GgaINT0107000 @ galGal4
Intron Retention
Gene
ENSGALG00000016169 | TMPRSS3
Description
transmembrane protease, serine 3 [Source:HGNC Symbol;Acc:HGNC:11877]
Coordinates
chr1:108743181-108744053:-
Coord C1 exon
chr1:108743888-108744053
Coord A exon
chr1:108743351-108743887
Coord C2 exon
chr1:108743181-108743350
Length
537 bp
Sequences
Splice sites
5' ss Seq
CGAGTAAGT
5' ss Score
10.15
3' ss Seq
CCCCTATCTCTTCATTTCAGCTT
3' ss Score
9.48
Exon sequences
Seq C1 exon
CATGTGGGATGCGGGCCAGCTATGGGCCACGGATTGTGGGAGGCAATGCATCCTTGCCCCAGCAGTGGCCTTGGCAGGTCAGCCTGCAGTTCCATGGGCACCACCTCTGCGGAGGGTCTGTCATCACCCCACGTTGGATCATCACAGCTGCACACTGTGTCTACGA
Seq A exon
GTAAGTCCCTAAATTGTCTTACTCAGGTGTCCCATTGACTCTACTTGCAGCACATCTTGGGGGATACTGCAGAAGAAGACTCAAGCATTGTGCTTTATCTTCAAAAAACCTGCAGAAGAGATTGGCTTAACCTTATTTCACGGACTTTATCAATAGCATTTAAACTGTCTCTCCTTTCTGTACCAGTGCAAATCCTTATGAAAAAGGATCTTCCACAAAAGTGTTCAAATCACACAGCCCAATTTTCAAAAATTCTGGAAACTCTCAGCTGCCTGGGAAATCAACTTAAACAACTGATAAATGTCAAATCATTTCTTTAGAATTCAGATCACTGATTTCTCTACGTTGCATGTGATTTAATGGCTCAGGAGGAATTTTTACTTGGCTGCTGAGTACTAAAGTACTCAGAAGCTCCTAAGTAAATGACAAGACCCTGTTCAATTTAATAGGATCAATCAGACTGTAAGCTTGGGAGACAAATGACAACCTGAGAGTTTTCTTAAAGGTTTCTCACTCTCCCCTATCTCTTCATTTCAG
Seq C2 exon
CTTGTACTTACCGAGCTCATGGAGTGTGCAAGTTGGCTTTGTGACTCAGCAAGATACCCAGGTTCACACGTATTCAGTGGAAAAGATTATATACCATCGAAATTATAAGCCAAAGACCATGGGAAATGATATAGCACTGATGAAACTGGCAGCACCGCTTGCTTTCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016169:ENSGALT00000026056:9
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:
PF154941=SRCR_2=PD(5.0=8.9),PF0008921=Trypsin=PU(19.4=78.6)
A:
NA
C2:
PF0008921=Trypsin=FE(25.1=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:
ATGTGGGATGCGGGCCAG
R:
CAAGCGGTGCTGCCAGTTTC
Band lengths:
326-863
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]