GgaINT1028055 @ galGal4
Intron Retention
Gene
ENSGALG00000012483 | TMPRSS6
Description
transmembrane protease, serine 6 [Source:HGNC Symbol;Acc:HGNC:16517]
Coordinates
chr1:51327971-51329061:+
Coord C1 exon
chr1:51327971-51328116
Coord A exon
chr1:51328117-51328962
Coord C2 exon
chr1:51328963-51329061
Length
846 bp
Sequences
Splice sites
5' ss Seq
ATCGTAAGT
5' ss Score
10.44
3' ss Seq
GCTTTCTGGTGGTTTCACAGCCT
3' ss Score
6.73
Exon sequences
Seq C1 exon
GTTGTGCGGCCTGCGGACCCTACAAGCTTATGCTGAGAGGATCCCAGTCACATCCTCTGCTGACATTGCCATTACCTTCACCTCGCAGATCTCCTTAACTGGCCCTGGTGTGCAGGCAGCTTACAGCCTGTACAACCAATCTGATC
Seq A exon
GTAAGTTCAGGATTCTTCTTTGCTCCTTAGAGGGGCGGTGGGGGTCCCAGATGGCTACCAGCAGCCCCCTGTGTGCATGGGTTATGTTAGGAGAAACACAAGGCACATCCCATGAGCTCCAGGTGCCAAGTGCCCTCCAGGAACATGTTCATGAACACAGTGATGCACACACCACTGATCTCCCAAAAAGAAGTATTTACATCTAAAGCTGCTTCAGCACTTATCTCTGACTCATGTTCCCAGAGCATTCTGGTGCCAAGGCCCAGCTCCAGAACACTGCCTGTGCCCACAGCACGGATTGGCCTTGGAATGGGAGGCCATCTCTGACTTGAAGTGGTGTTTGTTTGGACCACAAGAGCTCTTAAAGAGAACTGTTTCCTGCTGAACTTGGAATAGGTGCAAGTGAGAGAGAAATGAAACTACACACGAATACGCACGCATACATATGCAATCGTGCACCCATAGCCCTTTCCAAGGTTTTTCAGGTTCCCTCCCATAGGGTTGCTGTAACCCACGCCAGTCCCTGAATATGTGCACCTGGCAACAACTGTCTAAAAACAGCTCCTCTGTGGCCCTGACAAAGGTTTAATCACAGCCCCAGAGAAACGACTTCATTTTTGCTGCAGTGCTCAGGAGCCGTGGAACAGTGCTAGATCAAAGGTAGAGTGTGCCAGGCAGGTGGATGATGTGGCAAAATTGGAGGATTTTAGTGAGGCCACATACAAGCTGCTGCAGCTCGCGTGTAGTCAGGAAGGTATGCGGTTCCATGCTCCACTTTTAAGCCACTATGCTCTGCTTCAAGGTTTCCAGTTAGTGGGGACTGATTGCTTTCTGGTGGTTTCACAG
Seq C2 exon
CCTGTCCCAGGGAGTTCCTGTGTTCTGTGAATGGCTTGTGCGTCCCAGCCTGTGACGGAATCAAAGATTGCCCCAATGGGCTGGATGAGAGAAACTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012483:ENSGALT00000020394:10
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:
PF0043115=CUB=PD(35.7=82.0),PF0005713=Ldl_recept_a=PU(2.9=2.0)
A:
NA
C2:
PF0005713=Ldl_recept_a=PD(94.1=94.1),PF0005713=Ldl_recept_a=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCTGCGGACCCTACAAG
R:
CGCAGTTTCTCTCATCCAGCC
Band lengths:
238-1084
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]