GgaINT0071474 @ galGal4
Intron Retention
Gene
ENSGALG00000007657 | CDXB
Description
caudal type homeobox 4 [Source:RefSeq peptide;Acc:NP_989945]
Coordinates
chr4:12070610-12074015:+
Coord C1 exon
chr4:12070610-12070755
Coord A exon
chr4:12070756-12073241
Coord C2 exon
chr4:12073242-12074015
Length
2486 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
CATCACTTATAACATTGCAGGTA
3' ss Score
6.95
Exon sequences
Seq C1 exon
GTAAAACAAGAACAAAAGAGAAGTACCGGGTTGTTTACACAGACCATCAGAGACTAGAATTAGAGAAGGAATTTCACTGCAACAGATACATTACAATAAGGAGAAAGTCAGAACTTGCAGCAAACCTTGGACTATCTGAAAGACAG
Seq A exon
GTACCCAGAGACTAACCATCGCCTGCACCCCTTCACCAGACACGGCTGCTGTCAGAAGATACAAACAGCATTCTTGTTCTGTATGTAAAAGTAGTGCCAGGGCAACCATGATAGTTTGCAAGTATATTAGCACACAGTGAATACACCACACGATTACAAATTAATGCATAGATTAATTTGACAGAAATCAGGTAACTAAGCATTAGGTGTTCATCTATAATAGAAGTATGGAAAAGTAGTTATTTTTACTTGCAAAACAGCTTGCTAAGGCAGCTAGGAATTAAACAATTTGGCTTAACATTCTCTTAGCTAAGTCCTCAATTGTTATGACACGCTCCATTTTATTTTAGCATGTGTTAAGGAGATTTCACAGGCAATTTTCAAGTTAGGATTTCATTTGGCTGTCATATTCACAGGTACTACAAACACCTATTATGTACAGGAAGCTTTAGGCTGTGAAATTTGGTGCCAAATTTTTATACCCATCATACACGTAATAGACTATCTGCTCAGAAAATGTTCAAGTGCATGCTTAGATCAATTGCCTACTCGGAAAGCACCTCTGCATTCCAGTTAAGTATATAATTAAGCACTGTCCTGAATAAAGACAGCCTCCTGAGCTATCCTAGTTGTGTTCATACAAAGGTTAGAGGGATTCAGGAGTTTTCCCTAGAATCACTGTGTTGGAGCGCGCATCTATGAAATGCCTGCAAATGTAGCAACTGTTGCATCCAGTCCTCCTTATGTAACAATTTCAGTGGTTCTGCTACAGTTGGAAGATAAGGGAAGATTGGCGGTACTGAATAAAGCAGCTCATACCTTAGCAACCAGACTTACTGCCCCCAGGTAAATTTAAGTAAGAGACCTTTCTTTTTAGAATTTTACAAACTATTGTTTGTATACATACTCAGACCTTTAAAATATCCTCCTCTTTTGCATTCAGTCTGTGCAAGGACATGGAACAGAGAGGGATCACTTGAGGCTTGGAAGTATGAGTAGGCAAGCAATAAGGATGAGTAGGCAAGCAATAAGGATTTTAGACTCCAGCACTGGGTTTTTAGAATCATCCTGTAGTGCAGCAGTGTTCAGTCTCAAAAACCAAACAGCATGCAGACTACACTCCAGAGACTATAAACCAGATTGGATATTAGGAAAAAGTTCTACACTGAGAGAATGGTTGGGTACTCACAGCATGAGGCAGTGGTCACAGCACCAATACGCCATTGGACAATGATCGCAGGCACTGTTTAAGTTTTAGGTAGTCCTGCATGGAGCTGGGAGTTGTACTTGATGATCATTGTGGGTCCCTTCCAACTCGGGATATTCAATGGTTTGCTAAGCAGCTCTGGGTAGTAACTAAGAAAACAAGTCCACCACCGAAGAACTTCAGTTTGTCATGCACTACGATATAGCTCCATTGCACAATTTTCTGAGAACTGCAGTTATAGAAAATTCAACTGCCCTGTTCTAATGTTACAAGTTGGCTGATTGAGAATACAGACATACCTGGAATAACCAGTGATTCTGCACAAAACCAACTGTTAGTTTTATCTAACTGTTGCTCTTCTCTTAAAGCCATCCAATTTTTGATTGGTAAATTTTCTTCAGGTAAGATGTAATCAAAACATGATCTATAAGCTGCTGACACAGCTAAATGTATCTTGCTGTCATTACCTGTAAGGTAATAATGAAATAACTACTTGGAAAATAATAGATTACCTACAGCAAAGGTAGACCTTTCTATATAGTACTGTATTCAGTGTACCTCAAAGGATGTAAAAAAAAAAAAAACAGTGAAGTCAGAACAGGAAACATTAAGGAAAACAAATGGAGTTTTCTGCTCATTTACACCCTCACAAAAGGAAAAAAAAAATAGATACTTAACTAAAATTGGGTTTCACATAGATATGAGTCTTTCAGTATAAACAATTAGTTTGAAATTGACTGTCCTCAAATAGCACTGACATAGCTGTACACAGGACATACCAGAGAACCACAGAATCAGATGCCTATTAAAAAATTAAAAACAAAAGATATGCATCCATACACAAATCATGATAGAAGAAAATGCACTCTCACTATTTAGGTTTGAATTAATCTTTATCAGAGATGAAGAAGAAACCTTAAAAAGTTTTTTCTGATTGAATCTTCAAGTTTGGCACACGCTACTGTCCAAGTTTAGATGATGAACCACGTGGATGCTGAGTATAAGCGAGAAATCTGAATGCTATGTTCCTAAATAAAACACAGCAAGGTCAATTTACACCACATCTAAGAAAAGCAAATAATTCTCTATTGATTACGATACAGACAGTGAATACAGAGTAACTTCAGAATTTCCCACTGCACAAGTCCAGCACTGGTTTTTGGGAGTTGAACTCGGGGTGTTTATTTGTTTTGCTCACATTTATTTTTTTTGTTGCTACTTGTTGCTGTAAAAAGTTTGACTACTTTAAACTAATCAGACATCACTTATAACATTGCAG
Seq C2 exon
GTAAAAATCTGGTTCCAGAATCGCCGAGCCAAAGAAAGAAAAATAATCAAGAAGAAAATCTCTCAGTTTGATGGCAGTGGGGGCTCAGTTCAGAGTGACTCTGGTTCACTCAGCCCTAATGAAATAACAAGTTCCCTGTTCCCACCACCACACGGAATAAATGTATTACAGTCTGCTGACATCCATCAGGTCATAGTTTCAGAATGAACAGTGGGGGAAAAAGAAAAACAGAAAAAAGAGTTGTATGGATTTTTTGTTTTTGTTTTTAACTCCCTCTATTGAAAACTCAATTTTGCAAAGCACCATTCTTGTTTAACTACCTTCAGAGTACTTATTTCTACATAGAGGATCTGGAACTATTACCAAAATATTTCAATTAAAGAAATCTCAGGGAGTTCGTGCTGCTGCTAATACTCATCACTCAAAATCTTTTGAATAGAAGATAATTTACATCAGATACCGAAGCAGAAAAAGATACTGCTGAAGATTCAAGCAAACCTAATTCTAGTCTGCTCATGTATACAAAGAAAACTGTCAGTGAATTGATTATAGAGTAATACTGCATAAAATGTAAGATGCTGGATGTATTTAGTTTGTTACATTTTATATAATTAAACAGTAGATTTTATAAATATTCACATTTAATGTGTACTGAAAATTAAGTCATTTTTTGAAAACAACTTTTTAAACACTTAAACACTCAAGAGACATAACAATGTTACGCCTGGTGACACATTGCGTCCCATTAAATAAAATGAATAGTCTTTGTATTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007657:ENSGALT00000012401:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.245 A=NA C2=0.353
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(0.7=2.0),PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
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]