BtaINT0035987 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012014 | CDX1
Description
Bos taurus caudal type homeobox 1 (CDX1), mRNA. [Source:RefSeq mRNA;Acc:NM_001101947]
Coordinates
chr7:63472589-63474202:+
Coord C1 exon
chr7:63472589-63472738
Coord A exon
chr7:63472739-63473538
Coord C2 exon
chr7:63473539-63474202
Length
800 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
TCTGTTCTCTGACCCCACAGGTG
3' ss Score
12.12
Exon sequences
Seq C1 exon
TCAGGTAAGACTCGGACCAAGGACAAATACCGGGTGGTCTATACCGACCACCAGCGCCTGGAGCTGGAGAAGGAGTTCCACTACAGCCGTTACATCACCATCCGGCGGAAATCAGAGCTGGCCGCCAACCTGGGGCTCACTGAACGGCAG
Seq A exon
GTGTGTAGGGCCCCTACTTCAGCCACAGGAGCAGTACTGCGAGTCTGACCTCCAGGCTACCAGGCAGATTATGGAGCTCAGTCAAGGGAGAACAGAGAGGTTTTCTCCTGGCCATGGTCATACAACACAACAGAAACAGAGCTGCTGCCATGAATCCCCTGGCCAATAAAACCCAATATCCCTGGGCACCAATACAGGGATAGGGGGTCTGATTAATTCTAGGCTACAGCAGGCTTTGATCAGTGCTGTTTAAATCCAGAGGAGGGAGCAGTCACAGGGAGGACAGGGAGGGCTTCCTGGAGGAAGGGTGTTAGAGTATGGCTTTGGAAGATGGAGAGGAAGAGGGTTACAGAAAAAGTTGTCTTAAGAGTAAAGGAGCAGGGGTGGAGGGGTGGGTGTGGGGGTGGGAGGGAGGCTCAAAAGGGAGGGGATATATGTATACTTATGACTGACTCATGTTGTTGCACAGCAGAAACCAACACAACATTGTAAACCAATATCTTCTAATTAAAAATAAATAAAAATTTAAAAATAAAGTAAAAGGATGGAGGAACAGCTGCAACTCCTATATTTTGCTGGGCAGAATAAAAAAATATTACAGGAAAAAATAAAAGGCAGGGTAACAGGTTCCAGAAAGGGAGAACATGTTCACGGTACATGAACAGCTGGGGTAGCTGGAGCCGGAGGGAAGCCCCAAACGCCACATCAAGAAACAAGAGGTCCACTGCCCTCTCTCTTCCTCTTGCTCTGTCATTCAGTCTCCACACCTTCTGCCCCATCTCTGTTCTCTGACCCCACAG
Seq C2 exon
GTGAAGATCTGGTTCCAAAACCGGCGGGCCAAGGAGCGCAAAGTGAATAAGAAGCAGCAGCAGCAGCAGCCTCCACAGCCACCCCCACCAGCCCATGACATCACCTCCACCCCAGCAGGGCCACCCCTGGGGGGCCTGTGCCCCAGCTCTGCTAGCCTCCTGGGTGCCTCCTCCCCAGTGCCTGTCAAGGAGGAATATCTGCCATAGCCCCCTGACCAGCCTTGTGGGCTGGGGGCCTTGAGGACTCAGGTGCTGGGAATGTGGCTCCTGTGGGGGCCCAGGAGTCTGAGTCCCAAGCCATACCACTGACCTTCTGAGTAACCCTGGACAAATCACCCACCTATTCCCTGCATCCCCTGGGCCCAACCGTGCAGTGAACCTGTTGAATAGGACCTTTTCCCACTTTGGTGTTCTAGGCCTCAGGGGGATAAGGGTGCCTGGGGTGGGAAGTCTTAATTCCCAGGAGGCAAGGTGAGGAGGATCTAGCTCCTCCTCCATAGGCTCAAAGGTGGGAGGCTGTTGTAGGGACCAGACTCCTGGAGAAAGGAGATGGAATCCAGGGAAGATGGCTTGCAGACCATGACCTGAGGGGGTCCAAGGGAAGGGTGCCAGCCTGCCTTTTCCTGCAGGCTCACGTCTACCTGCCCCCATCATCACATGCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012014:ENSBTAT00000015934:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.300 A=NA C2=0.765
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=84.0)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=18.8)
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:
CGGACCAAGGACAAATACCGG
R:
GTCAGGGGGCTATGGCAGATA
Band lengths:
354-1154
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]