BtaINT0052800 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015238 | DSC3
Description
Bos taurus desmocollin 3 (DSC3), mRNA. [Source:RefSeq mRNA;Acc:NM_001178103]
Coordinates
chr24:26428892-26430915:+
Coord C1 exon
chr24:26428892-26429034
Coord A exon
chr24:26429035-26430690
Coord C2 exon
chr24:26430691-26430915
Length
1656 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
CTTTTTTTCTTTCTTCCTAGATG
3' ss Score
11.81
Exon sequences
Seq C1 exon
GTACAAAATATTGCATGATCCTAAAGAGTGGATCACCGTTAATGAAGGTTCGGGCTCATTAGAGACTTACAAAACTTTGGACAGGGAGGTTATAACTCCCAAAAATGATTTGTATAATATTACAGTCCTGGCAATAGATCAAG
Seq A exon
GTAAAACACGAGTTTTCATCTGGGATGTTATGGAGGAGTTAGAGAATAAACTGCAGTTATTTCTGGGCAGAATTACTCTTGTGCTATATGTGTGTGTGTGTGTGCTCAGTCTTATCCTACTCTTGGGACGCTATGGACTATAGCTCGCCAGGCTCCTCTGTCCATGGGATTTTCCAGGCAAGAATACTGGAGTGGGTTGCCATTTCCTTCTCCAGGGGATCTTCCTGACCCCAGGATCGAACCCGAGTCTCTTGTGTCTCCTGTATTGGCAGGTGGGTTCTTTACTTCTGCGCCACCTGAGAAACCCATATTCTTGTGTTGAAAGTGAAGTCTTAGTCGCTCAGTCGTGTCCTACTCTTTGTGACCCCATGGACTGTAGCCTGCCAGGCTCCTCTATCCATGGGATTCTCTAGGCAAGAATACTGGAGTGTATAGCCATTCCCTTCTCCAGGGGATCTTCTCAAGCCAGGTATCAAACCCAGGTCTCTTGCATTGCAGGCAGATTCTTCACCATCAGAGCCACCAAGTAGACAGAGTTCTTAGAAATTACTTTAAAGATTGTTTCTATTTATCTTAACCATAAAACAAGGTGAAACTGCTTGGTGGCATGAAACCATGCCTTCTTTATCTTTATGTCCCTAGCATGGCAACATCTTACAAGCTTATAGATCTCTGTGTCAGAGGGCAAGATGAAACTCAAGTCTAGGACTAGATGAAATGGTCTCACCAGACTCTTCTAGATCTCTTTATGTCTTTTTAAATTAAATCATTAAATAGCTCAGCTGACTATAGAGTTAAAATGATTTTTTCTTTACATTCTGTTCCTTAAGGAAACCCAGAATTTCTCAACCCTGGCTAACTATGAAAATAATTGGCGATGTTTAAAAGTAATTTCAAGGTATAGACACTATCTGAGACCAACTGAATTAAGAATCCCTGATCTAGGAGCCTGGACATCATATATATATATATATTTTTTTAAATCTGCCTAGATGGTTAAAATATGTACCAGGATTAGAAAAGTTTTTCTATGGTCACTTTACTCTTTCTGACATCTGTACCAAAAGGAACCCAAGGAACTAGAGAGTTTGAAATTCAGACATTTATTTTTATTTTTTGGTAAAAATTCTGGTTAAAGGTTTATGGGCAGTTATATCTGATACTATCAACAGCACAGTAGTCATTTTAGATGCTCTACAGGTTTCATTTATCCATCTACCTTCTTCTTTGCCATTTTCTCTAATTATCAGTTTATTTATTTAAAAAAACCCAGGAGCTTCCCTGGTGGCTCAGTGTTTTAAAAAAAAAAAAAAAAAATCTGCCTGCCAATGCAGGGTACTGGTCTGGGAAGATCCCACATGCTGTGGGACAACTAGGTCTGTGTGCCACAACTATTGAGCCCATGTACCCCAGAGTCTGTGCTCTGCAGCCAGAGAATCCATTGCAATGAGAAGCCCGTGCAGTGCAATTAGAGGGTGATCTCGGCTTGCCACAACTAGTGAAAGCCCACGTGCAAGCAATGAAGACCTGGCACAGCCAAAAATAAATAAATAAAATTAAAAAAATTAAAAAGTCCATGCATATTTAGAATCTAGCTGATTTTTTTTTCCCTTAAAAAACTGTGAACTACACTCAACTTTTTTTCTTTCTTCCTAG
Seq C2 exon
ATGGTAGATCATGTACTGGAACCCTCGCAGTTAGCATTGAAGATGTGAATGATAACCCACCAGAAATACTTCAAGATTATCTAGTTATTTGCAAAGGAAACATGGACTATGTTGACATTTCGGCTATTGATCATGACAGTTCCATCAACGGTGCTCCATTTTACTTCAGCTTGGCAAACACTTCTCCAGAAATCAACAGACTATGGACGATCACCAGAGTTAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015238:ENSBTAT00000048309:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.026
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=FE(51.6=100)
A:
NA
C2:
PF0002812=Cadherin=PD(14.0=17.1),PF0002812=Cadherin=PU(51.2=55.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTAAAGAGTGGATCACCGT
R:
TCTGGTGATCGTCCATAGTCTGT
Band lengths:
343-1999
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]