GgaINT1014924 @ galGal4
Intron Retention
Gene
ENSGALG00000015600 | HMX1
Description
Homeobox protein HMX1 [Source:UniProtKB/Swiss-Prot;Acc:Q9DE09]
Coordinates
chr4:80975027-80978215:-
Coord C1 exon
chr4:80977378-80978215
Coord A exon
chr4:80975736-80977377
Coord C2 exon
chr4:80975027-80975735
Length
1642 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TGCTGTGCCTCTCTCCGCAGCCA
3' ss Score
11.69
Exon sequences
Seq C1 exon
CTGCTGCCCGTGTGCCGGGGCCGGCACCGCCGCTCCCCCCGCGCCGGGATTTGCTCCCTAATTGACCTAAATAAGGAGCTCGTGAGTGGCAGCCCCGGGGCGGCGCGCACACGGACACACGCACACACACACAGCAGCGCCCGACCCCGGCCCCGCTCAGCCATCGCCCTGCTCTTCCCCTGCGGAAATCCCATTTGCCGCCGCTCTCCTCCAATCGCAGGATCCCCCCCTCTCGTGTACAGCGTTTAACTCGCATGACATTTTTATTTCGTTATTATCGTTTTCGCGCAGAATCTGGCGCCTCCGATGGGTTGTCGGGTTGCTTTTTTTTTTTCTTTTTTTTTTTCTTTCTTTTTTTTTTCTTCCCCATTCCCTTCCCTTCCTCCTCCTCCCCCCTCCCCTCCTAGCTTGCAGGAAATGATGGCAAACCGCGATCTGAAATGATTACTCCGGAAAAAAACCCTTTTATACCAGGAGAGCATCCACGGGGCTAAGCAGAGGCAGGAGGCGGCCGCGGGGCAGCGGGGAGCCGAGGAGCCATCCTCCGGCGGAGCCGGGACCCCCCCTCCCGCAGCTGTTTTATCGACGATGCCGGACGAAGCGACGGAAAACGCCGGCTCCACATCTGCCCGCGTCTCGTCCTTTTTCATCGAGGACCTGCTGGGCACCGAAGGCGGCGGAGGGACGCGGAGGGCGGCGGCGGGAGGCGGAGGTGGGCGCGGAGCTCCGCGCTGCGGCCCCCACTCCCCGCTGCGCCTCGGAGCCTCGGGCTGCCCGCTCCGCGACGCCGCCGTCGGTTGGTACCGTCGAGCTTTCTTGGGCTGCGCCAGCCCCGACA
Seq A exon
GTAAGTTCCCTTTCCCTACGGGGCCCTGAAGGAGATGGGGGGTGCTGCTGACCCCTCCCAGGGTGTCCGGTCCCGTCGCGGTCCCGAGTAGGGAGGGAGAGTGGTGCTGCCGGGGTGTCCTTCGCAGCCTTCACCCCTATTCTGTCCGGAGATTTCGGCTGCCCAAATTTCCGGAAATGCTCTCAGGGTGTTGGACACCTGGAGAGCCTCCGCCCCGCCTGCTGCTCGTCCCGAAATGTCAGCAGCGGGGGCTGTTCTCTCCCTTGGATTGTTCTCTCTCTTTTTCCTTTATTTCTTCCTATCCTTTTTTCTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCTTTTCTTTCCTGCTTTACGCTTCCCAGTAACCTCGAAAGCCGGGATCACCGTCCTTGTAGAAGAGTTCTGAGGCAGCCCTCTATAGCACCGGCCCTATAGCACCGTCCCCTCGGTGCAACCGAGGCCCCGCAGCCCTTTCCCCACCGCTCTCCGCGCACTGCGGGGCTCCGCAGGGAGAGGCTTCTCCTCCCACCCGTCTCCGGGGCACAAATTAACGTCTGAAAAAGTTTACAGGCTGCGATCAGCGGTTATTTTTATCCTGATAGAAAAAATATTGTCCATCGGAGCATCACTTTGATTCCGTGCTAGTCTATGGGGTTTGCACGCTTACTGAGTACTTAGTAGAGGCGTGATGTATAATCCAGAGGTTTTCTTTTACAGGGATGGGTTTATTTATATTCTTAATTTCTCTCTCAAATACGTCTAGAAAGAGAAAATAACCACCAAAACAACTGCTCGGTTTTCCTCACTTCTTTTTCTGTCTTTCTTTCTGCCTTCTGTTCTATAAATATTAGGATTTTTTCCCCCTTTAGAACTCCAACTGCAAAACACACTGTGGGAAACCACGGAGACGTGCTGGAGGCAATGTCCCGATATTAGAGCAGCTGATCCCATCGATGTGGTTTATGCAGCTGAGAATAACATGAAGCGAAAGCATTTGTTTTCCCCCTCTCTTCATACACACGCACTCACTGATATACTTACCTCATCTATACACACCCCAACATAGTTACATACGTTCTTGTAAACATATGTGTACATATGTGTGTAAATACATTGGTATATGTGTGTAAATATATACACGTGAGTGTATAAATGTGCAAGCACATAAGCGCATATGTATAAGTATATATATACATACATTAATATATACGTGTGTATATAAATGGACATGTTTATGCTGTATATACATGTGTACAAAACATATAAAGTGCACAGATGTTATATACGTGCATATATATCAGCGTATATGGATGTTATATACATACATATGAATATAGGTATGTGCGCATAGGTATATGCATGCACATAGGTATGTATGCACACATATATGAGTATGCACTTACACATGTGTATATGCATGACATATATTTTACGTATTTACTTGCCAGTATGTGCGTGAGTGTATGAACTCGCCTCTATATGGGAGTCCTTCACAACGCAAGGAGCACTGGCAGCGTCCTCAGCCCCGGGATCGCTGCCTCCGCACCGCGTTGTTTCCCCTTCCCATGCCCGGGCGGGGGGAGCCGCTCCTCGGAGCTCCCCCAACCCCATTGCTGTGCCTCTCTCCGCAG
Seq C2 exon
CCAGCGACCGGGACTCGCCGGAGCTGCCCGAGGACACGGAGCGGGCGGGCGGCGGCGGGCGGGCGGCGGCGCGGGGCCCCGCGGGCGGGAGGCAGAGCTCCGGAGGCCGCGAGGAAGAGGAGGAACGCGGCGAGGAAGCGGGCGAAGCGGAGCAGCGAGCCGCCGGCCGCAAGAAGAAGACGCGCACGGTGTTCAGCCGCAGCCAGGTCTTCCAGCTGGAGTCCACCTTCGACGTGAAGCGCTACCTGAGCAGCTCCGAGAGGGCCGGCCTGGCCGCCTCGCTGCACCTCACCGAGACGCAGGTGAAGATTTGGTTCCAGAACCGCCGCAACAAGTGGAAGCGGCAGCTCGCCGCCGACCTGGAGGCGGCCAACCTCTCACACGCCGCCCAAAGGATTGTGCGGGTCCCCATTTTGTACCACGAGAACTCGCCGGCCAGCGCCTTGGGCTTCGGCCTGCCCCACATGTCCCCCCCCTTGGTGGGCTTCTCCGGCGGCGTCAGTTACCCCCTGGGCACCTTCCCCGCCGCCTCCCTTCCCTTCCTTCGCTCGCAGATGACGGGACTCGTCTGAGCGCCCACCTGTGTCGGGACCGCGGCCCCGAGCCCCCTCCCTTGGCTTCCAGCTTCACCCTCGGACTTTTTCTTTCCACTTTCACCATTTTCCGCTTTTAGACTTTTATTTAAAAAAAAAGGAAAAAAAAAAAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015600:ENSGALT00000025153:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.749 A=NA C2=0.338
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=29.8)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACCGTCGAGCTTTCTTGGG
R:
AAATCTTCACCTGCGTCTCGG
Band lengths:
350-1992
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]