GgaINT0120025 @ galGal4
Intron Retention
Gene
ENSGALG00000016144 | TMPRSS2
Description
transmembrane protease, serine 2 [Source:HGNC Symbol;Acc:HGNC:11876]
Coordinates
chr1:108297493-108298999:-
Coord C1 exon
chr1:108298847-108298999
Coord A exon
chr1:108298673-108298846
Coord C2 exon
chr1:108297493-108298672
Length
174 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TTGTTCTTTTTTTTAAACAGGCC
3' ss Score
11.07
Exon sequences
Seq C1 exon
GGTGACAGCGGAGGTCCTCTGGTAACAAACAAAAACTCTGTGTGGTGGTTGGTTGGAGATACCAGCTGGGGAACTGGCTGCGCTAGTCCCAATAGGCCTGGAGTTTATGGAAATATGACTGTGTTTACAGACTGGATTTATAAAAATATGCAG
Seq A exon
GTAAAATGTTTCTATCTTTCTAAATGCCCCAAGTCATGAAACTTGAATTTAATCATTTATGTCCCTTGATTTATCTGACAATAGAGTTACTCCATTGAGAAGCATCCAAGCAACTGATAAGATGGTCTGTCAGCACAGCTAGAGCCTTTGTCTTTTGTTCTTTTTTTTAAACAG
Seq C2 exon
GCCAACAGATGACAACGCCATTTCTCATTCCGTGTTTCTGAGAACAAGAGAAAATGAAGCCATGGGTGCCTGGGATATTTATTCACTTTTACAAATGATTTTGCTCTTTGAATTTTTTTTTTTTTTTTAAATAACATGAAGGATTGCACACTGGATTACGTGCTGACTACAGTGACTGATTTTGGTCAGTGAGAGATTAGCACAATAGGCACCTTTATTGATGGGGTGCCTGGCAGAAAGGTGTTCTGCTAACTGCTTGCTGAGATTTTTTTTTTTTTTTAGCTGAGTAACTTTCACTTGGTAATCAGGTGCAGGTTTAACATGGAAATCTTAATCACAACTTCCGATTTTTGTAGCAGGATGCTGAGACAGTTGGTTTTGTAGGGTTTTAAATTAACTGTTAAGTAATGTGAGCATTGAATCTCTGAGCTGCTGGTTGGCAATGTAAGAAGAAATGAATGTTTTCTGGTATATATGAAGGGAAGTTTTCATGCACTACGGTAGTAGAGGCACAGAAAAAGAAATACAAACTGTATATTCAGGTAGATATAAATCCTCAGGATCGTGACAGCCATCATCCAACTCAGATTGCTCCAAGTAAGATCAGTCTGATCCACTGAGTAACTAAAAGTGCTCTTCTGCCTTAAACTGCTGTGAATCCTGAAAGGGCAGGACCTGCCGTCGCTCCCTATGTAGGTGACAGAGGAAGGAGGGAGCTGAGCATCCTGCCAGCGAGGTCCCCTGCCACGTGCATCCAGAGGATGTGACGCTGCTCCGTGGGGTGTGCTGCAGGCAGTAGACCTCTGGCTGCAGTGCCCATCTGGGGGCTGGGTGTTGAGGATGAGGAGACACAAACCCGTGTTTCTGCCTAACCAGATGAACTACCTCATTTATTAAATTTGGCTTTTAATACTTTAGGGCTCTCTTTTAGGTATCTGGATGATGTTTTTAGCAAAATGCAATGAATATCAGAGTGCCACTTTGACTAGGATTTGGAAAATAATTTATAATCATAGGACAGAGGATCAAAAAGCCATAACAAGTCACTTTTATTAAGAAGGATAATTTTTTTTTTTTTTTGTAATAAATGACTCTACTAGTCTTGTTTTCTGGTGGCACTGAAATGCAATTACCTTGCATGGAAATGCTGCACCAAATAAAAACATATATTTTTTTTTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016144:ENSGALT00000026003:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PD(19.7=88.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTAGTCCCAATAGGCCTGGA
R:
CAGTCACTGTAGTCAGCACGT
Band lengths:
250-424
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]