GgaINT0107002 @ galGal4
Intron Retention
Gene
ENSGALG00000016169 | TMPRSS3
Description
transmembrane protease, serine 3 [Source:HGNC Symbol;Acc:HGNC:11877]
Coordinates
chr1:108739756-108741104:-
Coord C1 exon
chr1:108741009-108741104
Coord A exon
chr1:108739899-108741008
Coord C2 exon
chr1:108739756-108739898
Length
1110 bp
Sequences
Splice sites
5' ss Seq
GAGGTATTT
5' ss Score
7.63
3' ss Seq
TTTGTTCTGTTTTTGAACAGGTG
3' ss Score
11.19
Exon sequences
Seq C1 exon
GTCACATAGAGCCAATTTGTCTGCCTAATTTTGGTGAACAGTTCCCAGAAGGAAAAATGTGTTGGGTATCAGGATGGGGAGCAACTGTTGAAGGAG
Seq A exon
GTATTTTAAATGCCTGCTGTCAGTTACAGTACATGAAAATATCTCACACAGAGGAAATATAGGATTTGGCTGGAGCAATTGATCAACATTAAATTGTCTAGGATATCTGGGGGGAAGAAGATGACATATTCCTAAATTTTATGGTAACCGTGGAAAGGGAGTTCAGTCTTTTGCAGGGGGGAATATGAGACAAAAGTGCTGTACTCACTCTTAACACAAGGAATGAACGGGAACACTCAATGGAAAGAATGAGAACCACATGTAGGTGCAGAGATGGTGCTCCATCCATCCTCTCATGTTTTTTATAACTTCAAGCACACGAAGCAGAGCAGAAATGCAAGAATCAAACATTCTTTTTTATTTTTTCAAGAGAGAGCATGTATATATTTTCAAGCGAGTTGGATGATAAAGAAATTAGATTTGTGAATTATGTTACAAACAAAAGGGACTATTTTATTTTTAGCATGACTCGTGGGTTATGTCAGTCAATAATATGTAGTGACTCACTTTCACTTCAGAGTGCCTGAATGCTCAGGTCATTGTTCTTTATTCATTCTTGATTTGTCTCATTTAAAATGTTCCCGTTGTTCAGAGAACACAATAATAGATAATAGCAAAAGGCGAGGAAAAAGAGAAAGCAACATTTACCACATGAAAAGATGATATCTAAATTGGAAGGAGAGTGTGCAAGTGCTCCTATTTGTGGAAATGATTCACTGAGACTCTGATGAATACTTGTAAAATAGAACAGATGTTTGCAGGTGATTTGTTGATGAACAGAACAGGGACTAAATTCAAAACAAATCTGTGCTCTAGAATTAGAAGACAGTGTCCAAATAGCTTTCAAGCTCACAATTGAAGTAGAAACATATAGCTCACCATTATTTATTACACACTATGATAATGCCCAGCTCTATGCAGTCACTAGTTACCAGATTACATACATGATGAGACTTTCATTGTGTTGTCATTATAACTATATTTCTCTCACTCTTGCTTGCCAGTTCTTCATATTGTAGAGCATCTTCTGGTTTTGGTTAAAGATTACTTTCAAGGATAGAGTGTTTTTCCTTGTTTGTTTGTTTTTGGTTTTGTTCTGTTTTTGAACAG
Seq C2 exon
GTGACACATCCGAAACCATGAATTACGCAGGTGTTCCCTTGATTTCTAATAGAATTTGCAATCACAGGGATGTCTATGGTGGGATCATAACCTCTTCAATGCTTTGTGCCGGTTTCCTAAAGGGAGGAGTGGACACCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016169:ENSGALT00000026056:11
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:
PF0008921=Trypsin=FE(14.1=100)
A:
NA
C2:
PF0008921=Trypsin=FE(20.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACATAGAGCCAATTTGTCTGCC
R:
CTGGCAGGTGTCCACTCCTC
Band lengths:
238-1348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]