HsaINT0113480 @ hg19
Intron Retention
Gene
ENSG00000116962 | NID1
Description
nidogen 1 [Source:HGNC Symbol;Acc:7821]
Coordinates
chr1:236139132-236142407:-
Coord C1 exon
chr1:236142295-236142407
Coord A exon
chr1:236141289-236142294
Coord C2 exon
chr1:236139132-236141288
Length
1006 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACT
5' ss Score
9.01
3' ss Seq
CTGATTTCTGCCTTTTCCAGGCC
3' ss Score
10.93
Exon sequences
Seq C1 exon
GAATTCCGTGGTTGCTCTCGATCTTGCAATTTCCAAGGAGACGGATGCTTTCCAACCCCACAAGCAGACCCGGCTGTATGGCATCACCACGGCCCTGTCTCAGTGTCCGCAAG
Seq A exon
GTAACTCTCCTGTGCTGTTACTGTTGGCATACTGGGGGCACATGGAGGCTCAGAGCCCACACTCTGGCTGCTACCCGTATGGCCACTAGTAGCCTTGATTATGCCGTAAGAGAGATCCAGTCCTTTGCATCCAGGGTCTTCATTAGCAGGTGAACCAGTTAAATAAACAGAAAATATTAGGTCATGAAGTTGTCAGGATGAGGAAAAGCATTGAGTTTTGGGCTGGATATAAAAGCATAGGGTCTTCAGGTTCCAAATAGTCAGGTTAGGATATTACAATGTTAGGATCTCTGCTCCTTTAAAAGTCCATCCATCTGGCCTAACAGCAATAACAATAATTAATAATAAGAATTGAAAACATATGTGTGGCACTTACTGTGAGCTATGAACTTTACATATATCAACTCACTTAGAGTTCTAAATACTTTGTATTTGTTAGTTCATGTAATCCTCATAGCAACCCTGTGAGGTAGGTACTATTATTATGTTCATTTCATAAATAAGCAAACTGAAGCAACTTGCTCCAAGTCACACAGCTCACAGGGGCAAGTCCAGGCAGCCTGGCCCTGGAGTCTATGCTATGCTGCCTCTTGAAGGCCTCTCCCCTCACCCACTTTCCTTCTCAGCTTCCCTCATCTTCTTCTGTCAGTGTGAAGCTAGGAGTGCAAGCTACATAAAAAGAACTTTGCACTTTAAAATTCCAATTCTATGTTATAATCAGAGCTGGAGAACTTCCCCCTGAGATCTGTTTAATAGCCTTAGTAGAAAATCTGCATAACCCCCAAGTTGGGAATCAGTGTTTGTGTCTGGTTTAATGCTGATAAAACAAACAATGGATCAGCTCAGCTGACTGCCTAGCACAGTGTCCCCATTCTCCTGAAGCCTTCCTAGCATGGCTTCAAGGAAACTAAAAGGGGGATCACACACAAGAAGGAGCCCACTATCTTAAATGGCTATGGAGTCAGATCAGAGAGAGGGCTATTGAACTGATTTCTGCCTTTTCCAG
Seq C2 exon
GCCATAACTACTGCTCAGTGAACAATGGCGGCTGCACCCACCTATGCTTGGCCACCCCAGGGAGCAGGACCTGCCGTTGCCCTGACAACACCTTGGGAGTTGACTGTATCGAACAGAAATGAAGACAAGAGTGCCTTATTTCCTTTCCAAGTATTTCACAGCAACACTCTACTTGAAGCAACTTGGTCCAGATTGAAAAGTGTCCTCTGGCTGAGTGGCCACTAGGCCCAGACCCAGCCCAGCCTGAGCCCCAACAACTTTTCCCTCACTGTTCCCCAAAACATGCACCCTGGACTTCTCTAATAGAAAAGTCTCCACCCCTACACAAGGACAGAACCCTCCACCCCTACCCCCAACCCTCAGACAGACTTATACACCCCTGAGTGAGGATTACATGCCCATCCCAGTGTCCTAGGACCTTTTCCCAATACTAGCCCCCCAGTGGTGAACAGAACCTCCCAAATTTGAGTTGCACCCTTCCCTGTGGCCTTATGAGCTCAGCCTCGCTTTGAGGTACCCACCGTCCTGTCAGCTCCTTGACCTATGAGCCGGGGCCTGACTAGGAAAAGTTGGGAGTTAAGGAGGAAATTAGCATTCCTTAATGTTTTGTTTTGGTGCTCTGAATTTCTTCTTTATTATAGTCCTATAGTTTTACTCCTCAGTTCCTCACCATCATCATCTTGTCTAAGACCCCCATTATAATATTCATGCGCTGCTTTTTCATCAAAACCTACCCTGTCCTAGAGATCTATGGGCATTTGGTGGATGATAATGAGCAGCCCCTCCCAGATAGAATGTCAATATTTGAGCAGTAGGATATTGGCATTTGTTAGTTAAAGGCTTAAATCAAAAGAATGTCCAATGGTAGGAATTTCAAGGTGTAGGTCAGATATTTGAGAATAGGGGATTTTTTTGATGTGCCTTAAATTATACCAAAGATTACTAATTATTCCTCTTTGCCCAAAATACTTGCATCCAAGGTTCTAGTCTCTGTTGCTGTGCTGGTCTTTAGCCCCACTGCTTGCACTGATGTCCCTCCTTTTCACGGAGACCTATCTGAGGTACAGGATGGGGCTGGCACCAGATGATGTCCCACCACAGTCCCTCACCTCCGGCCTCCACATGACAGAACCAATTTACACTCAACCATGACCTCACCCCTCCTTGGTTTCTCCCTCGATCTGTGGCCCTTTTTGGATGTATTCTTATCTAACAACACAATCCGGAAAGACTGAATTGAATATTTATACTAATGGTTCATATCCTTTATTGCTCAATGATCTAATTAAAGGGATCATTGCCACATTTCATGTTTATATTTCTACAATTTGTTTAGAAAACATCTCCTGACCATATCAGTAGCTCGTGTTATCTTTTTATCAACTGCTTCCCAGAGTCCTAAAACAATAGAAATTTTGGATTGAAAAGTTCAGCATAAGGAGTTTGAGTCAGTAAAGGATGGGATAAAGGAGTCGAGATGATTCAATGAAAAGTATCACAAAAAAGAGATTGATCAACAAGAGAAATAAAAAAGCCCAAGAGGAAGTGGTAGGGGAAGGAATTTAAGAACAGCAATAAGTAAAACTCTTAAGTAACTCCAAAAAGAAAATGGTACATTTTGCCAAAGACCACTTATACTTGAGAACATGGAAGAATTTGCCTGATACTCTCTTTGGGGAAAAGAGTCTCTCCTCTTTTCCTCAAACCCCAGTACACTCAGCCTCTCTGCCCCACCTTCTCCTGACTTTGTCCTCACTTGCTTCTGCAGTACATTGGAACCTGAATTGAAAGAAAGTCTTCCTTGAATAATTGGAGTTTGTCTTGAGAGGCAAATATAGCCCCAAGAATCACAAGATTCGAGGACCATGTAGGTCTTTTACGTAGCCCAAATCCATAAATTAGTCTCACTTTTTGTATTTATCGTTTCATATTAAACCCTCTATATCAAATGTTCATCATGATTTTGTATGATTTTTATAACTATTTTATTCATTTTATTAGATTTATTCTAAAATTTTTTAATGGTAAATTCTTAAACTGTGGAAACCACTGAAGGTGCTTATTAACTGTTCTCCCAGATTTGTACAAGTATTGGATGATTCCTTGAGTTTACAGCTGTACAAATAGTGTGGAAAATAAACTTTTTTTAAAAAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000116962-NID1:NM_002508:19
Average complexity
IR-S
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:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=75.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAGGAGACGGATGCTTTCC
R:
GGGAAAAGTTGTTGGGGCTCA
Band lengths:
346-1352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)