BtaINT0035990 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001726 | CDX4
Description
caudal type homeobox 4 [Source:HGNC Symbol;Acc:HGNC:1808]
Coordinates
chrX:82551923-82559474:-
Coord C1 exon
chrX:82558970-82559474
Coord A exon
chrX:82552069-82558969
Coord C2 exon
chrX:82551923-82552068
Length
6901 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
ACTCCTTTCTCCCCTAACAGGGA
3' ss Score
11.65
Exon sequences
Seq C1 exon
ATGTACAGAAGCTGCCTTTTGGAAAAAGAAGCGGACATGTATTCCAGCACTCTCAGGAGCCCCGCAGGAGGTGGCACCGCCGGGGCTGGTGCCACTGGGGATGGTGGGAGTCCTCTGCCAGCCTCCAACTTCGCAGCGGCCCCTTCTTATGCGCACTACATGGGATATCCACATATGCCCGGTATGGATCCTCACGGGCCACCGCTGGGAGCCTGGGGGTCACCCTATAGTCCCCCTCGTGAAGACTGGAGCGTGTACCCCGGGCCATCCAGTACTATGGGTACGGTCCCCATGAACGACATGAGCTCGAGCCCCGCCGCTTTCAGCTCACTGGAATATAGCAATCTGGGCCCCGCAGGGGGTGGAAACAGCGGTAGCAGCCTGCCAACACCAGCCGGAGGATCACTGTTCCCCATCGACGCCGGCATCGCAGACGCAGACGAGAGTTCTAGCAGAAGCCGTCACAGCCCCTATGCATGGATGCGCAAGACAGTGCAGGTGACTG
Seq A exon
GTGAGTAACCAAAACCAATGCTCTGATCCTTTTCCTTCCTTTGCTTCTTCTTTACTTCTGTTGGCCTTCTGGTCCTCCTACTTCTCAGACTTCTCTCCGGACAGCTTAGCTAAGGAGACCACTATGTGGCTTACTGCCCAGGGCCCCAGACCACAAGTGACCTCCTTCGCTTGTGCTTCTGCTCAAAAACAGAGTGTAGTGCTTGGAACTAAGCTGACAGTAGAGGACTTTTTCATCATTTTCTGATCAGCCAAAGGAGCAACCGCGGTGACAATGGACATACTGAGCCACAAAGATCAAGATCCAACCCCACAGTTGCCCAGATAGGAAAACATATTCACGGGGAAGGTCAGTGGGTGAATGAGGAGAGGACAACTATGTTTCTCTATGCTCAGCCACTGCTGTTTGCCTGTTCCATTTCAAAGCCTTCTCTATCTGAGCAGGTCGGCTTCTCCCCCAAATCTGGTGATGGTCAATTTAGATTCAGTGCTTGATTGGCAATAGGTGGTCCAGTTTAGCCACAAAGGCCCTGATGGCAAAATGGCCTCCTCACCCTGAACTCTCAAGGAAGCTCCAGTTTCCTTTGCCCAAGCTGGCAGGAGCCAGCTGAATTCAAACCCAATGCCTTTGTACAACTTTCCTTCCACCAATGGAAAGCTACAGCACACCACTGGGACATAATAAGCTGCTCAACCCTAACATCCCCGGGGTGTGCACCAGTATCAGCCCCAGCATCAATACAGTTAAAGGGATTAAAGCCCTCCAAACAGTACAGGCAGGCATTTCGAGATGCAGGGACTGAATACAGGCTTGTCAGGACACATAGGAAAGCCCAGAGATCTCAGCCTAATGCCAACTCACTCTCCTACCAGCAAGCTACTGGTTGGCGGCTACTGGGAGGAGGGTGTGCGCAGGGGTGTGGGGTGTGTGTGGGGGGGTACTCTGCATACTCTGCTTTAATCTTGGACAGGGGCTGGAGGAGGGAGGTGGGGAGATGTTTGTTTTCAGCTATAGTTGTGCTTTTATCACATTCTTATTATTCCAACTCATCACTGCCTTTCATTAGAGAAAATTAGTAAAATTCAGCCTAACACTTTCATCCCTCTGGGGAAGACATGACATTCCAATAGCATTTGCCCATAGTGATTATGCTTCTGCTCACAGTTCTGCACTTTTTCTCTGCTTAAAAATAGCAAAAACAAGAGGGTGGGAAGGGACCAAATTTTATCATTGAGAGTACTCAGCCTGGAGGAGGCAGTTCCAATTAATTAGGACATTACTAGGGTAGCAATCCCAAATTAAGAGTAGAGCTTAAATACTTAGCTCTAAAGTGTTTGTAAGTAAGTCTGCATATTGCTTTTTGAAATAAGAGTGAGTTGGTGGGCTAAAAAGAATAGAAAGTAAGCTTAGGGTGGGGCACTGTCAGGGCTGTTATTATATCTAATCTTAGGGTTGTAATTAACACCTATTCACTAAGACCTAACCATCAGCAAGAGACACAAAAGCCAGAAAAGTGGCTGCTCCAGTTTAGGATTATGTTTTGAAATACTTAAAAAGAGGAAAGTCACTAGTATGTTGTTTGGAAGACAAAACAATGGGAAGAAAAGAACAAGATAAAATAATTATCTTGAGTCATGAATTTTCTGTATAAAAGAGAAAATATGATGGGTTTCTCTGCTTAATAGTCTTCATTTGTATTTGTCAGAGTCTCTCTTTTGTATAATTCTGGTGCCAGGAAAAGTTTAGAACGGGACTCTAAATTACTCTATGGAGTCTTCATCATTAGCTCAGTCGTCAAACCTTGCTGTACAATACCATCTTCACAAGATTTTCTCTCCAACTTCTATGAGAAATTCTAAATTGAATGATTTTAGAACCTCACTAACTTGTGGCAGCCTATCCTATAGATGAGGCTTTATTAAATTCAATCACCATTTCATTTTAATGTCTTATAAAAATACCCCTTTGTTATATTCTTGCAGCCTAAGTACATATTTAGCAATGATTTAAGAATATGATGAAAAGTATGGACCCTCTTCCAGAAAAATGCACAAGGGCACAAATGCACATGTACACACTTCATTTTTTCCATCAGATTTTTTAAATTTTTATCTATTTTTTTGGTCTTGCCAAGCAGCATACAAGATCTTAGTTCCCTGACCAAGGACCAAACCCATGCTTTCTTCAGTGGAAGCACAGAGTCTTAACCACTGGACTGCCAGGGAAGTCCCACATATGTCATTTATTTGAATAATTTTGGGAGACTCATGGATCCACTGAAACCCCTTCCGTAGATCTCAGGTTATGAACTGATAACCTGAGAAAAAATTAAAATGATCACCTCTCTGTATCACTCCAAACCAAAAGGCACCCATTTGTATGCTTAGTACATAATGAGAGTTAAACAAATATCTGTTAAGTGAATAAGTCAGATCCTCCTAAATTTTATACTTCACTCTGTAGTATTATAGGACATTTGACTTACGGCTGAGAACAAAACAGATGATCTACAAAAATGGAAGTAACCCCTCCTTGATTATGGTAGTCAAATTAAAGCTCTTTATATTATTTAAGAATGTTTTAACTAGCCTTAAGTTAAAGAAACAAAAATACACATATTAGGGGACAATTGGAAAACATTTCATAGTGATTATCATGGCACTTGATTTTTGAATGACAGAAAGGGGACTGACATACAGAATAAATGACTGTCCACTAAGTGATTTGATTTAAAAGTGAGATATTTTTTCCCCCACTTTGTTCCCTAAGTAGTCTGTTTGAAAACACACCTTGTGTTAAAAATTATGTGAAAAGGAACCTGACAGAGATATTCACGAAAAGTTCATTATTTTAATATTTTAAGCATTGTCAGTTTAAAAGTTCAGTATTTTCATATTTTAAACATTGATAGCACCACTCTAGAAATTTTTTCATTTTGTTTTTATTTTACCCAGAGTTATAGCCTTGTATGAGTATTGGAAAGGCGGTAACCCTAGCAGGGCTGGAAAGCGGCTTTGGTTTTAGGGGTGGGAAAGAAGAGGAGAGAAGGAAGTGACTTTGAATAATTCTGATTAACCCACTGGACAAAAGACAGAAAACCAAGGAAGTTAAAAGGTTTTCTTCAGTTAGGACATTTCAGAAAATTAGTTACTTAGTAATTCCTAATATCATTATCTTTCTTGGTTTTGATCATTTTATTTTTATTTTTTTAAATTTTATTTTATTTTTAAACTTTACATAATTGTATTAGTTTTGCCAAATATCAAAATGAATCCGCCACAGGTATACATGTGTTCCCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCATACCATCCCTCTGGGTCGTCCCAGTGCACTAGCCCCAAGCATCCAGTATCGTGCATCGAACCTGGACTGGCAACTCGTTTCTTACATGATATTTTACATGTTTCAATGTCATTCTCCCAAATCTTCCCACCCTCTCCCTCTCCCACAGAGTCCATAAGACTGTTCTATACATCAGTGTCTCTTTTGCTGTCTCGTACACTGGGTTATTGTTACCATCTTTCTAAATTCCATATATATGCGTTTTGATCATTTTAATTGGACAGTTTTTATAAGTGAATTTGGATGCAATTTTTAACTAAAAGCAGCAAAAGATTACCATCGCATGGAAACTCATTATGATGGTGTTAATTACACTCTGTTCCCTATTGAAAGGGATTGGTGTTAATCATCTTTACCCTCGATGTCACCATCATCATAATCCTTAGGTTTGGAGAGTGCTTTTCTGCCTAACAGCACTGTCACAGCCAGTCTCTCAAATGAGCACATTTAGGTGATGATAAGTCATCATATATAATGACATTTGTTTGCAAACTCTGTAGGGATCCTGTCTCCTTATGGGAACTACAGAGGTTTGTCAAAGTGTTTGGTCAGGGCAAGTAATGATATCCTACCGCAGAGCTTTGAAGCAGCCCTGTAATACAACTTAAAGTTTGTTACTTTCCTAGATTAACTCGCAATAGTGCTGGAGAAGGGGATCCCACACCCTCGGCACTGTCATAGTCTCTGGGAGAAGAGAATGGCTTGAACAATAAAAGCTACTGCTTTTAGCACTTTGTTAGTGTTTTAGTATGGAAATATGGTTCTATGCTCCACTAGAAAATGTCCAAAACGCAGTCAATCAGATTTCATCATTTAAGGGAAGAGACAATGGAGTAAATGGAAAGAAAATAGCTTGGGAGGAGGGACACAAGAGGAGCACCAGGAAATGAGAATTCATTTCTCTTCGTTAAACGTGCAGTCAGTATTTCCAACTAATCTAGTGTTCTTGAGGTCTGAGGTCTTATCCATAAGATTGGGGCAACAGACTCTTTTTTTAACACTTTGCATGGCTTTGATATGCAGCCTGGCTCTTCCTCATCCCTCCTTTCTTTAGGGGTTATATTGCCGGAAAGGGTGAGGATTTTCATGGCAAATAAAGAGGCCTGGTATTGACTTTATTGTCCTCAGAAGAAACTGCAAGAGGGGAATTTATGACCAATGGGGGTGGGGAAGAATTGCAACCTTCCAGAATTCTTGAAGTCTGGTTATATTTACTGATTATCAAAGAGTTGAAAACAGACACACGCACATTAAATTTTAACTTCTGCCTCAAGTTAGAATTTAAACACTCAGTCATTTTGGTATTAGGAATGGTTTTAGGAAACATCTCTTCAAAGATATATTTTGATTCTAAGATTTGAGGCTCTAGAAATAAATTAAACCTCAATGTTTTCATTGTGGCCTCAAAAATACATTCTGCCTTTGTAACATACCAAATGCCAGAACTTTGGTTTCCTAGATTCAGAAAAGCAGCTGAAGTTTGTTTTCCGTACGTGTGAGTCTGTTTCTGTTTTGCATATACATTCATTTGTGTTATATTTTAGATTCCGCATATAAGTGATACCATATAGTATTTGTCTTTCTCTGTCTGACATTTCACTGAGCATAATATTCTCTTGATCTTTCCAGGTTGTTACAAATGAACCTAACACAATATTGTGAATCAACTATACTTCAATTTAAAAAATTGATATAAAAAAACCCATGAAAAACAAGCAAACAAAGAGAAAACCAGCTCATAGTTTGAGCCTTTGAGATAGATAAACTGATTGGAGCTCATCATTTTCCATTTTCAAGAAGGAAAGTTTTGTTTAGCTCCCTAGTCCATGAGTTAATCCTAAAACATATCTCTCATCTAGAATTTGTTTCTACATTCACGTCCCCCCCTTTTTTTTTCTTTCCTGGAGATGAAAGGGTGTCTGACATTTGTTTAGGGCTTGTAAATTCCAAACCAATTGGCTGGTGTTCCTGAATGTAAAGAGGGTTCAAGATGGGATCTGATGCTATGTAGCTCCTTTGTTAAGCTTGTGCTGCATCTTAACACCTCAATGGAGTTTAGGGAAACACTTTAAAGAAACCTTTGTCTTACAGATCGCTCCCCAAAACTTCACATCAAAAACAACCAGGGAAGATCAGAAGGAGTTTGCCAAAAGCTATAGAGAAAAGGAGGAAGATCCTGGAGGGGGTTAGAAAAATTGAAAAGAAAAAGAAACTTCCTAATCACCTTTGGAAAATTTAAAAGGAGGAATAAAACCCTATTTGATGGAAGGCATGAGAAATTAGTTAAACATTGTAACACAAAGCAAATGTTTGGATATCCTTTCAAAGAATACTAGAATACCCATTTTATTCTGGTAAAGTCAACACCCCCTACTTCCCCCTCTCATTTTCCATTAGGGAATAAAAATTTGTTTAAAACTCCCCCAAAAATCCCTGGAGAAGGAAATGGCAACCCACTCCAGTATTCTTGCCTGGGAAATCCCATGGACAAAGGAGCCTGGAGGGCTAGAGTCCATGGGGTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTCTAATAGGTGAAAAGAAAGTGAAAGTGAAGTAGCTCAGCAGTGTCTGACTCTTTGCAACCCTGTGGACTGTAGTCCTCCAGGCTCCTCCATCCATGGGATTCTCCAGGCAAGAGTACTGGAGTGGGTTGCCATGTCCTCTCCAGGGGATCTTCCTGACCCAGGGATTGAACCCAGGTCTTCCGCATTGCAGGCAGACGCTTTACCTACCGTCTGAGCCACCAGGGAAGCCCATAGAGCTCTTGTAGAACAGAATCCAAGTGACAAGAGATGTTTTCTTTTTTAAGTACTATCCAAATGAAATTCTCTCTAGAATGTGCATGTAATAAGAATGTCAGTATCATGAAACAGTTTGCTGCACTTGGGCCATTCTTATGCTGCCCAGCATATTTAAACTAGGAATAACATTTGGCACACTGGACTTGGAGTCAGTCAGGGGTATGTGTTTGGGTCCCCATTCCTAAGCCCACTACCACAAAGCCACTTACCTCTGAGCCTCGGTTTCCTTATCTGTACAATGGGAATAAGACACATTCTGCATAAGCTGAAAGGGTAGGTGAGAGAGAGGTTCAATAGGAAACAACATGAAAGAACTCTATACAATATAAATGGAAGTGCATGTATAATGGATGGTGCTACTATTGCCAATACTGCTGTCATATGTGAGTGGGAAGGGAATGAAAATCATGGCTAGTGTTTGCTTTAAAATGCTTTGGTGTAACAGTATGTCAATGGTGCTGTGATGGGTGTGTTGAATGTGTGTGTGTGTGTGTGTCAAATAGCCACGGATGACAAAGTACTTAATGAAGAAATGGACTTATGACATATTTGGTTCAAAAAATGTACTTGTTTTATATTTGAAAGTAATAGCTAAGGGTAGGAACAGTGGCTCTGATTCCTCCAACCAAAATAACCTCCAAAGAAAAAAAATATGATTAAATACACTCCTTTCTCCCCTAACAG
Seq C2 exon
GGAAAACCAGGACAAAAGAAAAGTACCGCGTAGTTTACACAGATCATCAAAGGTTGGAGCTGGAGAAAGAATTCCACTGCAATAGATATATCACCATTCGGAGAAAATCAGAGCTTGCAGTCAACTTGGGCCTTTCTGAGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001726:ENSBTAT00000002260:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.669 A=NA C2=0.061
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PU(97.5=92.3)
A:
NA
C2:
PF047317=Caudal_act=PD(1.9=6.1),PF0004624=Homeobox=PU(73.7=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]