GgaINT0091739 @ galGal3
Intron Retention
Gene
ENSGALG00000011054 | HOXA3
Description
NA
Coordinates
chr2:32524754-32527430:-
Coord C1 exon
chr2:32526899-32527430
Coord A exon
chr2:32525524-32526898
Coord C2 exon
chr2:32524754-32525523
Length
1375 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
TCTTTGTGTGATTTACATAGGTG
3' ss Score
8.28
Exon sequences
Seq C1 exon
TATTCTCCAAGGGTGTCAAGACCCTGTCAGTTTGCGAAATAAATATTGGGAAACAACGAAATGCAAAAAGCGACCTACTACGACAGCTCTGCAATCTATGGTGCCTACCCCTACCAAGGAGCAAATGGTTTCACTTATAATGCGAGTCAGCAGCAATATCCTCCATCTTCGTCACTTGTGGAAACTGAGTACCACCGCCCCGCGTGCTCCCTCCAGTCCCCTGGCAGCGCCGTGTCCCACCACAAGGCCAATGACATCAGTGAGAGTTGCATGAGGACTCTCCCCAGCCAGCCTCTGCAGCCCCCTGGCCTCACCGACCCGCAGGCCCCGCCGCAGCCACCTCCAGCCCCGCAGGCACAGCCTCCACCTCCATCCTCGGCCTCACCATCTCAAAATGCCAGCAGCAACCCTGCCCCGGCCAACTCCACTAAGAGCCCGGCTCTTAACTCGCCCACCGTGTCCAAACAGATATTCCCGTGGATGAAAGAGTCTCGGCAAAACACAAAGCAGAAAAACAGCAGTTCCAGTTCAG
Seq A exon
GTATGGAACACGCTACTTTCACGTGTCCTCTGGGGAGGCCTGGGCACCTTTGCTTTTGGGAGGGAGTGGAGGGTTGGGGGCTTGCTTGCCTCCCTGAGCTGCCCCCACGGGCTTGTTGGCTTGCAGTGGGATCTCGGTGACCGAACAACCCCCTGGGATCTTTCTCAGCCTTGCAGGATGGATCCAGTGTGATTTGGTTTCCTTGCGGCTCAAGTGTGCTTGTGCCCTCCTACATCTATCACATTTCGTAGGTAATCCCCCATCCAGTAAATCACGCCAGTGCCGAGCAGCCCAGGCCCCGAGCCAGGGGCCTGTCCCGAGTACTTTGTTGGCACAGTGCTGCTAGATTAATAAGACAGTGACCTATCTCTGCTGAAGTGTAACGCGAATAAAACAGCTCATAATCATGTGCAGTTGGGATCAATGCCCTGTGTGCAGTCTGAACCTCTTCCTACTTTTACAGGCTGATTGGCAAAGTTACAAGACCGGTAAACAAAAGTCTTTGGGAATGCCATAAACTTTAGCCCGTGAAATATTATTTGAGGCATGGCAGCGTACATTAACACTTTTATTACTCAAGGAAACCCAAATCAGTAACACCAGTGCTAGCTCCAGTGCACAGGAGTTGTGTTTATATTTACCTCTTCCTCTTTTTCTCTTAAATGTGCTTTGGAAATAGAGTCCAAATCTTTAGCAAAGGTCTCTGCCACTGTACTTTTAAAGCTCTGATAATATTGCTGTTTACAGACTTCCACAGCATGTATTTATTTTATTAAAAAGCCATAACAGTTAAATATGCCTGTATGCAAGCACAGCTGCCATATGCTCTTCTGATGTGCATTATACTTCCCAATCACTACCATATGTTTATGTTGGATGTGCGAGAAACACTATACTGCCAATTCTATGCGTTACGACATTATATGTAGATATCTGACCTTCCGACATCTATAGCTTATGTGTGTATGACAGGGTTATCAGAAGAAGGGGCTGTAGGTCTCTATGGTTGTGGAGAACAGGTAGTTCTCAAAGGGTCTGAGCCTGGTATGTATGTGGAGCAATAGGTTCACCTTTAGAGTTTCTAAAAGCTGCTTTATTTCCCTGAACCTTTCTTATTCCTTTATGCAAAGCTCAAGGTATGTTGCGCCCCGTCTTTCTTTGTTGGAGCAAGTATAGCCATACAGTGGTACCAGTGAAGTAAAGGAAGCCTGCTGGGGCTTGGCTTGGCGTGGCTGAGCTCGTGCTGGGGTTACTTGGTGCACATGTGGGCATCTCATGTCCAAGAGCTGGGCAGATGTTGACATTATTGGGCACTGTCTCTGGTTGCCATGTCTAGGTTTACCATCTGATTGTGTTCTTTGTGTGATTTACATAG
Seq C2 exon
GTGAGAGCTGTGCTGGTGATAAGAGCCCCCCAGGGCAAGCATCCTCTAAGCGAGCCCGTACGGCTTACACAAGTGCCCAGCTGGTAGAACTGGAAAAGGAGTTCCACTTCAATAGATACCTTTGCAGGCCACGAAGGGTTGAGATGGCCAATTTGCTCAATCTCACAGAAAGACAGATCAAAATCTGGTTTCAGAACCGCAGAATGAAATACAAAAAGGATCAAAAGGGCAAGGGCATGATGACCTCTTCAGGAGGACAGTCCCCGAGCAGAAGCCCCGTCCCTCCAGCTGCTGGGGGATACCTAAACTCTATGCATTCTTTAGTAAACAGTGTCCCCTACGAGCCCCAGTCGCCTCCGCCATTTAATAAGCCTCATCAAAACACCTATGGCATCCCCGCATCGTATACCGCTCCTCTTAATAATTGCCCACCTCCTCAAAAGAGATACACGGGGACAGCAGCTGTGACACCTGAATACGATACTCATCCTCTTCAAGGCAACGGTTATGGGAATCCACATATACAGGGAAGCCCCGTCTACGTAGGGGGCAACTACGTGGAGACCATGACCAATTCCGGGCCTTCCATCTTTGGTCTAACTCATCTCTCTCATCCTCCCTCTGCCAACATGGACTACAGCGGGGCTGGGCCGATGGGCAACAATCACCACCACGGACCTTGCGACCCGCACCCGACATACACAGACCTTACAGCTCACCATCCTTCTCAGGGAAGAATTCAGGAAGCGCCCAAACTCACCCATCTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011054:ENSGALT00000018005:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.854 A=NA C2=0.832
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.2),PF132931=DUF4074=WD(100=24.9)
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:
CCACCACAAGGCCAATGACAT
R:
GCTTAGAGGATGCTTGCCCTG
Band lengths:
347-1722
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]