GgaINT0018948 @ galGal4
Intron Retention
Gene
ENSGALG00000005679 | CDX-A
Description
Homeobox protein CDX-1 [Source:UniProtKB/Swiss-Prot;Acc:Q9DEB6]
Coordinates
chr13:12553550-12561961:-
Coord C1 exon
chr13:12561448-12561961
Coord A exon
chr13:12553696-12561447
Coord C2 exon
chr13:12553550-12553695
Length
7752 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGG
5' ss Score
9.63
3' ss Seq
CACTCTGCTCTCTCTGCCAGGCA
3' ss Score
9.81
Exon sequences
Seq C1 exon
GCTGCGTGACACCCAGCCGCTTCGGCACGGAGCGGCGCAGCGCGGTGCATCGGCACAGCATGAGCACAGAGCCAGGTGGAGAAGATGTATGTAGGCTATCTTTTGGATAAGGACACCAACATGTATCCCAGTCCCGTCCGGCATCCCAGCCTCAACCTCAACCCCCAGAACTACGTGCCGGGGCCACCCCAGTACTCGGACTTCGCCAGCTACCACCATGTGCCAGGGATTAACAACGACCCTCACCATGGGCAGCCCGCAGCCGCCTGGGGCTCACCCTACACCCCTGCCAAGGAGGACTGGCACTCATATGGCACCGCTGCCGCCTCCGCCGCCACCAACCCAGGGCAGTTTGGATTTAGCCCCCCGGATTTTAACCCCATGCAGCCCCATGCGGGCTCTGGACTCCTGCCTCCAGCCATCAGCAGCTCGGTGCCACAGCTGTCCCCTAATGCACAGAGGCGCACCCCGTACGAATGGATGAGGCGCAGTATTCCCAGCACCAGCAGCAGCG
Seq A exon
GTAAGGAAACCCCCAGCCCTACACCTGGGCTCCTTCCTCCACCTGGGAGCCCTCAGCTTGGAGTCCTGCAGGGCCGGATCCTGCTCTGGGACCTACCCCAATGGGGAGAGCTGTGGGGCTGGCGAGGTGGCATGGATTGAGGATGGGCATGGAGAGCATTGGTGTGCGGGTGACCCCGTTCTGCTGGCAGTCAGAATGAGAGCTCTGCTCTGCGTATGGGAAGTCCTTGTCATGGCCAGTCCAGGGTAGTCCAGGCTCATCGCCATGGTGGTGGGGTGCTCCTGTTGGAGCAGTGCTGTGCTGTGTGTGCAGGGTGCTGCAAGCAGTGCATGTGCACGGCACTCACTGTAAAGAATCAGTGAGTGCATACGGGCAGTACTGCGTGCTCAGGGTGCATGCAAGGTGCGGTGTGTCGGGGACGGTGCCACATGCAGGGTGTGTGTGGGTGCTCTGGGTGTTGCATGGCACACAGCGTATGCACAGCTCCTGTGTCTGGCACTGGGCAGCCATACTGTTCCCGTGCCCTATCTCCTGTCCCCATGTCCCATCCCCTGTTCCTCTGCCTTATCCCCCGTCCCCTGTCCCTGTATCCTGTCCCCGACCCCGGGGTCTTGTCCCTGCTGAACTCCTGACCCCGGCGGGGTGGGTGGGTGGAAGTGTCCGTGCCCCGCAGCCCTCCGCCCGTGGACGCCCCACTGCCCACTTCAAAGGCGGTGGGCAGTCCCCCCTTGGGGCCAGCCCAAATTGACACGGGCTTCGCTTTGTCATGGAGATGCCGCCGGCTCCTTTGGCATTGAGGCGAGGTTGGGGAGGGCCTTTGCCCTTTCATGTTCCCCTCCAGGGTTTCCAGCCCGACCGCAGTCCTCTCCGTCTCCCCCTTGTGCGGGGCTCCCTGTTTGAAAATGGTGTAAAATGCCTCATTTGTTGGCTTGCTTCTGGTTTCCTGGCATCGCTGCGTTGGGTTTTCCCCATGCATGGCGCTGGGGATGTGACAGCCAAGAGCTGCACGGAGACTGAGTGGTGCTGAAGGGTCTGGGCACGGCGATGCGCTGCGGTGCCCACATCCTCGCTGTCCTACCCCCTGCTCCTCTGCCCCATCCCCAGGCCCCATGCTCTGGAAATTGCATGGAAATTGCTGTGAGACTGTGCTGGATGCTGGGGTTGGGGTCATCCCGGTGGGAGCGGGGGTTGCGGTGGGGCTGAGCATCCCAGGAGGTGGAAAGCAGCGAGCTCTGCTCTGCAAGAAGGAGGGAGAGGCAGGATGGTATTTCCTGGTCCATTTTAAGCACTGAATATAACTCTTTAGGAAAATTGCCCCCCTCTCCTCATACGTGTTGAATGGGAGCCCACAGCTTCTGTGGGATTTGTAGGTCCAAACAGTTCGGTGTCTTCTGGGAAAGGTGGGAGGGAAAATGAAGGAGGGGGGGGAAATGTAAGGACACCTCTGGATGAAGGGAGTGAGACATAGCGAGGGCAGGAAGGTTCCCCTGCCTGAGTCACACAGCAATGGAGTGATTGAATTCTGGAAAAATCAGCCGTTGCGCAGTTTGTATCTCTTAGATTGAACGCACACAAAGGGACAAATGAGCCAGCTGTTGTCCCCTGCACGTGGAGGCAGAGAGGGCTGGCAGGAGCAAAACCCCCTTGGTTATATGGGACGCCTCTCTACAAACCCCCCCAGCCCTGAGGTTTCTGTCCATGGGACCGTGCAGCTGAATTCAAACCCACGGCGCCTGCCCAGGCTGCCTTTACATAAACCAGGAGGTGGGTTTGACACAGATAAGGGTGAAATGTTTTATTGGAATCAATAAACTGTACATTAATCAGGCTGGATGGGTTATACCCCTCTCCACGCTGTGGGAGTAGGAAATGAATGCGCGGGCTATAAATACGGAGAGCTCCATTGCGAGCGCTGTAAATCATCCGAGGGCTGTAAATTAAGGTTCCCTCTGTCTTCCCTTGTATAAACAGCCATCGGCCGCGGCGTGAAGGCGCTCGGAAGGAGCCTTGCCATGCTCAGAGGCAATGCAAGGCAGGGACGGAGCGTGCCGGGGGGTTCTGCCGGCGTGATGGAGAGCTGGGAGAAATCGATGAGAAATCTCCCAGTGACTCAGTGCGGAGTCAGACCTCATGGGGCGATGAGCTGATATAGCTGCTGCTAAGAACGTGCGTGCCTCACCCAGCAGAGCCAGCCACGGCACAGGGCAAAGCTCAGCCCAGGTAACGGATGCTCAAGTGCCCTAAATTGGGAAACAGGAGGAACAAGATGTCCCCGTGCCTCCTTTCTTCCCGAGCATCAGCCCTTTTTCTGCTCATAAAATCTTCACGAGCACAGTGTCAGACCCTCACGCTTCCTCCTTACTCGTAATTATTTGCAAACTTCCTTGTGAATGGCACCCCTGCTCTATAAAAAGCTCAGGAAGGCGCTGGAAACGGCAGCGCGCTGAACTTTGAAGTTCACCCCCCCCCCGCCCTCCGTCCTGCTCGTTAGCTATGTAAATGACGTGTGCAGCCTCCAGGTCACTAATGGACCCGGCTGCAGAGCTCTGTATCGCAAGGGAAAGTGTGCCCGGACATCCCTGGGGAGGTGAATGTGCATAGGGCAGTGCAGGGTGAGCAGCCGTGGTGGGAGCATCCCAGGGTGTGGATGCCTCAAACACGGGCAGAAGGCAATGTACTGAGCGTGCAGCTCTCCGCTCTGTTTCAGCTCTGTTTTCACTCTTTCTGGCTCAGTTTTCCAGCTCTGCTTGTTCAGCCCTAGGAAAGCTGCAGGAAACGTGAAATCCCCGTGAATGAGACACCAGGCCAGGGGAGGTTCGAGATGGGCGATGGGGGTGGCTGGAGGACCTGGTCCTGTTTTAGGGACACAGCTGCTCCCCGAGAAACCCTCTGCTCCCCTGGGTCACCTGGAGTGCTGCATGCCGCCGGGGGCCCTACTGGTCCTGTCCCCTTGAATTATTAACCCACAGCCTCCTGCTCCTGGCTTCTGCTGGGGTTTGCTGAGCGCTTAGCCTGCTGGCCAAGGTACAGGTGGTTCAAACTTCCTTAGGATTGACTTTCCTTGAACAAAAAGGGCTTCCCTGCGGGTACCTACGTGATGGGCTCTGCTGGTTAATACCCTGGGATTAGCTGAGGGACAATTAATGCTCTGGCCAATGGGCGGTGCTTCCTGCAGGAGACCCCTTCAAGGACGCCCACCTCAGTGCTGTTAGCTTTGCGATTCTCCTGGATAATGGGATGGCTCCTTCCCCTGCACTGAGCCCCATAGGGCTGTGAAGGGGCAGGGAATCCCAGTGCCCACCTGGGACCCCCGCTGTGCCACCGGCTTACTGTGGAACGGGATGGCAGCTCTGTGCCGTGGGTCTGGCTGTGGATCCACTCCACGCGGGCGATGCTCCGTGCTTGCAGCCCACACGTCCCTGCATTGCGGTCTTTGACCCAGCGCTGGAGCCCGGCTGGCGGCACTTGGCGAGGTGCTCATAAAACCAAGGAGCAGCCCCAGGAACGCACCGGTTGCCAAAATAAAGGCTTGAATCACTGCTCTGCTGAGAAACGCTCGTCCCAACACCCAACCTGGGGCTGCTGCTCCTTGGCCGGGGAGTGGGTCTGGGCCGGGGATGCTGAACAGAGCCAGACTGCCCCAGTGTGAGGTCTGCGGACCCGGCTCTTCCCTGCCTGCTCTGTTCCTTCTCAATCACTGCAGCCCTGGGTGCTGCTGTCCTGGTCCATGCTTCTCGGATTTGCACCCCAGAAGTGCAGAGTTTGATCCTCTGCGTGCGGAAGACTATAAAACCACTGGGAGCTGTGGTGCGGTTTTGTAACTGAAACATTCCCAGTGTGTGACATATCAAAGCCAAATGAGGTTTTATTGCCAGTGGGGTGGCACTGCTGCTTCCTCTGAGATCTTTGGCACCAGGAAGATCTCCCTGGCTTGGTTTGGTGTTGGCTGACAGCCCTGCGAGGAGCTGCCCTGGGGGCTGCAGGGCTGCCTGGGGGTGGTGGCCACGGTGAGCCCTTCCTGCAGCCCAGCATCTCAGCAGTGCCCATTTGTGCCACCTGGAGCAGGAGCTAGGGCAACCTGGGCAGGGCCACGGGGTGGGGGCTCAGCCAGCATCCCCTCCCTCTGCAGTGCGAGCAGAGGAGGGGCTGGGGTAGATCCTCTCACATGGCTTTGGAAACCCAGCAGTTGTCTAAATCCAAGGGAAAAGATCTTGGCAGGATCTCATGGAGGTGGGATGCCTTCTGGTCGACAACAATAAGGGGGTCCATGTGGCTGCAGTCCTCCATGCTACGTTGATTGCCCCATCCATCACACCACGCTTCCTGAGGTGGATGGGAAAGAGCTGAAAATATTGCATGGGAAGGGGAAGTGAAAACCCTCTGGTTCCCAGCAGGCAGGGGGAGCGGTGGGGCTTAGACTCCAACAGAGGGGTGAGCATAATGGAGATAGATCTTGGGGTGTTCAGAGTGTGCGTAGGGTGCTCAGGCTTTGGGGCTGCTATTTCCAGATGGTTTGGGAACAGTAACGTGTTCTGGGCTGTCTGAGCTGAGTATCAGCACGGTGTGGCTGTGGTCCCCTCTGCTCAGCAGAGGGAGCATTGACCTCTCTGTGCAGGCACAGCTGGAGCACATCTGGCTGCCAGATGATGGTGACCCAGCTAGGAGGGTCCTGAGTGCTGGGAACAGACCCCAGCCCTTGTCCCAGGGCTGCACCGTGCAGCATCGCTCTGCTGGCTGCAAAAGCAGTGGGAGCTGTGAGGGTGGAGAGGGAGTTGAGCTTCCCGTGGCTCTGACCCCGGGACTACACACTGATTTGGTGTTGCTTCTGTGCCTCAGTTTCCCCACCCATAGCATTGCCCAGGCTACCTTGGGCATAGGGGGACAAGGGGGGGAGATAGGGGGAAAGTTTTCATAGAGAATTTTCCTGGGAAGAAACGGCAAATAGGACTCTCATCCACAGTGTGTTCCATGCACTGCTCCCAGGCTGCTCGGGGCAACCCAGTCTTTCTGTGCCGGTCATGCAAAGAGCTGCTGGGCAGCAGGGCGTGCAGAGCCTCGGCTCCATCCCCACCAGCACCTCCCATGCTAAATGCCCTGCACAGTGCCTGGCACCCGTGTTGCCATGTGCCCGTGTCCCTGGGCCTGGGGGCCTCTGCAGCTGGCAGCGGCACGGCTCTCATCTCTCCAGCTCCACGGCCCCACTTGCTGTGCTCTGATCTGATCGGAGCCCTGATGGCTGCGGTGCTGCTCAGAATGGAGCCAGGGCTTGCAGCCACTGTAATTTTGAGCTGCTTTGACCTGTGAAATGGAGACCTTTGGGGAACAGCGTAGGATTATACTCTTGCCTGGTTTGATCCTAGCATTTGCTACAGCTGCCCTGCATCAGCCTCAAAACTCTACTGCCCATCTCTTTTAGGGGGTCTGTGTCTTGTTGAAAGCCATCCTTTAGACAGGTTAGGGCTGGAGAGGGTGAATTACAGCCCCATAACAGCCTCCATCATCCCACGGTGCCTTCCTATGCCTGTTTGTGACAGTAGCCCTGTGGGTGCAGAGCTGGAGACAGAGCGCACAGAGCTGGGGTTGGGTTTTCCCTTCTTCCCTCTGTTCTGGAGGGAGGGAAGCAATAATGCTGTGTCACTCAGGCTGCATGACCTCAACGTGGACACCTCAGAGATGCTGTAGTACTGTGGTCAAGGGCAGGGAACTCCTGTCTCCCTATCCTTGTCCCCATCCCCATCCCCAGGGCTGCCATGTGGAGCAGATCAGGGCGGGGGGTCTCCCTTAACGTGTTTGCGAGTGTGTGTGCACGCATACTCAGGAGTGTGTCCTTTGGGGCCTGTGCAGCACATTGAAGCTATTCCCTTATCTAATCATGGCTCAGGTGAGTGCTATTAGGGTTATACATTAACAGCAGTAACGATGCCCTCTCCCCAAGCTTTGGGCCCTGCCTTGATCCCAACGCTGGAATCCTTCCTTCTGGCCCCATGGATGGCTCAGTTTGGCTGCTTGAGATGTTCCTTTTGTCTTTGGAGGACAAGAAGGAGGAAGTTTGAACGTGTGCTGGGGCTGGAAGGTGCTGGCAGCAGGGGGACCCTTGTCCCATTCATGCTCCCACCCATGGCCCCTCCAACAGCCGTGGGCCGTGCCAGAGAGCTGGCACAGCCCCAACCCCAGACTGCCCCCATCCCACTGCTCCTCGAGATCCCTGCAGGCATTGGGGTCTTCCCCACAGGTCCCCACGAGGAGCCATGACGGCTCATCCCAAATTTCCTCTTTCCTTTCCCAGAGCCATAAAAGGGCCACCGAGGGCGAGCGAAGTGTAACCCAGCATTGATATTCAAGGTGGCCGCATTATTCATTGTCAATAGCATTTCTTGCAAGTCCCTTTCTTCTCCCTGTGAATCTCTCACAATGCATTCCTGAATTCAGCAAACATCACTGAAAACTGCCGTTAGCCAAGGCGAGGAAATCTCCATCTCTGGGTTGGCAGCGGGCAGAGCCTTTGCTCCCTGATATTTGCAATGGGCACCCAGGGCTGCACCGGGGTTCGCCAAGGACGAGCAACAAGGAGACAACAACAAAGCACGGGCGGTGATGGATCTATTTACGGCTGCAGCAGGAAATAATAATTCCTGCTAAAATTCCTGGCAGATGCAGTACCCACAGACCGCCTTGTTTCCTTACTCTTTAATTTTTTTTAACATTAGCTGTCAGTTCCATTGCGTTCCAGCTGTTTTTTCTTCCACCACGCAGTGGCATTTAAATTGCAATATCGCAAATAAGATCACTTTTCAGTCATTATCTCTTCAGAAAGGGTATTGCTTCCAAATGAAAAGGGAAAGAAAAAGGATTCACGTGTGAAAGAAGATATCTTGAGCCCTGGTTCTGGAGGATGCAGTTTTCAGCCCTATCTGTGGTGCAGCCTTGCTGTCCCCCCACCTCATCACATCATGGTATATGCACTGTGCTGGGGGCACGGGCAGGGCTGGACCACTGCTACCCGGTGCTGTTGCACACCGTGTTTTTCTAATAGGAAGCAGTGCTCTCGGCACCATGTGTTGGCTATCTTCTTGCTCAGGTGAAATGTGGGGCTCAATGGAGCTCTGACCATAGTTGAGGAGACCCAAGGGCAGATTCAGGCTGGTTATGGCCTGAAGCATTGCTGGCTATTGAGTCCATCACTGGGAATGTTTGTGCTTAATGTGGGCTCTCCCTGTCGTAGCTTTAATGGCTACACCATTCTTTTGTGAACACAGCGTGGAGACTATGAAAACCTCTCTTGGCAGAACAATACTGTCACTCCTGGGTTTTCCCTCTATTCCTGTCCTGATCTGTGTGCCTTCAATTGATGGCACTGTGGGTTTGGGCTCTGTGGCACAAAGCTGGGCTTCCTGCAGCCCTCTGGGCTGGACTTGTCCAGGCAGCGTGTCCTCCACCTGGGCTGCAGCTCTGCTCCTCCTGAGGTGATGATCATGGCACATGGGATGTGGAGACCACTATGTTGGGATGTTACTGAGTGCCTTCTTCCCTTCCTACCACGAACGGCCCTATCCCCTGCTGCTCTCCAGCATGGAAAAACACCCTGTTGCTACCCAGGATGGGTATCAAACCCCATAGGGGCCAAGGACTCATATCCTCTGGTCCCATGTTCCTCCAGAGCTCTCTGTGTGCTCATGCAGCTCCTCCATGCCATCAGCGATGCTCCTGTCCCCCAGCCCTCTTGTCTCACCCTCACTCTGCTCTCTCTGCCAG
Seq C2 exon
GCAAGACGAGGACAAAGGACAAGTACCGGGTGGTGTACACGGACCACCAACGCCTGGAGCTGGAGAAGGAATTTCACTACAGCCGCTACATCACCATCCGCCGTAAGGCCGAGCTGGCTGCTGCCCTGGGGCTCACTGAACGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005679:ENSGALT00000009108:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.785 A=NA C2=0.286
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=WD(100=91.7)
A:
NA
C2:
PF047317=Caudal_act=PD(0.1=0.0),PF0004624=Homeobox=PU(73.7=85.7)
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]