GgaINT1014532 @ galGal4
Intron Retention
Gene
ENSGALG00000026563 | HAPLN4
Description
hyaluronan and proteoglycan link protein 4 [Source:HGNC Symbol;Acc:HGNC:31357]
Coordinates
chr28:3312673-3313483:+
Coord C1 exon
chr28:3312673-3312857
Coord A exon
chr28:3312858-3313120
Coord C2 exon
chr28:3313121-3313483
Length
263 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
GAGCTCCGTGTCCTTTGCAGAGG
3' ss Score
8.53
Exon sequences
Seq C1 exon
TGGCGATGGGGGGTCAGATGTGATGCTTCCCCCCGTGCCGCGGTGTTGGTGGGTGCTGATGGCTCCGCTCGCCCCCCAGATGTGTCCCCAGGGGCCCTGGGCTGCGCTGCTGCTGCTGGTGGGTGTCCTCGCCTCCGACACACCGCCCAGCGCCCGGGGAAGGAAGAAGGTGGTCCACGTCCTGG
Seq A exon
GTGAGTGCTGGGGGGGGTCCGTGGTGGGGGAGCGGGTGCCCCTCCATAGCCTTTGGGGAGTGGGGTTTAACATTCATGGAAGCACAGCGGGGCTGTCCCGTGGCTTGCAAAGCTCCCCAAAAGGGGGAATCCTCCCCAAAAGCTGCTCCTGCCCGACCCTGAGCCAAGCGACCGCTCTGCCCCACCGCATCTCCACCCCATCTGACTCTGCAATGGGGCAGCTTTGGGGACGAGGACCCCTCTGAGCTCCGTGTCCTTTGCAG
Seq C2 exon
AGGGGGACAGCGGGGCCGTGGTGGTGCAGACAGCCCCGGGGAAGGTGGTGACGCACCGGGGCGGCACCATCATCCTGCCCTGCCGCTACCACTACGACGTCTCGGCCCACGACCCCGACGAGATCCGCCTCAAATGGACCAAAGTGACGGAGCCGATGGCCTTCGTGGACGTCTTTGTGGCTCTGGGGAAGGCGCGGAGGGCGTTCGGCAGCTACCGCGGGCGCACGGCGCTGCAGGAGGACGGCTTTGGGGACGCCTCGCTCATCATCCGCAACGTCACCCTGCAGGACTACGGGCGCTACGAGTGCGAGGTCACCAACGAGCTGGAGGATGACACCGGCATGGTCAAGCTGGATCTCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026563:ENSGALT00000045053:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=WD(100=94.3),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGAAGAAGGTGGTCCACGT
R:
GGTGACGTTGCGGATGATGAG
Band lengths:
307-570
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]