BtaINT0103150 @ bosTau6
Intron Retention
Gene
ENSBTAG00000046140 | NPDC1
Description
neural proliferation, differentiation and control, 1 [Source:HGNC Symbol;Acc:HGNC:7899]
Coordinates
chr11:106192705-106194241:-
Coord C1 exon
chr11:106193879-106194241
Coord A exon
chr11:106192840-106193878
Coord C2 exon
chr11:106192705-106192839
Length
1039 bp
Sequences
Splice sites
5' ss Seq
TGGGTACGG
5' ss Score
6.54
3' ss Seq
TGGCCCCTCGACCTCGCCAGGGG
3' ss Score
5.28
Exon sequences
Seq C1 exon
AGTGGGTGGGGCGAGGGAGTTCCCATAAGTGTCAGGACTGTTTGTCTTCCTGGTTCTGATCCCTGATGCGGGGGAGGCAGGGCCTGCCCAGAACAATGGCCGGAGCCGGCTTGGCCAGCTCTGGGGTGGGGGCGGGGTGGCCAAGACAGCACCACTTCTGGGCAGGGGCTGAGTCAGGCCCCCTGAGATGCTTTTCTTCCTCTGCTTCCTTCCCAGATACAGCCGCCTGTCCTGGGAGCCTGGACTGTGCCCTGAAGAGGCGGGCACGGTGCCCCCCAGGTGCACATGTCTGTGGGCCCTGCCTCCAGCCCTTTCAGGAGGATCGGCAGGGGCTCTGTGTGCCCAGGATGCGCCAGCCTCTGG
Seq A exon
GTACGGCCTCTCCCCTCCCCCCAACCTGGTACATCCGCTCTCTTCCTTAGCACTCGGCTCGGGTGTCCTGTACTTTGTGGGATGCCAGGACTCGCCAGTCTCCCTCCAAGTGGCCTGGTGACCCTTTCCGGATGGCACCATGAGGAGTTGGGTAGTGGGCTGGGGCCTGGGGCAGTCACCCTTCCCAGGGCCACCGGTACCCAGCATGAAGTGCCAGGGTGACCCCAGGAGAGACAAGGTCAGTTCCCCAGGCCTGAGTCTCCGCAGAGTCAGGCTCCCACCTCTCCACCCCGCGAGCTGCCTCTGCTCTTTGCCCAGCACCTCTTCTCTCTCCATCACTCACTCGTCCTGTCTGCTTGAATGCCCTGGTGCTGCCCTGACCCAGCGTCTGTTGGGATGGTGCCAGCCAGAGTGACTTCAGGTGTGATGGGGCATTACAGAGGGTATTGGGGCTGAAGTGTTGGATAGGGTGGGAGGGGCTTCCAGGAGGAACATGTCCCTGGCAACGAGTTGGGGGGTGGGCCCTGAAGGCATGTGGTCTGGGATGGGGAGGCCCATCCACAGCCCCTCCCTTCCTCCTGGTGACCAGGCAGGGGTGGGGGTTAGGACGGGGCTTCTCTGCGTCCCTTGGGAAGTCCTGCCCCCCTCGGCCGAGGAGGCCCACGCAGCCCGGGTGACGCACTGTCCCTGTGTTCCTCCCACCACTTTGTGGGAGGCGGGTAGGGAGAGGGCCGGCACCCCTGTCCTGTGCTGGCTTCTGCGTGTTCCCCCTGCACTTGCTCCTTGCCTACTCGCCTGGGAATTGCCGCTCACACAGTTGCTTCAGCTGTCACCATGGCGACTAGGATGGCCAGGGCCTCGGGCTGGCACCTGGTCCTCTGGCTCCTGGGGCCTAAGAGGAGCCTGTAGGGAGGAGACCCAGGCCTGGGGACTGGCTGGCGGATGGGCCTTCCGGCTCTCTCTGGGAAGGCCACCTGTAGCTGGTGTTGCCAGGGAGGGCCCAGGGCCTCTCCAGCTGATGGCCCCTCGACCTCGCCAG
Seq C2 exon
GGGAGGGCTTGCACCAGCCCAGACTGGAAGAGGAGATCGACTTCCTGGCCCAGGAGCTAGCCCGGCAGGAGGCAGGGCGCCCCAGGCTCAAGGCCCCACCCCAGCTTGAGGCACAACAGCGGCCCCCAGAGGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046140:ENSBTAT00000065575:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.935
Domain overlap (PFAM):
C1:
PF068096=NPDC1=PU(26.8=67.8)
A:
NA
C2:
PF068096=NPDC1=FE(19.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTTCTGATCCCTGATGCG
R:
ATCTCCTCTTCCAGTCTGGGC
Band lengths:
351-1390
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development