HsaINT0077281 @ hg38
Intron Retention
Gene
ENSG00000105997 | HOXA3
Description
homeobox A3 [Source:HGNC Symbol;Acc:HGNC:5104]
Coordinates
chr7:27110115-27119595:-
Coord C1 exon
chr7:27119516-27119595
Coord A exon
chr7:27110761-27119515
Coord C2 exon
chr7:27110115-27110760
Length
8755 bp
Sequences
Splice sites
5' ss Seq
ACGGTACAA
5' ss Score
4.76
3' ss Seq
TGCGCTTCTCGCCCCACCAGGTC
3' ss Score
10.75
Exon sequences
Seq C1 exon
TCTCACTAGCCTCAGAGCACTCTCAGAAGTTCAGAAACTAAGACCAGAAAAGAGAAGATTTTTAGACAGCTCATGAAACG
Seq A exon
GTACAATGTTGAAATTAGTGGGCAATGTCATCAGGCAGAAGGCAGGAGTAGGGGTGGAACCAAGGGTGGGAGCAGCTTATTTGTTTCAGTTAGGTTCTTCCTGAGCACAGTTGGTTCTCTACTGGTTTTCTGCTCAAGATTATTTTGAGAGTTCTGAAGGGGGCTCTTTCTCATCTTTGAGTTGATATCTCTATAGGAACTTGTGTGGGGGTGGGGAGAGAATTTGCTGGTGGACACAGAATTGTCTTGGAAAAGTGGGTGGACAGACCTGCCTGTGGAGAGGGTCCCAGATTGCCTTGTTAACTTAAGGCACTCCAGTGAAGGTTGATTCTTTTTCTTTTTTTTCTTATTTTTTTTGGGGGGGGGGGTCTCTTGCAGAGCAATTAGATCATTTCCTCTGATATTTTTTATGTTTAGAAACTTATAATTCCATGTATCACTCAGTTGTGCACTGAGGAAATGCTTAAGTGCAAGTTTAGTCAGGGCACTAGGTTTCTCTAGATTTTGCAAAACCCGGACCCACCACTCTATAGCCAAGCACATCTTTCCTAGTGGGCTCCCACTGAACAAAACCAACTGGACTTGGAGGAGATGCTTTAACCTTTTGTCAGGTAATTATGTGCCTTTTTGGTGTTTCTTGCGTCTGTAGTGTATGGTGTGGGTGTTAGCAAACTCCATACAATGGCAGGCTGTGAGGAAGTCCGCTGTCCAGGCCAGTTATTTCTGGGCCTGCCCCTTGCCTTTTGATATACTGGCCTGTGGGCCAGAGGAGACTGGGGTGCATGGGTGTGCAGGATCCAGCTTGTCCGTGGGTGGGAGGCTGTAAGGAAAGTTAAATGGATTCTAAAAATGTGAATAGCATTGCTGTAACCCTTGTGTTTGGAGGGTGTGTAAAGAAATATAAGTGGAGATAAGCTTGTATGTCTTATATGGCATTCATGGGAGGATGGCTCCAAGCATCCTATTGCTTAGACAGAACTCTTAAACTCAAAACTGCTGGTCAAGGTTCCCCACCTACCCTCCCCCAAAGCTAAATATTCTGTTTGGAAACCTAGTTCCTTCAGTGGTTCCCTATTTCAAATAAAAGGATTTAAGTTGACGTATGACCACGTGAGCACATAATACAGCGCATTATTGTGGCATTTGGAGCGGAGACCCAGACAGGCTTCGCCTGTGATTACGTTTTCTAGATTCTCTACAGAGCCAGAGCTTTCCCCCAACCCCCACGCACCCACCTCCTCCTTCTCCTTCCCCTTCTCCGGAGAGCGCTCTCTGAGCCGATTGCAGTTTTCAGCACTCATGGAGCGGTTCTGGGCGAGCTAGCCGATGGAAGTCGAGGCTATACCAGGAGGATGGAATTTATTTTAAGGTATTTCCGCCGATTGTTCATATCTAGAGTGAGTTATGGCTGTGAGAGACAAAGGTCAGGCGAGGAGACCCTGGCTCATGGACAGGACCCTCAGCCTCTCTCTTCCTTTGTTTCTCTTTTAGAACCGAAACCATTTGAAAGATTCCCAGTAGCGCCTCAGACTCTGAATTTAATTCCCTGGAAAGTGTTGGGGGTGTAAAGGAGGGGGCACTAGGGGGGCTCCTAGGTGGGCCCAGTGGCCCCCAGTGCAAGGGTGGCTTTGTCCACTGCAGCAGGGCAGGGCTGGAGTCTCAGGAGCTGATCCCCAGGCGGAAAGAGGGTCCAGAAGCCAGGTGCAGGCAGAGGTGGACCGGCTTGCAGGGCTAGATTGCCTGGGAGGGGTGGGGGATGGGTGGGTGAGAAGGGGAATCTCTCCCAGGATGGCGGTGTTTTCAGGCAGGGGATGGAGGATTAGGGGCTGACCTGAGCAGCCGGAGCAGCTGGAAGAGGGAAATCGATGAGGGAAATGTGCAGATGCGCTGCCATTTTATTGATGATGCTTCCAGGCACTTTGTTTAGTGCCAGATTGCAGAGCATGCTTCCCCACAAGCCGGACCCAAGAAGCCAGACCCAAGGATCTGAACCGGAGGGCCCGCCATTGTTTCCCTGAGCACCCTCTGCCCCAGAGGGTTGAAGAAAGACAGCTCAGACCTAGGAGAGCCTTGGGGTGGGGTGAGCATGCTGGATGCCCAGGGGCTCCTTATTCTAACATTCGGGAGACAGAGGAAGGAGGGAGCCAGGATTAGGTTTGGACTTCATCAGTGCGCCTGGTCTGGGCATTCCTTGTGTACCCCCAGCTGGCTTGGAGAGTTCCAGAACTGGCCAGTGGGCCCTGGGTTGGAGGGAAGTCCAGAGACAAGAGTCCTCAGGAAGCAGAGGCAGACATCTCTCCAGCTTCAGAGCCTCCAAAACAGAGCTGTAGCCAGGGTGGAGGCAGATGAAAGTTAAACTGCATGTTTCCAGATTATTGGGAAAGCCCCAGCTAATTGGGCTTTGGGGACCCCACACTCCTGGGAAGGGTGGGAACTCCCTGGAAAGGTGCAGGAAACTCTATTATGCTCCTTGCAGTAGGGAAAGGGATGCTTATAAGGAGTCAGAGGTCGGATGTGCCCCTTTCACTTCTTAAAATATAGATTATTTCTTTCTGTACGTGAAAAAAAAATCAAATCAGGCATCCCCTACTTGAGTGGGATTTACTACCCCAGAACGAAAGGGCCCTTCTGCCCTCCCCAGTGCCGGCCTCGGCAGTAACCAAGTGTTTAACTGAGGCCCTTTCAAGTGCTCTAAAACACCCCTTGGAAATAAAATGTAAGCTTTAATTGCTGTTCAATTACTTGTCAGCATTTCATATGATTTATGACCTAGTTCTGGCGCATTTTTGACCCAGTTAAAGACTCATAAATAATATAGTTTTGCTAGAAAGAATGAGAGAGGGAATAGAGGTTTGTTAGAGGCATCTTTTTATTGTTGCTTCAGTGCCAGCAAGCTGAATAAATATCTAAGGATGGACTCTGGTTCTACATAAAAGCATGCACAGTGAGAAGCCAAGAGCCACATTTATAGAGCTCAGATTGGTTTTTCCTCCCATGAAAGTGCTAAAGTGAGTCCATTACGTATAATGCTAAACTATTAGATATCAAAAAAGGCTAGTCCCCTTCTACCTCGAAATGCCAGCTTCACCCTCACAGGCAAGTACATTTCCTCAATAATTTTCCTCTCTATTCTGTGATTTTGGTGCCTCTTCTTACCCACGATATTCCTCACCTTCCTCCCCGGCTGCACAGCCTTGGAACCGCCAGAGGCCCTCTCAGACGCCTTCAGGAGGACACCCCTTGAATGGTAGAAAGACACCACGGGCACCTTTGCTGCTCCAAGTATTCTTCTAGTGCTGAGAAAATCTTTTCTTCTAGTCCCCCTGGATGAGAGATCGGGAGCCACGGGGATTTGGGGGAATTGGTGGAACCAAGGGGTCCTCTCAGTAAAGAAAAGCTCTGCGGTTTTGGGGGAGCCGGGTGAACTGCTGTGGGATTTGTCTAGAAAGGGCGCAGCGGCGGCGGCTGGTAATTTCTGGAGGTGGAAATCAACAATCGGCATTTTCGCTTAAAAAACAAAACACCAATAGCAAACCAACAAATAAAAACCTTCCGCCAGCATAAATTATTATTTTAAAATAATCTCGCCTACGCTTGCTCCAAAGCCAGTCCTTTGGATTTAAGCAGAGCGGCTTGAGGCTGGGGCACCGACCATCTGCATGCCAGGACGCTGGACCTTCATCTTGAGGTCGGAGCCCCACTTCTGCCCGCTGAGGCCCGCGGCCCAGGAGCCACGTATCGGGGCGGATAGAGGCCCTGGCCGGAACGAAGCTCCCGCCCCAGATCTCCCTGGGCTCCCACGGCTCCTCAGGTCTGGTCCCCGCGTTTTGCCCGGCAGGGTCTTGGCGCCAGTGGAAAGGTATGCTTTCAGGGCGCCCCAGCCCTTGCTCGGGAGCCCTCGGTCCCCTTGGCCCAGAGAATCCCTTCCCCTGGCAGGTTCTTACGGAGAGCTGGCCTTCCCGGCAGCTGGCTTAGCTGAGAAGGCGGTGAGAGTCGCGTCAGCAGTTTGGAGGAGAAAGTGCGGGTTGATTATTGACCCACGCCTTCTTTCTTCAAATGCCACATCCGACCGGGCGGGTTTGAAGAGAAAATGCCGCCGAACGGATTTTTGCGGCTGGCTCTCACCTCCTACGCGGCCAGCTCCCCCTTTCAAGTTGCTCTGCAATATGCCATAAGGAGCAAGTGTTTGCTGTTTTGTGCTCTGTTTACAGCTTTGGGGCGCCGAGTCATAAATCTTGCCCAGCCATAAATGACAAAAACCATTGGTATGCATGAGGCCACCCTGGCCCGGAGTGCTTTTTGATTTCTCCCTTTTCCCCTGGCTTTGTTTTTGCTCTAAGGTGACACTTTGGCTCCTTGACAGTTTAAACATACTACTTATATTTTTAACACCTTCCTTTGAGAAGGACCCGCCGTTGACGCCTTGGGATTGCAGCAAAAGAGAGAAATCTCCATTTCTCTTTTTGCCACACTCGTACCCTTGCAGAGTTTGCTTCTGAAGCTGGGAGCAAAGGAGGCTTTAGGAGGAAAATCATCCACTTTCAAGTTGTGGCAATATTACCAGGCAAATTCGGACCTTTCTTTTGCCCAGCTCAGCGTTACTCCATCCCACTAATGAGGAAAATATGTATATACATATATATAATATATATTATATATATAATATATATTATATATATAATATATATTATATATATATGTATGTTTTAGGAATCCGTTTGAGAAACCACATATTCCTCTGCCCTGCGTGTGTGTGTGTGTGTGTGTGTGTATGATGTCGGTTTCTCTTGGGGTCAGAGCTTTCTCTGTCTTCCCTGTGGGTGAGCTGCGTGTCTGCACTCTGAAATGGGCACATGAGCCCTGGAGATCCGCGTTTCTAAACACCCTTGTTTGTACCTGAGCCCAGAGCATCCCATTTCACTGCTGGAACAAGTACCTGTCTCTCCCAGGACATTTTTCTCCTGGCTGCTAGGATGTCAGCAGTTTCTGCCTGAAAATTTAACCAAAGAGAGCCCAGTTGGCTCTTGAGGGTCTCTAGAGAAAAGCCTTATCCCAGCTCCCCACACCCCCACCCAAAGATCTGTTTGGGAGTTGCAGGTGAAGTAAACTGGGCAAAGTCTGGGAAACTCACTTTTCTTGGTTCTCTTTCCCCTCACCCCACAATTGGAAGTGTCCAGGGCAGAGGAATACGAAGTTTCTCAAACGAATTCCTAAGAAATAGAGCCCAGCAAGAGAGCCCCTTTGTGAGAGCCGTTTGTCCTCATTAGCATAATTTTCCTGGACTTTCGTGACGCCTGGGAGCAGGAGAGGGAGGGCGTTGGGGGGTGGGGGGAGGCTGCCCTCCTCCCGCCACCGCCGAGCTCCCCTTCTCCCTCCGGTCCCTCCCCTCGCCTCAGCCCCATCCCCCACACCAGCCCGCGCTTCCCCAGCCGCCTTGGTCTCCCCTCCCGCCCGCCCCAACACCCCCCACCGCACCCCCGGACCAGACGCTGCTCCGCGTGTAATATTCATAAGAAACATACCCAAGTCGGTGCCACTAGCCCAGGCAGAGCCCGGCGCCGCACTAGCGCTTATCTCCGGGCCGCGGCTGCTGCCCTCGGGAAGGGCAGGGGGCGGGGGTGTGGGGGAGGGGTGGGTGGGTGGGGTGGGTGGGAGGGGGGTCCAAGCCGCCCCAGTCGGCCCTGGGCGAGCCGTGCTGGAGCAGCGAGGCGGCCACGCTCTGCGCGGCGGTGACCGGGCCTCGGGGTCTCCAGCCCGCCTGCCATCTCGGCTGATGCTGAGGGTCCGTGCCCATCCCGCGCCGAGGGGACCCGGCCGGGCCGCCAAGCCAGGCCGGGGGCCAGAGCCCGTGTCGGAGCCTGAGCCCGAGCCTGCGCTCGTCAGAAGTTAAGGTAAGCAGGGCCGCAACCGGCCGCTCCCGGCGCTGAATGGCGGAGTTTACGTCTCGGTGATTTATGGCTGCAGACTTAAATCTCGGTTCAAGAAGAGTTCACAAGCCGGAGCTTCCTTCCCGGCAGTGACTGATACCCTTACACTTCGAGTTCAGGCCGCTTTCCCATCCCCGCCCCCACCTCTTGCCTCTCCCCTAGCCCAGCCTTAACTTTTCTGGGTTGCAGAGGGAAGGAGAGGTGGGCAGGGGACTCGGGGCTCCTATCCGACGAACCCGCTCAGATTTGGGGTGAGGGAAGGCTAAGAAAGAGGAGGGAATGGGAAGAGGGAGCGATGTCTGAAGGACGGAGGTTGAATTTGGGCACATCTTCCAGAGAGACAATAGGGCTTGCTTCTTGCACTCAATTTAGCCTCTTCAACTCTCTTTCGGCTCTTGCACCTGGGGATTATTGTCCAGAAACAGATCTTTGTGGAGGAATCTCCCCTCATCCCCAGCCCTTGCTTGGCGGTACAGAGCAAAGTTTCCTGGCTGGCAAATCTCCAACTTCTTTACTAGGTTGCAAACTTTGGGGGCTGGGTTGGGGTGGGGGGATGTATGAGCTCCAAGGTGGTGGTCTGCTGACCTCGAACAATAGGAAGGATTTTGGTGGGATCCCAGAATCGAATTTATATTTTAAGTTTACGAGGGCTGTTGTATGCTCTTTGATTTTCAAAGATATTTTTGTTATTTTGTAAGACAATGCACAACTTGATAAAAAGGCTTAACTAAGTAGCAGGCTGGTATAACGTGATAATGGATTAGCAAGTCACTAGAAATATTGCATGTGCAAAATCAGCTTAATTTTGTTTTATCTAATATCTTGCTGTTCGAGTGTCTAATTTTCTTAACCTGACATTTTATTTTACACAAGCCTGGTATCTAAAAAATTTGTAATGGCAGACATTGACACTGCCAAATGTAATAGGAACTGTTTTCAGTAAAAGAAAAGGAAACGGATACACTAAATTGCTATTCAGTTTTAAGTTTTACTTTATCCTTTATTTACTTTCAACCATGGTATGTGTAGCTTCCTATTTCCAAAAGAGAAACAATGCTCCAGGGCTCATGATCACTGACAATAACTCTGGATAAGCGATGCTGTAATTTTTAATCGAGGTTCTGGAAAATTAATTGTGCCTGTTTTGCAGATGTTGGTAAGATTGTTGGCTTAATAATGAAATCTAAAGGAGTCCATTATCAACAATGGAATTATAATCATCTACTGGTAGATGCAATACATTATCTTTTTTTTTCTAGTTAACAAAGCATCTAATATTCCTGGAAAACTTGAATAACTCTGGGACTCAATATACATAGTTGGATTGCATGTTAACCATTTTCTTTTGAATTTGTTATAATTTTCTTGAGTGGTCAGAGGGACTAAGATTCTGAGTGTGTGTGTGGGTGAATATTTGAAACTCACATGGAACTTTTCTGTGCTGAGAACTAGAGGTTGACCATGCAGTGGTTGAAAACAAAAAGAAAACAGATTTAACTTTTGCAAACTGCTTTCTAAATGAAAGAGGGTTGAGGAGGTTTTCAACTGCTTTTTAGATTTTCAGGGTTATCCTTTACTTGGTATTTCTGAAGCAGGTAAATAGGCCAAGTAACAAAATATCAACAACAACAACAGCACACAAAGATCAGGAAACTCTGGCAGGATTTTATGGCTTGTGCTTCCATCCCTCGTCGGGAGCCAAATGACCCCCATACATCAAATTACATAGCAGTTTCTAAGACAGAACCTATTATCGTTAAGTTGGAAGGAGAGTTCAAACTGTGGTCATGGAGATGAACGCTGGTTTTTCAGGTTCCTGGAGGGGTTTTTTTTCCCCCTCTAATCCATCATGTTTTAACAGGTAGAATTTGATAGTTGCCCCGAATAACAGCACCTTAGAAAGTCCAAGACAGGAGGTTCTGGGAACCTTCTGTAACTGGGGGAAAGAAGTAAAGAAGTGGGGGTGGCTTGCTGGGAAGTGCCTGAGAAACAGGGAGAGGAAAGGAGTAAAGAACTCTCCAGGATTTTAGTTGTGACTTGCTGGGTGGGGTGTTACTGTTGGTCCCTCACCCTAAACACACACACACACACACACACACACACGCAATGTGTTCCACACAAAGTTTTCCCTCCCCCCTTGGCTTGGCCACAAGGGGTTCATTTGGAGGAGGTGAGTCATATCCCCAACAAGGTGGATTAACTTCCTAACAAGCTCAGCTTCTGAAATCCAGCATGGTTGGATGGGGCAAATTGCCTGAAATTTTTTGTGCAAACCTCTCTTGGGAGCAGGAAGGTCCAAGAAGGAGCTGGGTGGGAAGTTACCCCATCTCAGGGCTCTTTTGGCAAACATCAGTCCTAAAGCGGAGAAAACATTGGCGACCCAAGCTCCCCTTTGCCTCCTCGTTCCCTTCCCAACATTCCCAGAGTGGAGGAGTCTTGGGCCCTCTGGAGGAGGCCAAGGAGCAGAAACTAAGCGACACCCCAAGTTTCTTCTTCCCTGGAAAAGAAAGATCCCAGCCTTTTTCCTTTCTAGCCTATCAAGCCTTTCTCCTTTTGGATCCCGGCTCCTGAGAATCAGCTTGCAGCCCTCACTCATTCTCCTTCTCCCCGGAAAATCCCCCAACTCCAGACGCAAGTTAAGCAAATATTTGTAGCTGCCAGTAAATTCCAGCGGTTTTTTATAGCACGGCTCCCTGCGCCCGGGGCCAAGTCGTGCTGCTAAATATTGCTGACCACTTTTTCTTTTATGGCTTTCATGTCACTTAGCTATTGAGAGTAAGATGGATTTGCGCGGAGCCCTCACCGCGCTGCGCTTCTCGCCCCACCAG
Seq C2 exon
GTCTGCGCGGGGCGGCCATTGGCGGCGGAGTGTCACGTGACCGCGGGGGCGTGCCAATGTGCGCCCTCACGGGTGTCAAACCCCTGTCAGAGTGTGCGATCAAGATCGTGAAACAACGCGATGCAAAAAGCGACCTACTACGACAGCTCGGCGATCTACGGTGGCTACCCCTACCAGGCAGCCAACGGGTTCGCTTATAATGCCAATCAGCAGCCGTACCCGGCGTCCGCCGCTTTGGGCGCCGACGGCGAGTACCACCGACCCGCCTGCTCCCTCCAGTCTCCCTCCAGCGCCGGGGGCCACCCCAAGGCACACGAACTGAGTGAGGCGTGCCTGCGCACCCTGAGCGCCCCACCTAGCCAGCCTCCAAGCCTGGGAGAGCCGCCCCTGCACCCGCCGCCGCCCCAGGCCGCGCCCCCTGCCCCACAGCCGCCTCAGCCCGCACCTCAGCCCCCTGCACCTACCCCTGCCGCGCCCCCGCCTCCCTCTTCTGCCTCCCCTCCTCAGAATGCCAGCAACAACCCTACCCCTGCCAACGCGGCCAAGAGCCCCCTGCTCAACTCACCCACAGTGGCCAAACAAATCTTCCCCTGGATGAAAGAGTCTCGACAAAACACAAAGCAGAAAACCAGCAGCTCCAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105997:ENST00000396352:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.869
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development