BtaINT0052921 @ bosTau6
Intron Retention
Gene
ENSBTAG00000039483 | DSG3
Description
Bos taurus desmoglein 3 (DSG3), mRNA. [Source:RefSeq mRNA;Acc:NM_001192685]
Coordinates
chr24:25988940-25991099:-
Coord C1 exon
chr24:25990960-25991099
Coord A exon
chr24:25989168-25990959
Coord C2 exon
chr24:25988940-25989167
Length
1792 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
CTAAAATGTTATTCTTACAGGAA
3' ss Score
8.26
Exon sequences
Seq C1 exon
ATATGTCTTGGGACGTAATGACGGTGGTTTGCTAATGATTGATTCAGAAACTGCTGGAATCAAATTTGTCAAAAACATTGATCGAGACGTTACTTTCATAGTTAACAAGACAATCACAGCTGAAGTTCTGGCCATAGATG
Seq A exon
GTAAGAAAAAAATATTATTCCAATTAGCATTTTTTTATGAATAGATGCTTTTGATTACTAACATATTACATTTATCACTGCATGCATATGTGCTAAGTCACTTCAGTCATGTCCAACTCTTTGCAACCCCATGAACTGTAGCCCACCAGGCTCCTCTGTCCATGAAATTTCCCAGGCAAGAATCCTGGAGTGAGTTGCCATTTCCTTCTCCAAGGGATCTTCCTGACCCAGGGATTGAACCTGCATCTCCTGCGTAGCAGGCAGATTCCTTACCACTGAGACACCAGGGAAGAACCTTTATCACTAGATAAAGTTGATTACCTTAGGGGTCTTGGGTCTTAAGTCTGAGGTGGCTAAATCTAGGCGATGACTAAGCATCCTAGCTTCTCAATGGAATTCACTGGACCAGTGAATTCTGGGTTTAGTCCTACTATTTGCTGTAGTTGGCGCAAGAATTTCTTGATTTGAGAATGTGGACAAAGATTGATACAGAAGGCCTATCAGGGAAGTTCAGCTCAAATGTGAGGTGCCTTTGTGAGTTACTTACACACAGAGTGAGTTACTTACAGAGACTTATATGCTTATATCATAGAACAGGAAAAATCTTCTGAAAAATTTTCTAAATGAAGCACCTTGACTATGTGCTTGACTATGTGCTTCCCTAAGTGTAAAATTAATTTATACTCAAGGCAATTTCAGCAAACATAAAAATAAAATAAAAAATCATATTATCTGGAAAAACAGAAAAAAGCACTAAGGGAAACAACAGAAGTAATTCTTAATCCCACCACTGAGAGATCTTATATCTTGGGTAATAAAAATAAATCATAGTTTATTCCAAATACTTTGGTTCAAGCTTTTAAAGCAGAAATCTTCCACACAGTCTGGGTTCATACACTAGAATATATTTAAGAAAACTATTATTTTTATGTTGATTTCATTCATAATCAGTGAATTTATCACCTTAAAGGTCTTGGTTCCAATCACATTGAATAGCTGATGCTACTAATTAAGGTGGCTCAGAGGTAAAGAATCCACCTGCTAATGCAGGATTCCATCTGTGGGTCGGGAAGATCCCCTGGAGAAGGAAATGACCCACTCCAGTATTCCTGCCTGGAGAATCCCATAGACAGAGGAGACTGGCAGGCTCCAGTCCATGGGACTGTAAAGAGTCAGACATGACTTAGTGACTGAACAACAACAAGCTAATTAAACTAATTAAAGACAGCAGGCAAGCTGATAATTAGATTTCCTTTTAACCAGGTACAGAAATTGGGTGACATCTTTTTATTTGTAGGAATAACAGACACAATTTCATGAGTATGTACACTAATCTGGTGCATGTGAGATCGTTTTTTTCTAATATTTATTTATTTATTCCCTGGTTGCACTGGGGCTTCTTTGCCGTGTTCAGGCTTTCTCTAGTTGCAGCAAGCAGGGGCCACTCTCCAGTCGTGGTGCACGGGATTTTCATTGTGGCGGCTTCCCTCGTTGCGGAGCACAGGCTCTCAGCTTCAGTAGTTGTAGCGTGTGGGCTCAGCAGTTGCAACTCACAGGCACTAGGGCACAGGCTTCGCAGTTGAGGTGCACGGGCTTTTACTCCACGGCATGTGGTGTCTTCCTGGACCAGTGATCAAACCCATGTCCCCTGCGCTGGCAGGTGGATTCTTATCCGCTGTGCCACCAGAGAAGTCCATGCATGTGAGAGACATTTTAAGGGCTTATTTATGTTTCTTTATTTTGCACAACTTGCTCTGTATAGTTCTCTAACTCTAAAATGTTATTCTTACAG
Seq C2 exon
GAAACACCGGTAAAACTTCAACAGGCACCATATTTGTCCTAGTACCTGATTTTAATGAAAAGTGTCCAACAATTGCCCTGGAAAAGGAAGCAGTCTGTAGTTCGTCACCTTCCGTGGTTGTCAGAGCTTCACCACTGGAAAGGGATAAATATGCTGGCCCCTATGAATTTTCAGTGGAACACCAAAGCCTAAAACTTCCAGTTGTATGGAGTATCTCAGGAAGAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039483:ENSBTAT00000002538:10
Average complexity
IR
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=FE(51.1=100)
A:
NA
C2:
PF0002812=Cadherin=PD(16.3=19.5)
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:
CGTAATGACGGTGGTTTGCTA
R:
TCCTGAGATACTCCATACAACTGGA
Band lengths:
348-2140
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]