BtaINT0070469 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001765 | HAPLN4
Description
hyaluronan and proteoglycan link protein 4 [Source:HGNC Symbol;Acc:HGNC:31357]
Coordinates
chr7:3940462-3941465:+
Coord C1 exon
chr7:3940462-3940794
Coord A exon
chr7:3940795-3941178
Coord C2 exon
chr7:3941179-3941465
Length
384 bp
Sequences
Splice sites
5' ss Seq
CGGGTGCGT
5' ss Score
7.91
3' ss Seq
TCCTACCCACCCCTCTGCAGGGC
3' ss Score
9.01
Exon sequences
Seq C1 exon
GTGTAGTCTTCCCTTACCACCCTCGTGGAGGCCGCTACAAGCTGACCTTCGCCGAGGCTCAACGCGCGTGCGCTGAGCAGGACGGCATCTTGGCGTCTGCTGAGCAGCTGCACGCAGCCTGGCGCGACGGTCTGGACTGGTGCAACGCGGGCTGGCTGCGCGACGGCTCGGTGCAGTACCCGGTGAGCCAGCCCCGGGAGCCCTGCGGCGGCCTGGGCGGAGCCGGGAGCGCCGGGGCTGGCGGCGGAGCCTCAGGAGGTGTGCGCAACTACGGCTACCGCCACAACGCAGAAGAACGTTACGATGCCTTCTGCTTCACATCCAACCTCCCGG
Seq A exon
GTGCGTAGGCCCCACCCCTGGGAGGAAGGTCCTGCCCACCGCTGGCCCGGGCCCCGCCCCACCCATGAGACCCCACCCCCACCCCCAGGCCTGTCTCAAGATTCTTTCCCACTGGGCCCAGTTTTCTCTCCTCGCCTTTCCTCTCCACACCTGTCCTCGGATGTCCGGACCCGGAGGTCCCTAGTATAGTCAAGGCGCGGCAATCAAACAAAGCCTGGCACCAGCACTTCTCTAGCCGAGGCCGTGGTCCCGGGCTGCAGGGGAGCGGGTGAAGTTTCTGAATCCTGAGGCTGTTTCCTGGGCGGCAGGCGAGAGGGAGTCCTGAAATCCGAGGAGGCGCAGCCCCAAGAGCAGCCCTAATCACTCCTACCCACCCCTCTGCAG
Seq C2 exon
GGCGCGTGTTCTTCCTGAAGCCACTGAGGCCGGTGCCTTTCTCCGGAGCGGCGCGCGCCTGCGCAGCGCGCGGCGCCGCCGTAGCCAAGGTGGGGCAGCTCTTCGCCGCGTGGAAGCTGCAGCTGCTGGACCGCTGCACCGCAGGCTGGCTGGCGGACGGGAGCGCACGCTACCCCATCGTGAATCCGCGCGCGCGCTGCGGCGGCCGCCGGCCGGGTGTACGCAGCCTCGGCTTTCCAGACGCCTCGCGCCGCCTCTTCGGCGTCTACTGCTACCGAGCGCCTGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001765:ENSBTAT00000002313:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0768612=V-set=PD(1.7=1.8),PF0019312=Xlink=WD(100=94.6),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=95.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCTTCCCTTACCACCCTCG
R:
AGTGGCTTCAGGAAGAACACG
Band lengths:
354-738
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]