GgaINT1014926 @ galGal4
Intron Retention
Gene
ENSGALG00000023414 | HMX2
Description
H6 family homeobox 2 [Source:HGNC Symbol;Acc:HGNC:5018]
Coordinates
chr6:31021291-31023370:+
Coord C1 exon
chr6:31021291-31021568
Coord A exon
chr6:31021569-31022463
Coord C2 exon
chr6:31022464-31023370
Length
895 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
GCGCTGTGGCTGTGTTGCAGGCA
3' ss Score
7.76
Exon sequences
Seq C1 exon
GATGAGCAGCAAGGAAGAGCAGAGCAAGTGCTGCCCGCCCGCTGCTCCCGGCTCCACCTTCACCATTCAGTCCATCCTGGGCAGCGGCAGCGCCGACGGCCCCCGGGAACCGGGCCCCAAGGCGGCCCCGTGGCCCCCCCGAGGTCGGAACCTCTCCCTTTCCTCTGACGAAGAGGAACCGAACGAGAGCTGGAAACACCGCGCCTGCTTCTGCCCCGAAGCCCACGGCCCCGCCGAGCCGTGCCGTAAGCAGCAGCCCCTCGGCTTCGCCCGTCTCG
Seq A exon
GTGAGTAACGCTGCCCCGACGGCGCGGCCGCACCTCGGGGCTGCCGGGTGTGAGCCGGCCTTGGCTGGAGGGGGGATGGATCTGCTGGAAAAACGGGGCGGCTTCGGTTTTTCTTCCCTATTTCCACCTCAGCAGGGTTCGTTCTCGCCCTGGCGAAGGGGCGAGTTTGGAGTGATAACGAACGTTCCCTTATCTCCTGCTTATTTACAACGCTCTGCTGAGGGAGAGAAAGATGTTTATTTTTAGCATTAGTTCTGATGAAACGGCGCGTGAAATGCGGTGCTGTAAAGCAAAATGCGCCGGCAGGAAAGCAGCACTGAGCCCGGTGCTCAGGTGCCTTTACTGTGACATATCACAGAATCATCACAGACTCATCGTTATAAAATCACAGAATCGGGGAATATCCCGAGCTGGGAGGGACCCTTAATGATCATCTTGTCCAACCCCCGGCTCCACGCAGGACCCCCCAAAACCCAGTCGCTGTGTCTGAGAGGGGTGTCCCGTTGCTCCCTGAGCTCCGGCAGCTCGGGGCCGTGCCCCCTGCCGTGGGGAGCTGTTCCGTGCCCATCACACTCTGGGGCCAAACCCTTTCCCTAACAGCCAACCTGGCCTTTCCCAACGAAGCTTCATGCTGTTCCTCGGGTGATATCCATTCGTCCGTCCATTTTTCCGCCCCTCCATCCACCTGTGCATCCCTCCATCTATCTGCTCGCTTGACCATCCAGCCCTCCCTCCATCACGCACCAACCCCTGACGCACACCCACCCTTAGCAAAAGCTTCTCCCACCCTCGCTGCCGTTTCCTGCCGCTTTCCCTCTCCTCCCGGCTCCCCGGAGCCGTCGGGGCCGCGCCGTCGGGAAGTGCCGGTGCGACCCGCGCTGTGGCTGTGTTGCAG
Seq C2 exon
GCAGCACCAAGGGCAGCGGAACGGCTGCGGGCGGAGCGGAGCGGCCCCCCTTCCTCTCGGCTTCCCCGCAGGACTTTAAGGAGGACAAGGAGAAGCCGCTGGGACCCCCCTCGCCCTCCTACGGGGACCGACAGCGCGACAGCGGGGACCGGCAGGCCGGGGCCGCCAAGAAGAAGACGCGCACGGTGTTCAGCCGCAGCCAGGTGTACCAGCTGGAATCCACCTTCGACATGAAACGCTACCTGAGCAGCTCGGAGAGGGCCTGCCTGGCCTCCAGCCTGCAGCTCACCGAGACCCAGGTGAAGACGTGGTTCCAGAACCGCCGCAACAAGTGGAAGCGGCAGCTCTCGGCCGAGCTGGAGGCGGCCAACATGGCCCACGCCTCGGCGCAGACTCTGGTGGGGATGCCGCTGGTGTTCAGAGACAATTCCCTCCTGCGGGTGCCGGTGCCGCGCTCCATCGCCTTCCCCGCTCCTCTCTACTACCCCGGCAGCAACCTCTCGGCCTTACCGCTCTACAACCTCTACAATAAGATCGAGTACTGAGAGCCCGCCCGCCCCGTCGGGGCTGGGAGCGGCCGCGCCTCCCGGCTTCGGCTCCGGGACCGCCTGCGGGACTTCGGGCCCGGGACTTCGGGATTCGGCTCTGGAGGTTCTGCTCCGGCTCCGAGGCGCCGGGTCCGGGGATTCGGGATTCGGGGTTCGGGGCCGCTTCCAGCGGCAATCCGGAGAGGTTTGGAACTGGATGGGGGGTGGGAGGGGTGAGGTCGGGCCTCCCCCTCCCCCGCCAGCGTTATTCTGCCACTTAGAAAAAGAAAAATTAAAATTAAAAAAAAAAAGAAAAGAAAAGAAGAAGAAGCAGCGCTATTTCAGATCTGTACATATTTTTAAAGGAAATAAAACGTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000023414:ENSGALT00000038675:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.871 A=NA C2=0.337
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=31.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
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:
CTGACGAAGAGGAACCGAACG
R:
GCGTTTCATGTCGAAGGTGGA
Band lengths:
353-1248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]