GgaINT1014534 @ galGal4
Intron Retention
Gene
ENSGALG00000026563 | HAPLN4
Description
hyaluronan and proteoglycan link protein 4 [Source:HGNC Symbol;Acc:HGNC:31357]
Coordinates
chr28:3313979-3315920:+
Coord C1 exon
chr28:3313979-3314281
Coord A exon
chr28:3314282-3314999
Coord C2 exon
chr28:3315000-3315920
Length
718 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
ACCCCCCCCCTCTTTCCCAGGCA
3' ss Score
10.09
Exon sequences
Seq C1 exon
GCGTCATTTTCCCCTACCACCCGCGCCTGGGCCGCTACACCCTGAACTTCCACGAGGCGCAGCAGGCGTGCCTGCAGCAGGACGGCATCCTGGCCTCGCACGACCAGCTGCACCAGGCCTGGCTGGAGGGCATGGATTGGTGCAATGCAGGCTGGCTGCAGGACGGCTCCGTGCAGTACCCCATCTCACACCCGCGGGAGGAGTGCGGCCGCAAGGACACGCCGGTGGGTGTGCGCAACTACGGCTACCGGCACAAGGAGAGCGAGCACTACGATGCCTTCTGCTTCACCTCCAACCTCAACG
Seq A exon
GTGAGTGGGGAAACTGAGGCACCGCTCTGCTTTTAAGGCAGAGGTTCCCCTTGGAGAGAAGGGGCCGTTCGCAGTACTCTCCCTGTGTCGCAATGCCGGGGTCCTGCTGGATGGTGCTGGGGGTTCCCAACCCCAGGAGGTGGCTGCACATCCCCGCGTCACATCGCGAGGGGTTTGGGAGTGGGGACCCCCATCCAGGACCGGGGTCCATCTGTGTGCTGCCGTCACCCGCTGCTCGGGGGCACTCACTCTCAGCCCAGCTCTGTGTTCCCTGGGCAGGAGCAGGGGATGGAGGTAATTGCAGCTGCGAGTGGCCCGGGTGATGGATGAGGCCCGGGCCACGCAAGACAGATAGGAGCCACGAGGGCTCTGGGGCTGTGTAAATTCCTCTTGGCTGGCAGGGCAGTGCGGGGGGGGCTCTGCGGATGTTTGTTTAATGGTGGCAGGCAGGATAAATAGCAGGCAGCACCGCCAGCACCGGCGGCACCACGCAGCCCCATAAATCTGCCCGTGCTGAGCGGGGGTCCCCACGGCTGGCCGCTTGCCTCCTCCATCCCTTCCAATGAGGATTGGGGTGGGGAGGCCCAGAACCCCCACAGGGATGGATGTGGGGGGGCTCACACCTCCCGGCCCCATCCTCACCCAATACCCCATTCTCTGGTGCTGCACCCCATCCCCAAACCCCTTTCTTTCCCACCACCCCCCCCCTCTTTCCCAG
Seq C2 exon
GCAAAGTCTACTTCCTGAAGACGTTCCGCAAGCTGAGCTACAGCGAGGCGGTGCAGGCCTGCAAGAACAACGGGGCGGCCGTGGCCAAAGTGGGGCAGCTCTATGCTGCCTGGAAGATCCAACTGCTGGACCGCTGCGAGGCAGGCTGGCTGGAGGACGGCAGCATCCGTTACCCCATCGTCAACCCACGGGCACGCTGCGGTGGCCGGGAGCCCGGCGTGCGCAACCTGGGCTTCCCGGACAAGAAGTACAAGCTTTTTGGGGTGTACTGCTTTAAAAAGGCTGGCGATGCTCCTCCCGAGAAGAAGCAGGGCGAGGGGCATCCCAACCGCGTGTGATGCAGCGCTGGGCTTCCCCACGAGGCTCCCCCAGCCCTGCATGGCTGCGGAGCGCCCTCGGACTCTTCTGGGAGCCCTTAGGGTTGAGGCTGTGCACGTGGAACTGGAAGAGCTCAGGTGATGCCAGCGGGTGCTGTGCTGTGCCCGGGCCCGGTGATGCCTGGGGGGAAACTGAGGCACCGGGAGGAGAAAGCACTGAGCTGCCCGGGCAGGAGGATCCAGCACCAACCTGGCAGAACCCATCTGCAGTCATCGCTTAGAAATCAGCGCATTGCATGTGCAAAAAGCCCGGCCAGAGCAACGCAGGACTGAACCCCGCGTCCCTGTGCTCTCCAGCTCTGCGCCGGGACCAACCCCGCCTCGGGGTGCTGCAGGTAACACACAGCAGGGGGGGCATAGCCCCAAAATCTGGCACCAATGCAGGCGGTGCCCGCTCGGGGCAGCAGCCTCTCGCCCTCGCGCTTGGCTTAGTGCAGAAGCTGTCCTGAGCTGCTACCCCCGGCCAGGGGCAGCTCTGGGTGTCATGCAGCCCCAGGGCTGTGAGCTGGACTTAGGTGAAATAAAAGCTTCAGCTGCTTTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026563:ENSGALT00000045053:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.107
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=81.4)
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:
AAGGAGAGCGAGCACTACGAT
R:
GGAGCATCGCCAGCCTTTTTA
Band lengths:
344-1062
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]