HsaINT0077282 @ hg38
Intron Retention
Gene
ENSG00000105997 | HOXA3
Description
homeobox A3 [Source:HGNC Symbol;Acc:HGNC:5104]
Coordinates
chr7:27106184-27110760:-
Coord C1 exon
chr7:27110115-27110760
Coord A exon
chr7:27108721-27110114
Coord C2 exon
chr7:27106184-27108720
Length
1394 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TCCTCTCTCTGTCCTCGCAGGCG
3' ss Score
12.35
Exon sequences
Seq C1 exon
GTCTGCGCGGGGCGGCCATTGGCGGCGGAGTGTCACGTGACCGCGGGGGCGTGCCAATGTGCGCCCTCACGGGTGTCAAACCCCTGTCAGAGTGTGCGATCAAGATCGTGAAACAACGCGATGCAAAAAGCGACCTACTACGACAGCTCGGCGATCTACGGTGGCTACCCCTACCAGGCAGCCAACGGGTTCGCTTATAATGCCAATCAGCAGCCGTACCCGGCGTCCGCCGCTTTGGGCGCCGACGGCGAGTACCACCGACCCGCCTGCTCCCTCCAGTCTCCCTCCAGCGCCGGGGGCCACCCCAAGGCACACGAACTGAGTGAGGCGTGCCTGCGCACCCTGAGCGCCCCACCTAGCCAGCCTCCAAGCCTGGGAGAGCCGCCCCTGCACCCGCCGCCGCCCCAGGCCGCGCCCCCTGCCCCACAGCCGCCTCAGCCCGCACCTCAGCCCCCTGCACCTACCCCTGCCGCGCCCCCGCCTCCCTCTTCTGCCTCCCCTCCTCAGAATGCCAGCAACAACCCTACCCCTGCCAACGCGGCCAAGAGCCCCCTGCTCAACTCACCCACAGTGGCCAAACAAATCTTCCCCTGGATGAAAGAGTCTCGACAAAACACAAAGCAGAAAACCAGCAGCTCCAGCTCAG
Seq A exon
GTAAAGGAGTGCCTTCTGGAAGAGGGTCCTCTGGCCTGGCTCCTGGTCCCCAAGCTACTGCCCACGACATCCAGCACAGCCTAGGAGCGATGGAGCATGTCTGGAATTCACTGCTCCCACACCACTGCCCACCAAAAAGGTTTTCATAGTCTTTGCAACTTAGGGAGGTGATAGGCCTCTGTAGGCTGGAAAACACCAGAGACCTGCTGGGAGTCCCTCTGGACTTCTCCAAGGGCAAGTAGGGTCTAGTGCAGTTGGAATCTCTTCTTGCTCCACTCTTGGAGTTAGGACCTCTGTGCAGAAACAACCTGAGCTCCACTGTCTATCTTTTTAGCACAGCTCTTCTAATGAAACAGTGACATCCTCCCCTTACTGAAATGTGGCAGAATAAAAACAGGCCTAATCACCCTCCAAGACAGAATCAATGCTTTGCCTATAATCAGAGCCAATTTTTGCTCCAGCAGATGGAGTGGCTGCCTTACCTCTGGGAAGACCCTACTCAGACTTAGTACAATGAAAGCAGCCAAAGATCTCCTGGGGGAGGGGGATGCAGACTTATCATCCTAATGGGAACCACATGGGCCTCCTGAAAGCGGGCTCCAGTAGAGGAAAGGCCCCAGGCTTTAGGCTTCCTAGCATTTTGGTTACCTTTGCCCCTGCCTTCTCCAGTTGCCAGTGCCCTGCTCTGAGCCTGAGCATCTGGGACTTCCAGAGCTAGGATCTGGGGGGCCAGGGAAGACAGAAGGGTACAAGATTAGTGGACAAAAGCTGGGGCTGGCTGCTTGATGACATAGGGAACCCTAAAGAATAGGACCTAGCATGAAGGGCCTAGGCCTCCCCACCAGAAATACCTTCAATGGGATCTCTTCTTTGGGCAGAGAAGGCCTTCCAGTTTGAGGTTTCCAGTCTGCCCATCTCCTCTGGGTAGAGAGAAAAAAGTGGCCAGTTGAAGCTACTGCCTAATTATTGTCAGACAGTGTGGGAGGGAAATGAGTGTGTACATTAGGTTTCCCACATTTCAGTTACTGTGAAGAGAATGGAGATGCTGAGACCGGCCCACAGGGAGGCTGTTGTCCGATAGGCCAAAGGGACCAGTAAATGAGTCAGAAAGTTAATAGCTCTAAACAGAAAATCCAGACCAGGAAGGCAAACCGGGGGTTCTACTTCTCTGTCCTTTCCCCCGAGAAGGCTGTGATTTGCTCCTTGGCTAAATGAGGGAGTATCACTGTTTTACCCACCAGGAGAGAGGATAGCACCTAGTTCCTACTTCTCTCTGGGACCTGACGGATGCAGGAACCTTTGGGGCCTGGTGGAAGGAGGGGCCGGGCTGGGTCAGGGGCTGGGCGGGGCCGCGGCAGCCCCTGACGCCGCTCTTCCTCTCTCTGTCCTCGCAG
Seq C2 exon
GCGAAAGCTGCGCTGGCGACAAGAGCCCGCCGGGGCAGGCTTCGTCCAAGCGCGCGCGCACGGCCTACACGAGCGCGCAGCTGGTGGAGCTGGAGAAAGAGTTCCACTTCAACCGCTACCTGTGCCGGCCGCGCCGGGTGGAGATGGCCAATCTGCTGAACCTCACTGAGCGCCAGATCAAGATCTGGTTCCAGAATCGCCGCATGAAGTACAAAAAGGATCAGAAGGGCAAGGGCATGCTAACGTCATCGGGGGGCCAGTCTCCAAGTCGCAGCCCCGTGCCCCCCGGAGCCGGTGGCTATCTGAACTCTATGCATTCGCTGGTCAACAGCGTCCCGTATGAGCCCCAGTCGCCCCCGCCCTTCTCCAAGCCCCCCCAGGGTACCTACGGGCTGCCCCCCGCCTCCTACCCTGCGTCCCTGCCCAGCTGCGCACCCCCGCCACCCCCACAGAAGCGCTACACGGCGGCAGGGGCGGGCGCAGGGGGCACCCCCGACTATGACCCGCACGCTCATGGCCTGCAGGGCAACGGCAGCTATGGGACCCCACACATACAGGGAAGCCCCGTCTTCGTGGGGGGCAGCTATGTGGAGCCCATGAGCAACTCCGGGCCAGCCCTCTTTGGTCTAACTCACCTCCCCCACGCTGCCTCGGGCGCCATGGACTATGGGGGTGCCGGGCCGCTGGGCAGCGGCCACCACCACGGGCCGGGGCCTGGGGAGCCGCACCCCACCTACACGGACCTTACCGGCCACCATCCTTCTCAGGGAAGAATTCAGGAAGCACCCAAGCTCACCCACCTGTGATAGTGGGCTTGGGGCTACGCGCCAGGAGAGTCTCCCCCCACCCACCTTTTTTCTTTGGTTGCTTTTTTTTTTTTTTTTTTTTAGGTTCTTCCTGCCCTTTCCTTCCTTCCTTTTCTCTCTTCTCCGCCCCGCACTCCGTTTCCCGGTTTCCCCCCTCGTTGGTAAGGCGTTTTTATAGTTTATGTGACGTAGCAATCTTGGTTGCTGGAATGGCTGTATCATAGCGATATTTATCTCTTCCTGCTCCTCGATAGGCCACTGGCCCTGCACCCTTTACCTTCTCCACTCTTTGATCAGAAACAGGGTATATGAACAAATTTTCTAGTCGAGTTTTCAATGTGAATTTGTTCTTACATTATGGCTCCCGAGGGGAAGCGATTACTTTTTTTAATTTTAAATTTTTTTTTTAATTGCACTTCTTGTAAAGAGTGAGAAAAAAAATCAAAGGCGCTTTGAAACAGGGGCTCTCTGTGCAAGGATGACTAAGTGTACGTCTTTCCGTGTGTGTATGCTGGTGAACAGTCAGATTTATTTATATTTTTTTGCAAGCATTGAATAATCTAAGTTTTAAATATTATTTATCCCCATCCGTTCGTATTTATATTAAAGAATTCTGTACCCTGATGGTTCAGAAGGGTTCTTGGGCCTTTTGTTCAATTGTGTATTGGCGTACTTAGAATTTTTTTTATTTGAAAGAGAAATATAATTCCTTTAAACGGTAACGATACAATAAAACCAGAGAAGATCCAGCTTTTGAAAACAGTGATTTAGGTTTGTAACATCCGGCAAAACTGAAAAAAAAAATCTGTAAACGCGAAAAATACTAGATTTGTTTTGAGAGTTCTTCATTCCTTGCTGCTCACATTCTGAGAAACAAAAAGAAATAAAGTTTTTATTCTGAATAATATCCGTGTTAAGAAGGGGTTCTTTGGCCGAAGACGTGGGTCTGCGTGGAATTCAGGCCGAGGCGAGCCGGCAGAGCAGGCCGGACGCAGCAGCCCTCTGGCTCCAGCATGGGGCCTGGCCAGGCTATTCGCCTGGAAGCTCGGCGAATTCTCAGGATGGCGGCTGGGGCTCCAGGCGGCTGCGGCAGCTCTGGTAACGCCGTGCGGCGGGCCAGCTGGGCTGCCCGGTTCCCAGCTGCTGCGGAGGCAGGCTGAGGGCGCAGGGGCTGCCGAGTGCTGTGCACGGAAGAAACAAAGACATCCCGGCCCAAGGCGCAGCGGGAGCGCACAGGTGCCCCGCGGCCCAGCCGGGGGATAACGCAGGGCGGTCTTCTGCTCCATGCTCTTCCTCGGGTCAAAGCGGACCAACTAACGCCTAAACCTCGGTATTAGCCAGCCGCGCAGAGGATGCCGAGCACTTTCCGGGAGCAATCGGACTCCTGGTCTCCTCCGGGGATGCTTCGCGGTCTGTTATCGCGTCAGGAGGAAAGAATTGCTCCAAAAATCTGCACGCGGAGCGAAACAGTTTGAAAGGGACTGAGGCTCACCCAGGTCTCCAGCAAACGGAGGACTGAACTGGGGAGAGTCACCCTGAGCCAGCCCTTCCCTGGACTGCCGGAATCCCAGCATTAGCTTCCTGCTGAATGTAGTATTTGGCATTCTCTGAATTTATTTCCTCTCCTTCCCCCACCCAGCTTTCTTTTTATGGCCCCAGGGGGAGGGGGAGAGAGCAAGGAGATCGGTATCTTTGTAATAAAACTGCAATTTTATAAATTTTTCATTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105997:ENST00000396352:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.869 A=NA C2=0.843
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=21.2),PF132931=DUF4074=WD(100=24.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCCAGCAACAACCCTACC
R:
TACTTCATGCGGCGATTCTGG
Band lengths:
350-1744
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development