GgaINT1014530 @ galGal4
Intron Retention
Gene
ENSGALG00000013234 | HAPLN2
Description
hyaluronan and proteoglycan link protein 2 [Source:HGNC Symbol;Acc:HGNC:17410]
Coordinates
chr25:509021-509779:-
Coord C1 exon
chr25:509580-509779
Coord A exon
chr25:509372-509579
Coord C2 exon
chr25:509021-509371
Length
208 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGG
5' ss Score
6.35
3' ss Seq
GGTGAGCTGGTGCCCCGCAGCCA
3' ss Score
2.54
Exon sequences
Seq C1 exon
GGCAAACACTGAGATGATTGCTGCCCATGTCCCTGCTGCATCCCCCGGTCTGTCCTGCTGCGTGGCCCTGACCCCTTCGCTCCCCCCAGGCTTTCTCCAGTCCCCAGCCCTAAAGATGCACCGGGTTCTGTTCGCATCCCTCTGGCTCCTGGCAGCATCCCCCACCTCCAGCATCTTCCAGAAGCCAACAGGGAGCCCTG
Seq A exon
GTAGGGAGCAGGGATGGGAACAGGACACTGCTGCTTGGGGACGGTGTTGGGAGGTTTGGGCAGGGGCTGGGCTGAGCATCCTGGAGGCTGCAGCAGCACGGAAATGAGTGGGGAAGGGTGCTGGAAACCAGGCTGTTGAGGGTGGTGGGGAGGTCCTGAGGGGCAATGAGGCTGTGGCAATGCCTCGAGGTGAGCTGGTGCCCCGCAG
Seq C2 exon
CCACCCCACGCCTGCAGTACCTGCTGGAGCCCCTGCACACCGCAGTGCACACGCAGCGAGGTGCCACAGCCACGCTGCCCTGCGTGCTGCGCGCCCTGCCCCGCAACTACCGGGTGAAGTGGAGCAAGGTGGAGCCAGCCAACTATGGGGAAAGCGTTATCATCATCACCAACGGGCTGTACCATAAGAACTATGGGCCGCTGAGCCCCCGCGTGCGCCTGCGGCACAGCCACCGCTACGACGCCTCGCTCACCATCACCAACGTGGCCTTGGAGGATGAGGGACGCTACCGCTGCCAGCTGGTCAACGGGCTGGAGGACGAGAGCGTCTCGCTCACGCTGCACCTGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013234:ENSGALT00000021612:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.103 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=PU(6.3=27.6)
A:
NA
C2:
PF0768612=V-set=FE(92.1=100),PF0019312=Xlink=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:
CTCCAGCATCTTCCAGAAGCC
R:
GTTGGTGATGGTGAGCGAGG
Band lengths:
298-506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]