HsaINT0077282 @ hg19
Intron Retention
Gene
ENSG00000105997 | HOXA3
Description
homeobox A3 [Source:HGNC Symbol;Acc:5104]
Coordinates
chr7:27145809-27150379:-
Coord C1 exon
chr7:27149734-27150379
Coord A exon
chr7:27148340-27149733
Coord C2 exon
chr7:27145809-27148339
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
GCGAAAGCTGCGCTGGCGACAAGAGCCCGCCGGGGCAGGCTTCGTCCAAGCGCGCGCGCACGGCCTACACGAGCGCGCAGCTGGTGGAGCTGGAGAAAGAGTTCCACTTCAACCGCTACCTGTGCCGGCCGCGCCGGGTGGAGATGGCCAATCTGCTGAACCTCACTGAGCGCCAGATCAAGATCTGGTTCCAGAATCGCCGCATGAAGTACAAAAAGGATCAGAAGGGCAAGGGCATGCTAACGTCATCGGGGGGCCAGTCTCCAAGTCGCAGCCCCGTGCCCCCCGGAGCCGGTGGCTATCTGAACTCTATGCATTCGCTGGTCAACAGCGTCCCGTATGAGCCCCAGTCGCCCCCGCCCTTCTCCAAGCCCCCCCAGGGTACCTACGGGCTGCCCCCCGCCTCCTACCCTGCGTCCCTGCCCAGCTGCGCACCCCCGCCACCCCCACAGAAGCGCTACACGGCGGCAGGGGCGGGCGCAGGGGGCACCCCCGACTATGACCCGCACGCTCATGGCCTGCAGGGCAACGGCAGCTATGGGACCCCACACATACAGGGAAGCCCCGTCTTCGTGGGGGGCAGCTATGTGGAGCCCATGAGCAACTCCGGGCCAGCCCTCTTTGGTCTAACTCACCTCCCCCACGCTGCCTCGGGCGCCATGGACTATGGGGGTGCCGGGCCGCTGGGCAGCGGCCACCACCACGGGCCGGGGCCTGGGGAGCCGCACCCCACCTACACGGACCTTACCGGCCACCATCCTTCTCAGGGAAGAATTCAGGAAGCACCCAAGCTCACCCACCTGTGATAGTGGGCTTGGGGCTACGCGCCAGGAGAGTCTCCCCCCACCCACCTTTTTTCTTTGGTTGCTTTTTTTTTTTTTTTTTTTTAGGTTCTTCCTGCCCTTTCCTTCCTTCCTTTTCTCTCTTCTCCGCCCCGCACTCCGTTTCCCGGTTTCCCCCCTCGTTGGTAAGGCGTTTTTATAGTTTATGTGACGTAGCAATCTTGGTTGCTGGAATGGCTGTATCATAGCGATATTTATCTCTTCCTGCTCCTCGATAGGCCACTGGCCCTGCACCCTTTACCTTCTCCACTCTTTGATCAGAAACAGGGTATATGAACAAATTTTCTAGTCGAGTTTTCAATGTGAATTTGTTCTTACATTATGGCTCCCGAGGGGAAGCGATTACTTTTTTTAATTTTAAATTTTTTTTTTAATTGCACTTCTTGTAAAGAGTGAGAAAAAAAATCAAAGGCGCTTTGAAACAGGGGCTCTCTGTGCAAGGATGACTAAGTGTACGTCTTTCCGTGTGTGTATGCTGGTGAACAGTCAGATTTATTTATATTTTTTTGCAAGCATTGAATAATCTAAGTTTTAAATATTATTTATCCCCATCCGTTCGTATTTATATTAAAGAATTCTGTACCCTGATGGTTCAGAAGGGTTCTTGGGCCTTTTGTTCAATTGTGTATTGGCGTACTTAGAATTTTTTTTATTTGAAAGAGAAATATAATTCCTTTAAACGGTAACGATACAATAAAACCAGAGAAGATCCAGCTTTTGAAAACAGTGATTTAGGTTTGTAACATCCGGCAAAACTGAAAAAAAAAATCTGTAAACGCGAAAAATACTAGATTTGTTTTGAGAGTTCTTCATTCCTTGCTGCTCACATTCTGAGAAACAAAAAGAAATAAAGTTTTTATTCTGAATAATATCCGTGTTAAGAAGGGGTTCTTTGGCCGAAGACGTGGGTCTGCGTGGAATTCAGGCCGAGGCGAGCCGGCAGAGCAGGCCGGACGCAGCAGCCCTCTGGCTCCAGCATGGGGCCTGGCCAGGCTATTCGCCTGGAAGCTCGGCGAATTCTCAGGATGGCGGCTGGGGCTCCAGGCGGCTGCGGCAGCTCTGGTAACGCCGTGCGGCGGGCCAGCTGGGCTGCCCGGTTCCCAGCTGCTGCGGAGGCAGGCTGAGGGCGCAGGGGCTGCCGAGTGCTGTGCACGGAAGAAACAAAGACATCCCGGCCCAAGGCGCAGCGGGAGCGCACAGGTGCCCCGCGGCCCAGCCGGGGGATAACGCAGGGCGGTCTTCTGCTCCATGCTCTTCCTCGGGTCAAAGCGGACCAACTAACGCCTAAACCTCGGTATTAGCCAGCCGCGCAGAGGATGCCGAGCACTTTCCGGGAGCAATCGGACTCCTGGTCTCCTCCGGGGATGCTTCGCGGTCTGTTATCGCGTCAGGAGGAAAGAATTGCTCCAAAAATCTGCACGCGGAGCGAAACAGTTTGAAAGGGACTGAGGCTCACCCAGGTCTCCAGCAAACGGAGGACTGAACTGGGGAGAGTCACCCTGAGCCAGCCCTTCCCTGGACTGCCGGAATCCCAGCATTAGCTTCCTGCTGAATGTAGTATTTGGCATTCTCTGAATTTATTTCCTCTCCTTCCCCCACCCAGCTTTCTTTTTATGGCCCCAGGGGGAGGGGGAGAGAGCAAGGAGATCGGTATCTTTGTAATAAAACTGCAATTTTATAAATTTTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105997-HOXA3:NM_153631:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.878 A=NA C2=0.840
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)