BtaINT0035989 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001819 | CDX2
Description
Bos taurus caudal type homeobox 2 (CDX2), mRNA. [Source:RefSeq mRNA;Acc:NM_001206299]
Coordinates
chr12:32321317-32322605:+
Coord C1 exon
chr12:32321317-32321462
Coord A exon
chr12:32321463-32322371
Coord C2 exon
chr12:32322372-32322605
Length
909 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TCCACCTTTTTCATTTCCAGGTT
3' ss Score
12.06
Exon sequences
Seq C1 exon
TGAAAACCAGGACGAAAGACAAATACCGGGTCGTGTACACGGACCACCAGCGTCTGGAGCTGGAGAAGGAGTTTCACTACAGTCGCTATATCACCATCCGGAGGAAAGCCGAACTGGCCGCCACGCTGGGGCTCTCAGAGAGGCAG
Seq A exon
GTGGGAACCCTCCAGGGCCCCGTCACCAACTGGGAGGCTCCAGTGGGGAGGGTTAGAAGCCAGGCCCCAGGATCCACCCAGTTCTGTGGGCAGATTAAGCAAGAGAATCGAGAGACTTTTCCTTCTAGATGCTTTTTTAAAAAGGCTTCTTCCATGTCTACTTGTCTTTTTAAAAAACATATGTATATTGTGATTTTTTTTTTTTTTTCTATTTCGGGGGACCTGGGAGGTAAAACACACACACACGCACGCACACACACACACACACACACAAACTGAGTTTAGTTTAATGCAGAATCCGATTTGGGTCAATAAAGACTTATTCTCTTTGTACCCAGTTCTTTATTGGGGGAAAAATTAATGTAGGATACCAGCCTCTGTCCAGAAAAACTATGGAGGGGTGAGGCTTAGCTCCTGAATGCTCTAGATTGTCAAATTCACAGCCAGGAAACCCCTCATTAAAACTCATTCTCAGCCCCAAGGCAAGGACTATTTCATTTCCGTTTAGCTTTGAGAGGCCAAAGGTTGTCATTTTGAAGTACATCTAGCCCTAGCCTCCTTGCTTGGTGTAGAAAGGACCTGGCAGTTTCTGTCTTCCTTAGTTCTGAGACTCTGAACTTTTCCAGTAAAGTTGTAGATAAAGGTTGCTCTGGAAAGAAACCTGAGGAACAAAGAGGGAGAGAGAGGCACTTCCCTCTTGAGACTGCATGGAGCTTGGGAGAAGCTCCAGCACTGGGCTGTTATATGGGCTGTCCAAAAAGCTGGGTGATGGGCTGCTGTCCTTCGGGTGCAGTGGGGACCTCTTTGGCTGGAGAAGGAGGCATTGGATCTAGTGTCAAATACTGTCCCTTTATGCTTTCGCTGTCTTCTTCACCGCCTTCTGTTTTTCTCCACCTTTTTCATTTCCAG
Seq C2 exon
GTTAAAATTTGGTTTCAGAACCGCAGAGCAAAGGAAAGGAAAATCAACAAGAAGAAGTTGCAACAGCAGCAGCAACAGCCGCCCCCACCTTCTGGGCCACAGCCTCCCCAGCCACAGCCAGGTCCGCTGAGAAGCGTCCCAGAGCCCCTGAGCCCCGTGTCTTCCCTGCAAGGCTCAGTGCCTGGGGTTCTGGGGCCAGCTGGGGGGGTGTTAAACCCTACTGTCACCCAGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001819:ENSBTAT00000047376:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.265 A=NA C2=0.831
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=16.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAAATACCGGGTCGTGTACAC
R:
GGGTGACAGTAGGGTTTAACACC
Band lengths:
357-1266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development