BtaINT0035988 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001819 | CDX2
Description
Bos taurus caudal type homeobox 2 (CDX2), mRNA. [Source:RefSeq mRNA;Acc:NM_001206299]
Coordinates
chr12:32317772-32321462:+
Coord C1 exon
chr12:32317772-32317821
Coord A exon
chr12:32317822-32321316
Coord C2 exon
chr12:32321317-32321462
Length
3495 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
AACTTTGCCTTCCTCCACAGTGA
3' ss Score
9.41
Exon sequences
Seq C1 exon
CCTGTGCGAGTGGATGCGGAAGCCCGCGCAGCCGGCGCTGGGCAGCCAAG
Seq A exon
GTGAGCTGGCGGGCGCCGGGGGAAGGCGCGGTCCCCGCGCGTCCGGGGACTCCGCGCAAGGGGGGCGGGGCGGGGCGACCGCGTCTAGGGGGCTCTGGACCCTCCCCCCCGGGGGTTGCTGCTCTGGACCCTGAGTAGGGGATAGCGGGGTCGGGAGTGGAGGTCCTGGTCTCAGGAGCCGCGTTCAGTGTAAAGCAAAGGGGAGGCTCCCTCCTTCCCACCGCCCTTCCTTCGTAAGGTCGGGTCTTCAGACCCTCGGGAGACTCCCGGGAACGTGGCGCAGCGCGGCTGCAGCGCAGTGATCGCGTCCGCCCGGCTTGCTGCCTCCTGTCCTCGCTCGGTGCGCGGCTACCCTGCAGCTCCCCAAGGCCGGGCTTTAGGGGCACACCGTCCTTCCCTGTCCCGGCCACTCAGGAAGAGCAAGGGACGGGGGTCCGGGAGGGCGGCGCGGTCGCGCGAGGGACCAGGTTTAGCCATTGGAACCAAAGGTAAGGATCGGAGCTGCCGCGCTGGGGAAACTGGGCGAAGCTGCCGAAGCTGAAAGAAAGTGTTGGTCCCGGGAACGAAGTGGGGAAGAGGTGCGGCTCGGGGGTTGGGGGAGCACCCGGGTCTTCAGACCTTTGATCTGCGCAGGGGTCATTTCAATCAAAAGCCGGAGGGCTGGGACTGGACGCCCCGGGAGTCCCCTCGTGTCTGCAGAGGGAGAAGGGGAGGCAGGGGTCGTGCGCGCTCCGCCGCTGCTCTAGACGGAGATCGTTTCTCCGGAACCTTCCTCCCCAGGGTCTGGTGTGTGTGCGCGTGTGAGTGTGTGTGTGTGTGCGCGCGCGTGAGTGTGTGTGCGTGTGTGCGCGCATATTCGTTTAACGAGCTTGCCCCAGAGATGTCTCTGCAGAGATCCCGGGTTGGCGGGACTGAGCAGGCTCTTGGGCTCCGGGTCTGCCCCGTCTGGCGTCTGAGTGTGTCCAGTGGGGAAGGAGCTCCAGTAGGTGTGGTGGGAGAGTCCTGCTGGCTCCGCTTTCCCTCCATGAAGTCTTTCCCAGCCCTCTGCACTTCCGCTTTTTCCTCTTCCCTCCTTTCAGGCCCAGCCCGGCTCGCATGCAGGTTATGGCCACTTTGCAGGGGTTTTATAGCCGATTACAGCCGCATAAATCAGAGTAGCCGTTGGGGGCTGTCTCCCGGGATCGGTTTTTTGCGTCACTGCGCACAAACCGGGACCCATCACCGGGGGGAACTGCGGCGGTCCGGGGAGGAGGCCTCGGGGCCGACCTGGAGGGTCGGCTGGGTCCCTTCCCCCGAGAGGAGGCGCGCTCGCCTGGACAGAGAGCGCGCCCGATGAAGGCCCTTGGCTATCCTGAGCCTGCCTGGGGCGCCGGCCCGCGGGGCCGGGCCGGGATCCTTGGTGCGTCCCAGGAGAATGCGCGCTGAGCAGGCTCGGGCGGGGGGGAGAGGGAGGCGTGCCACCGGAGCCTGGGCCGCGGGGTCAGCGGAGGAGAGGCCGCTGTGAAGTCCTGCGCCAAGGTGGCAAGGCCGCAGTCGGCGCCGGGCGCCCTTGTGATGTTAATGTGGGGCGGCCCGCCGGCCGGAGCCCGACTCCTCTGCGGAGCCTCATCCGTCAAGGGGCGAGTGGGGAAGGGGGGGCGGGTGGGACCCGACCCAGTCCGCTTTGATATACACCTTCCCATCCCTGCCATTGTCTCTTTTAGGGCCCGGAAAGAGGGTGGTGACTTTCGCAGTCAATAATGAATTCTGACAAGTCCCTCTCATCTCTCCCCTACTCCAGCCCCCTCCTTGGTTCCCAGGGGGTGCGGGGCATCTCCAAGGTCCTCGGGGCGCGAGCTGCAGAGCACACTGGGGCCTGGTCGCGCTGCCCCGGCCTCTCCGGATACTGAAAGGACAGCCCCCAGTCAGAGCCGCTCCCGAAGGCCCCAAGGCGAGTCCAGCTCCTGGAGAGTCCGGCTCGGAGAACTCCCCTGCGCCCGGCTCTCCGGCCCGGGGAGGTGTCCTTTGTGGCTCCCACCTGGCCCCCGTACACCATCTGCGTGGTGATCTAGTCTGATCCTCAGTTTGCCCCTCTGTACACAGGGGCCACCACCGCGGGCGGGCTGGGGGCGGTAGCGCAGGTTCCCAGGACGTGTCAGCTGCCTTTCCTTTCCCGGCGGGCGCAGGGTCGGGGCCACCGCGCGCATTCAAATGCGCCCGCCGCCGTGTTGATGTTAATGCGCCTGGCGGGGAGGGGGATGAAGGCCGGCCCGCCATTTGCTCAGTAGTGGTAATTCAAACAGAACGCGGTTGTTATTAAGGCATTGAAAGGGCTTTTCTTTGATAAGATCGCCTTGTCCTGCATTGTTTGAGGCTGTGTTCTCCTTTCAGCGGCTCCGGGGAGCTCCCTCTGATCCGGCCTGTATCTTCCCAGGGCGCTTTTGTTGTGGTTTGCAAAGGGTTTTACCTGAACAAAGTCGGCCTGCGGGGCATTAAACACCTCCGAGCAACTCCCCAGACCCTTTAGATCTTTCTGCAGCCCCGGGGCACCGGGCGATTGAACCTGTTCTTTTGGGGAGAAGACCCCGACCTGGGGCCGAGCGAGAACAGCTCTTGAGTTGGGGGATTCTGCCGAGGGTCGACCCGGGACAGACTCGGTGGAGACGCGGGGCTCCGGGCTGCTCTGACTCCAGTCGCACTATTTGTCAAGGCCCTTCAGTAAAACAATCAATGCAAGGTTTAATATGTTGACTCAATCCAATGAGCAGTAGATCACTGGTTAGGATAGCTCTGGCAGGGTTTGCAGCAGAAATAAATGGAGGATTAAAAAGAAAAGTGTGCCAACCCAGTTTCGCCCAGGTATAGAGCGTCCCCAGCGAGAGGAATTAGCGGCCTGCTAGACCCCTGCTTAGAATTCCACCGGATACGCTGGTGAGCCCGGGTGGGGGGGCGTGTGCGGTTTCTAGTGACCTGAGGGGACAGCTGTCAGCTGCTGCACCCCCTTTCCACTTCTAATAAAACAAACAGAAAGGGAATCCTCCCCCCACCCACATACCCACAATCCCAGCTGTTTTTACTGTGAGCTTTTTTTTTTTTGAACCTCTGATGGGCCTGGAAATCTGAATATTCCCAGGACTGTTTTCCTTTTGGGCCTCATCAGCTCAGGTGCTGTATTTGCTTTACAAAACCCCAGATGGGGTTCTGCTGTCACCTGTATGTATTTTTCAGTTCAGTCGCTCAGTCGTGTCAGACTCTTTGCTACCTGTATGAATTTTTAGTTTCTCTTTAATTTTCAAAAAACCACTTAATTCCAAGACTAGGTTAGTTGTCCTGAATAGCACCCCCCCACACACCCTCTGGAGGGGGTCTTGTCAGACTCAGCAGGAACCAGCCAAACCGCGGCCCCCCAGGGCGATGGAGGAAGAGAAATGGTTCCTGGGTTAGGGAGGTTTGTCATTACCCATGACTGATGGGCTGCCCGGCAGTTCTCGGGGCTAACTTTGCCTTCCTCCACAG
Seq C2 exon
TGAAAACCAGGACGAAAGACAAATACCGGGTCGTGTACACGGACCACCAGCGTCTGGAGCTGGAGAAGGAGTTTCACTACAGTCGCTATATCACCATCCGGAGGAAAGCCGAACTGGCCGCCACGCTGGGGCTCTCAGAGAGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001819:ENSBTAT00000047376:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.412 A=NA C2=0.265
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=85.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development