BtaINT0099708 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001764 | NCAN
Description
Bos taurus neurocan (NCAN), mRNA. [Source:RefSeq mRNA;Acc:NM_001193082]
Coordinates
chr7:3968334-3969278:-
Coord C1 exon
chr7:3969151-3969278
Coord A exon
chr7:3968628-3969150
Coord C2 exon
chr7:3968334-3968627
Length
523 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
TCTCCCGCGCCTTTCCGCAGGCG
3' ss Score
10.28
Exon sequences
Seq C1 exon
GTATCCTATCACCCAGTCCCGTCCTGGTTGCTATGGTGACCGTAGCAGCCTTCCGGGGGTGAGGAACTATGGGAGGCGAGACCCACGGGAACTCTACGATGTGTATTGCTTTGCCCGTGAGCTGGGGG
Seq A exon
GTAAGTCTGGGGCTGGTAGAACGCCCCCTTCTCTGAGCCCCTTTATCCTTCCTAACCCCCCATCCTTCCCTAAGTCCTTGCCTAGCTCTCCTAAGTTTTATCCCTCTCTAAACCCACAGCCAAGACCTGGACCCGCCGGTTTTTCCTCCACTCCCTGAGCCCCTCTCCTTTGTGCCCCTTCCCTTTCTCTGAATCTCTCCCCCTTCCTGCCCCCTTCTCCCTCTTCCTACTTCCTTCCTCCTCACACCTTCCCCAAGCCCCTTCCTCTCTCTGAAGCCCAACTCGTTCAGGCGCCTCAGTTACCTCATTTGTGAAAAGAAAGTGAAGCCCCCTCTTAGCACTGCATGAGAGGCAATGGCAGTGATGCTCTGGCGACGGGGGCGCGCAGCTGCGGCTGCCTCCATCTCGTTTAGCCGGAACCCAAATCTGGCCAGATCAGGGCTATTTGAGATGGGACTCCCTTCCCGGGCTCCGGGGGAGGGTCCGTGGGACACCTCTGACCTTCTCCCGCGCCTTTCCGCAG
Seq C2 exon
GCGAGGTCTTCTACGTAGGCCTGGCCCGCCGCCTGACACTGGCCGGCGCACGTGCCCAGTGCCGACGCCAGGGCGCCGTGCTGGCCTCGGTAGGACAGCTGCACCTGGCCTGGCATGAGGGCCTGGACCAGTGCGACCCGGGCTGGCTGGCCGACGGCAGCGTGCGCTACCCGATCCAGACGCCGCGTCGGCGCTGCGGTGGCCCAGCCCCTGGCGTGCGCACCGTATACCGCTTTGCCAACCGCACCGGCTTCCCGGCACCTGGAGAGCGCTTCGATGCCTACTGCTTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001764:ENSBTAT00000002312:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.141
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=98.0)
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:
CGTCCTGGTTGCTATGGTGAC
R:
GGTTGGCAAAGCGGTATACGG
Band lengths:
352-875
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]