RnoINT0102520 @ rn6
Intron Retention
Gene
ENSRNOG00000013895 | Npdc1
Description
neural proliferation, differentiation and control, 1 [Source:RGD Symbol;Acc:1303156]
Coordinates
chr3:2627752-2629086:+
Coord C1 exon
chr3:2627752-2627898
Coord A exon
chr3:2627899-2628945
Coord C2 exon
chr3:2628946-2629086
Length
1047 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGG
5' ss Score
7.13
3' ss Seq
GAAGGCCCATCACTCCTCAGGGG
3' ss Score
5.4
Exon sequences
Seq C1 exon
ATGCTCCCACCTGCCCTGGAAGCCTGGATTGTGCACTGAAGAGGCGGGCAAAGTGCCCACCAGGGGCACATGCCTGCGGACCATGCCTTCAGTCCTTCCAGGAGGACCAGAGAGGGGTCTGTGTGCCGAGGAAGCACCAATCTTCTG
Seq A exon
GTATGGCAGAGTATAGATTCAGGGAAATAGATGCATGAGATGTGTTTCCTCCCTCTCTTCCCTGCCCTGTGGGTCCAGACCTAAGAATCCTGAAGCCTCATGATAGTGGCCACCCATTCCTCTGAGCATCGTGGAATGCTCAGGTCCAAGACCAGAGTGACAAGATGGTGCTGACCCAGTGTTGGAACTAGGCTGAGGCCTATGGCAGCTGGGTCCTCCAGGTAGAGGATGACCTCAGGAGGAGGTGGAGAGGTCAGACTGTTAGGTTTGGACCATGACAGGTCCCCCAAGCCGTTCCAGTTGTCTACTTTGCACCCTCTAGGCAACCTGCTGTTCTCTCCTGCTCGCTTATCCTGTGCTCCCCACCCCTATCTCAGCATGTTGGGAGGCAGGGTTTCTCTGTGTAGCCCTGTGTATCCTGGAACTCACTCTGTAGACCAGGCTGGCTTTGAACTCACAGAGATCCACCTACTTCTGCCTCCCAAGTGCTGGGATTAAAGGCCATGCGCCACCACTGTGTACCCAGCTTGGGAGCTTCTCTTTGGACTGTGAAGTATTAAGGGAGAACGGGCCCATGTCCACCCCTATCCCCGCCCTACCCCCCCTCTGTATATGCCTGCCCCCACAGGCAGCTTCTTTTCTGATGGCCTGGGAGTTAACTAGATGTCTGGGTAGACTTTGATTTGCTCCCTCCTTCAGGATTTCCTTTCTCCTCTTAGGCAGAGAAGGGGCCCGAGGGTGGGCAAGGTAGGATATGTATTGACTTCCAGTGCTCTGCCCACCCTCTGTGCCCACCAGCTAGAACAAGAGATTCCATTTCTTTCTCCTATCGTGGGTCTCTGCACATGCCCTGGCCTTCCTCTCCACTCTTCTCCTCTTCCCTGCCTCCTCCCTCCCCCACCTCTGACTCAAAGAAGCTCCCTCAGTTGTCACCATGGAAACCAAGATAGTGAACTTTGGATGGGTCCCTCCATCTCAGGAGGCTGCTTGCTGCAGGCATTGTCGAGGGTCTGGGGCCTCTGTATATGAAGGCCCATCACTCCTCAG
Seq C2 exon
GGGAGGGCCTGCCCCAGCCCAGACTGGAAGAGGAGATCGATTCTCTGGCCCGGGAGCTGGCACTGAAGGAGAAGGAGGCTGGGCACCCAAGGCTCACAGCACAGCCCTTGCCTGAGGCTTCCCAGAAGCTCCTGGAACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013895:ENSRNOT00000018927:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.896
Domain overlap (PFAM):
C1:
PF068096=NPDC1=FE(14.8=100)
A:
NA
C2:
PF068096=NPDC1=FE(14.2=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:
ATGCTCCCACCTGCCCTG
R:
CAGGTTCCAGGAGCTTCTG
Band lengths:
288-1335
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]