BtaINT0070467 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001740 | HAPLN3
Description
Bos taurus hyaluronan and proteoglycan link protein 3 (HAPLN3), mRNA. [Source:RefSeq mRNA;Acc:NM_001098981]
Coordinates
chr21:20871465-20873387:-
Coord C1 exon
chr21:20873085-20873387
Coord A exon
chr21:20872439-20873084
Coord C2 exon
chr21:20871465-20872438
Length
646 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TCACGCCTTGCCTCCCACAGGGC
3' ss Score
10.55
Exon sequences
Seq C1 exon
GTGTGGTCTTTCCTTACCAGCACCCCCAAGGGCGCTACAAGTTCAACTTCCACGAAGCCCAGCAGGCCTGCGAGGAGCAGGACGCGGTGGTGGCCTCTTTCGAGCAGCTGTTCCGGGCCTGGGAGGAGGGCCTGGACTGGTGCAACGCGGGCTGGCTGCAGGATGCCTCGGTCCAGTACCCCGTCACGCAGGCCCGGCGCCCCTGTGGAGGTCTGGGGCTGGCCCCCGGCGTGCGCAGCTACGGCCCGCGGCACCGCCGCCTGCACCGCTACGACGTGTTCTGCTTCGCGGTTGCCCTCAGGG
Seq A exon
GTGAGTGGACTGGCCAAGCATGGGCCTGTGGGTGGAAGGGCAGCCTCTGGGGGGGCCTTCAGTCCTCTCTGCCCACCCTGTTGGCACTTCCAGCTGAAGCCCTGTGCCTTGATGCTGCTGCTTCACACCGATCATCGGTTCAGTCAATCATCCAACATTCCCTGAGTGCCTACTAGGTGCTCGGTCATCATAGACAGAAAAAACACAGTCTGCCCTCACAAAGGAGCTCATTTCATGGGAAGATACATGAACAAAAACACATCGTTTCAGTGCCATATCCCAGTTTGGCACTTAGTAGGTGCTCAATAAATGGCTGAGCAGATGAGAGATTCTTGATTGGTCCAGCAGAGGTGGGGCGCCCACCTAGAGTAAAATTAGGAAAGGGCTGGGACAGAGTACAGACCTGATTGTGGGGAACCCGGTACCATGGCTGGGGGGGATGATGCTTTTGGAGAGGGGCTGAGATTTGGGAAGGTGCCCCTGACCATCTCCACTGCAGACGCTCCATAGTGTGGCAGCTCCCTAAGTGCAGAGAGTTAACAGGTCTTTTGGGGGCTGGGTGGTGGGGTCTGCATGGGCTGGCCTTGCCCCAGGCCCTCTCTGGCTGCCCTCTCCCTTCTCTGTCCTCACGCCTTGCCTCCCACAG
Seq C2 exon
GGCAGGTGTACTACCTGGAGCACCCTGAGAAGCTGACGCTGGCAGAGGCAAGGGAGGCCTGCCAGGAAGATGGCGCCCAGATCGCGAAGGTGGGCCAGCTGTTTGCTGCCTGGAAGTTCCGTGGCCTGGACCGCTGCGATGCTGGCTGGCTGGCAGACGGCAGTGCCCGCTACCCTGTGGCTCACCCACGTTCCAACTGTGGGGCCCTGGAGCCTGGGGTCCGAAGCTTTGGCTTCCCCGACCCACACAGCCGCCAGTACGGCGTCTACTGCTACCGGCCGCGCTAGCTCCAGGTCGCTCTATACCCTGCCCCCTCCCCTCACGGGCGGTATTAATTATTGAGTAGTTCGTTGTCCCTCGCAGGTTGGGGCAATTTTCATCTTGTTTTTATACTTTCCAACTTAAAATTATTTTTAAATATTATTTTTTGGGTAAATCCCACAGATCCCAAATCGTCCCTTTACTCGGGTCCCTTTGCCAAGGCTCTCACCCTCCCTGAATCCTCCTGCCTCTCTCCTCTGGGACGTTTGAAGTCCTTGGGCTCATGAGCGCTCTCTGCCATCGCGGAGTCCATCCCCTCTCCCAGCCCTGGGGAGGTTGTTCCCAGAGCCGGTAGTGGCAGTGGCACGAGGAGCCAGGGCTGCGACCCGTCCTCCGCCTCCGCCTGGGGACGAGGGGGCAGCCAGGTGGCTCTGGAGCTGGGGTTCGGGCCTGGTGGTCTCCTGCCCCTTGTACTTCTTTGGGGAGCAGCTGGCCCGTGTCAGCATGGCGGAGGAGCCTGGGCAGGAGGTGGGTCCCTGGGCTTCCACGTGATGTCCCAGGGTAGGGAGAGAGATCCCGCCCCATGTTTTCCTTCTCTCTTGGCTCCAAAGAGTCTGTGTTTTGTTCTCATTTTTCTCTGTTTGGCGAGTGGCCCTCAGGTCTGTGTACTATTTTGGACAATAAATGGTGCTGTGACCCCTCCCTCCATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001740:ENSBTAT00000002282:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=WD(100=94.1),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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTACGACGTGTTCTGCTTCG
R:
GGTATAGAGCGACCTGGAGCT
Band lengths:
342-988
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]