BtaINT0035470 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015058 | CDH4
Description
cadherin 4, type 1, R-cadherin (retinal) [Source:HGNC Symbol;Acc:HGNC:1763]
Coordinates
chr13:55674130-55675426:-
Coord C1 exon
chr13:55675193-55675426
Coord A exon
chr13:55674364-55675192
Coord C2 exon
chr13:55674130-55674363
Length
829 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
CGCACCCTGCCCCCACCCAGGTG
3' ss Score
7.61
Exon sequences
Seq C1 exon
GGATTCCCCCGGCCAGTGGTACTGGGACCCTCCAGATCTATCTTATCGACATCAACGACAACGCCCCCGAGCTGCTGCCCAAGGAGGCACAGGTCTGTGAGAAGCCCAGCCTCAATGCCATCAACATCACAGCGGCTGATGCTGACGTGGACCCCAACATCGGGCCCTATGTCTTCGAGCTGCCCTTTGTCCCGGCGAGCGTGCGCAACAACTGGACTGTCACCCGCCTTAATG
Seq A exon
GTGAGCCCACCATGGGCACCTGCCCACTGGCTGCCCGGCTGCCGGGAAAGTCAGACCGAGTCCAGAGGGCAGCCCCACCCGGGCCTGTCACCCGGGAAGCAGGAGCAATGGAGTCAGGAGTCAGTCTCACAGGGGCCACGCAGCCCTCTCCTGCAGGGCAGGGGCCCTGCTGACTCCAGGGCTCAGCCACCAAGGAGGCCCCAAAGCACGCCCCAACCTTGTCCTTTAAAGAGCTCCACGTGACCATTCTACCACTGTAACCACACGTGACTGAGACCACTCCCTGAGCCAGTCATCAAACAATGGGGACCCCAACACCACCATGTTCCCTGAGGCACTTTCCTAGCCATGGTCTTGGTGGACAGGGCTTCCAAGTTCTGGAGTTCTGATAGCATTTACTTGTTCCCCAAACCCTTGCCAACACAGCATTATTGTTTTAAAATCATTTTTCCAATTTCTTAGCCAAAATCACTGTTTCCACTTGCATTTTATAACTACCAGTGGACATTTTTTCATCTATTTGCCATTTTTTGCTTCTGTGAATTATCTGGTCAATGTCCTTCACTGTTTTTCTTTGGAATAGGTTTTTTTTTCCTAATTGACTTGGTAGAACCCTTTCCATATTAAGGAAATAATTCCTTCATCCCACATGTTGCAATTGCTCTGTTCCTGAATTGCCAAGCCTCTTAACCTTACATGATGAGAGATGTGTGTATCTACGTGTGTCTTAGCCAGACAGGCCGAGCCTGTGCCTATTTGCCTGCGTTCGTCTCGCTCAGGAGGCAGGGCTGGCTGCCCACTGAGCAGAGCGCACCCTGCCCCCACCCAG
Seq C2 exon
GTGACTACGCCCAGCTCAGCCTGCGCGTCCTGCACCTGGAGGCCGGGGTGTACGACGTCCCCATCACGGTCACAGACTCGGGGAACCCGCCGCTGTCCCACACGTCCATCATCAAAGTCAAGGTGTGCCCATGCGACGACAACGGCGACTGCACCACCGTGGGCGCAGTGGCAGCGGCCGGGCTGGGCACGGGTGCCATCGTGGCCATCCTTATCTGCATCGTCATGCTGCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015058:ENSBTAT00000020042:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 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
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:
CCAGCCTCAATGCCATCAACA
R:
ATGCAGATAAGGATGGCCACG
Band lengths:
349-1178
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development