
GAATTGTGGGCAGCCTTAATCCAGAAAACAAAGTTGATCTCAATAATCCACAATATACAGTTGTGGTGGAAATAATAAAGAATGTTTGTTGCTTGAGTGTGGTGAGAGACTATGTTCTATTCAGAAAATACAATCTACAGGAGGTAGTGAAAAGCAACAAAGACGACACGCAACAAAACCCATCAAATGTGTCTGAAGAGCAGAACTCAACAGCCGTAAAACCAGAAACCATGGAAGAGAACTTGAAGGAAGTAAAACAAGAACAAGAGTGATGGTGAGATGGAAGCTGAACTCCACGGGAATTAAATGTAAACAGTGTAGAAAGTGTGGTAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002134:ENSGALT00000003334:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.444
Domain overlap (PFAM):
C1:
PF087955=DUF1796=PD(35.8=34.5),PF0292612=THUMP=FE(58.0=100)
A:
NA
C2:
PF0292612=THUMP=PD(24.5=38.5)
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:
GCATGCTCCCCATTTCTGGAA
R:
GATGGGTTTTGTTGCGTGTCG
Band lengths:
358-947
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]