Special

HsaINT0032186 @ hg19

Intron Retention

Gene
Description
cadherin 4, type 1, R-cadherin (retinal) [Source:HGNC Symbol;Acc:1763]
Coordinates
chr20:60503248-60504900:+
Coord C1 exon
chr20:60503248-60503481
Coord A exon
chr20:60503482-60504666
Coord C2 exon
chr20:60504667-60504900
Length
1185 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TTACTGTTGCTTTGCACCAGGTG
3' ss Score
9.55
Exon sequences
Seq C1 exon
GGATACCCCCGGCCAGCGGCACCGGGACCCTCCAGATCTATCTCATTGACATCAACGACAACGCCCCTGAGCTGCTGCCCAAGGAGGCGCAGATCTGCGAGAAGCCCAACCTGAACGCCATCAACATCACGGCGGCCGACGCTGACGTCGACCCCAACATCGGCCCCTACGTCTTCGAGCTGCCCTTTGTCCCGGCGGCCGTGCGGAAGAACTGGACCATCACCCGCCTGAACG
Seq A exon
GTGAGCCCGCCTTAGGCCACGGGGAGGGTCAGACTAGCCTGGGGTGCAGGCCCCTGGGAGACCCAGCTGGCCTTGGAAGAGTGGGCACCAGAGGTGGGTGACAGTCCTCCAACAGGACTGTCCCACCAAGGCTGGGGACACTGGCCACGCTTCAGCTGCTCAGCCTCCTTCACCTGGCCTTGAGGAGGCCACCAAGTCATTCCCAATTTCTTGCTGCTTTAATGAGGCCAGCCGTGAACATCCTTGCAGCTCTGCCCATGTACATCCATGACAACTTCCTGTGCCGGTTGTCAGTTGACTGGACCCTGACTGATATGTTTCCTTAGAATACTTCCCTGGATGCAGATCTGTGGTATAAAAGGATATCAAAATTCTCAAGTTTTGGCAGTACTGTGAAAATGTGCTCTAAACATGTCTACTTCCATCGGGAGAGTGCCTGTTTGTTTCCTCAAACCCCACCAACACTGAACATTATTGTTTTAAAATAATATTTTATTCTGCCACCTTTAGGCCAAAGTCATTATTTCCATTTGTATATCCTGATTACCAGTGGAAATTTTTTATATATATTTATTGGCCATTTTTGTTTCTTCTGTGAATTGTCTGTTCAATGACTTTGCCTATGTTTTCTTTGGGGAGTTTCTTTTTATTGATTTGGTAAAACTCTTTATATATTCAGGAAATTATTTCTTCATCCTACATGTTGCAATTGCTTTTTGGTTGTGTCTCCAATGTCTTTTTTTTTTTGAGACTGTTGCCCAGGCAGAAGTGCAGTGGCACAATCTCAGCTCTGCAACTCCACCTCCCAGGTTCAAGCAATTCTCCCACCTCAGGCTCCCAAGTAGCTGAGATCACAGGCTTGCACCACACGCCCGGCTAATTTTTGTATTTTTTACTAGAGACAGGGTTTTGCCATGTTGGCCAGGCTGGTCGTGAACTCCTGACTTCAAGTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGGGATTACAAGCGTGAGCCACCACACCCAACCTCCAATGTCTTTTAACTTAATGATGTAGCACAGGTGTATGTATGTATGTGTGGTAACCAGGCAGCCATTTCAGATTTCCATGCCATCGGACTTTTAGTCTTTTCCTTTGGACGTCTTGCTTGGAAGCGAGGGCCGGGCTCTGGTTGAATGTTTACTGTTGCTTTGCACCAG
Seq C2 exon
GTGACTATGCCCAACTCAGCTTGCGCATCCTGTACCTGGAGGCCGGGATGTATGACGTCCCCATCATCGTCACAGACTCTGGAAACCCTCCCCTGTCCAACACGTCCATCATCAAAGTCAAGGTGTGCCCATGTGATGACAACGGGGACTGCACCACCATTGGCGCAGTGGCAGCGGCTGGTCTGGGCACCGGTGCCATCGTGGCCATCCTCATCTGCATCCTCATCCTGCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179242-CDH4:NM_001794:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):

C1:
PF0002812=Cadherin=PD(15.8=19.0),PF0002812=Cadherin=PU(54.3=64.6)
A:
NA
C2:
PF0002812=Cadherin=PD(44.7=53.2)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGGACCCTCCAGATCTATC
R:
CACATGGGCACACCTTGACTT
Band lengths:
348-1533
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Genotype-Tissue Expression Project (GTEx)
  • Autistic and control brains
  • Pre-implantation embryo development