BtaINT0070463 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015784 | HAPLN2
Description
Bos taurus hyaluronan and proteoglycan link protein 2 (HAPLN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001075684]
Coordinates
chr3:14254486-14255711:-
Coord C1 exon
chr3:14255529-14255711
Coord A exon
chr3:14255111-14255528
Coord C2 exon
chr3:14254486-14255110
Length
418 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TGACCTGCTTCGGTTCCCAGGTC
3' ss Score
9.98
Exon sequences
Seq C1 exon
CGTGGACCGAGGGTCTGGACTGGTGTAACGCGGGCTGGCTGCTAGAGGGCTCCGTGCGTTACCCTGTCCTTACGGCGCGCGCGCCCTGCGGTGGCCGAGGTCGGCCCGGGATCCGCAGCTACGGGCCCCGCGACCGGAAGCGCGACCGCTACGACGCCTTCTGCTTCACCTCCGCGCTGTCAG
Seq A exon
GTAAGGGGGCGGGGCGAGCCATCCTCCGCGTTAGGAGCGGGCCGGGCCTGTCCTGCACGCGACAGAGGAGGATCCGACCTGAGAATGAGGCGGGGGATGGGGGAGGGGGGGCGGGGCCAGAACTCGGGCCTCAAGAATGCGGCGGGGAAGGTAGAAGGCTAGAGGCTTGAGGTTACAGGCCAACTCCTTTGAAGGCCTCGCCCCTCCGTCGCTCTGCCCACCCAGCCTCCAGCCTGCCTTTTACAACCTCACCTGCACCCCCAGTCTCTATACTCCCACTCCTCCTACCCAGGCTCGGACCCACCGATCCACACCTGCCCCTCTCCCCAACCCCGACTCTGCCCCCTGGGAGTCTGAATTCCACCACGCCCCGGCCGGCCCTGCCCTCGGTCAGTTGGTGACCTGCTTCGGTTCCCAG
Seq C2 exon
GTCACGTGTTCTTCGTGCCCGGGCGGCTGTCGCTGTCTGAAGCCCACGCGGCCTGCCGGCGGCGCGGGGCCATGGTGGCCAAGGTCGGGCACCTCTATGCCGCCTGGAAGTTCTCCGGGCTGGACCAATGCGACGGCGGCTGGCTGGCGGACGGCAGCGTGCGCTTTCCCATCACGACGCCTCGGCCGCGCTGCGGGGGCCTCCCGGATCCCGGAGTGCGCAGCTTTGGCTTCCCCAGACCCCAGCAGGCGGACTATGGGACCTACTGCTACTCCGAATAGGGGCCCACCGCACCCCCTCCAGCGCGCGCGACAAAGTCTGGGAGTCGTGGCGGGGGTCTCTCGCCACTTTCCCGAGAGCCTCCCCTTCCATCGGACGAGGAGCAGCTCCTCCTGACCCGCCTTCTCGACCGAAGGCTGCGGGCCAAGGATCCCGGCTGGCCCGGCGTCGGGAGGGGAAGTGGTGGCGCCCCGGGTGGTAGTGCGCAGCTACGAACCTCTGACCCGAGGCGGTTCCGCCCCTCCACCCCGCAGCAGACGACGCAGCCACGGCTAGGTGACGGGAGAGGCGTCCAATGGGCATTAACTGACTTCTATCCGGCAATAAAAATAACCTGAGGACTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015784:ENSBTAT00000020956:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.081 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PD(57.9=88.7),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=96.8)
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:
AGGGTCTGGACTGGTGTAACG
R:
GAGGCGTCGTGATGGGAAAG
Band lengths:
357-775
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]