GgaINT0048444 @ galGal3
Intron Retention
Gene
ENSGALG00000012444 | AVR2A_CHICK
Description
NA
Coordinates
chr7:36180802-36182504:+
Coord C1 exon
chr7:36180802-36180932
Coord A exon
chr7:36180933-36181938
Coord C2 exon
chr7:36181939-36182504
Length
1006 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
CTGCCTCTGTTTGCCCGCAGGGA
3' ss Score
13.11
Exon sequences
Seq C1 exon
GCCCAGTAGATGAGTACATGTTGCCATTTGAAGAAGAAATTGGCCAGCATCCTTCCCTTGAAGACATGCAGGAAGTTGTGGTTCATAAAAAGAAGAGACCTGTTTTAAGAGAGTGTTGGCAAAAGCATTCT
Seq A exon
GTAAGTAGTTCTTAGTGGTACTATATTTCAAGTATGAACGGTTCTCTTAAATGTTATAAGCAGACAAGTTTTTGTGGTGTCCAGCATTAAGTACTGCACCAGGTTCTGTCGTTATTTGAGTTTCAGGTAGTGTTAATCCCGTGTGGTGTTCACGTGGGTGTCTTTTAGCAAGAATTTAAGCACAGTAAAAATTAAATGGGTTTATGAACACCATAAAAAGTTCCCTCTCGTCTTGAGTGAATCGAAAGTACTTTTGGTTAAAGAAGAGATCCTTTGGTTTTATGTCTGAAATGAAAACATGCATGATAAAAATGAACGTTAAGAAATAATAGCCTTGATTTCCTCCAGGAAGGCTACGAGCAGTGCATGCAGTAACACAGGGTAAGCAGTGTCACGTGGGGAACTGCTGGGAGCCGTTAGGGAGGAGTAGCTTCTGTGAGTTGGCTTTTGGCTACAGACTTGCACTGATGTCGCTGTGCATTCCTCGCACTGTTTTATTTTGATTGGTTTTGTTTTGCTTTGTTTTCAAAAAATGGGTTATTGGAAACAATAGATGACAGTGTCTGCAAGGCAAATGTGTGCGCTGCCATCTGCTCCCTGTAATCAGCGCACTGCTGTATCGGCTCGGTGCTGCGCTGGAGAGAAATGAACCGCTGCCGGATGCAGATCCCCGTCTGTGCCGTTGGGTTTCATGTTGTCCCTGCACAGCTTCACCTCTCTGAGCGTGAGACCTTACGAAGTACCACAAGGACTCCCAGCAGACGGCAGCATGCTGTAGTGAAAAGCACCGGCTTGCTGTTGGCCTTATCACCAACGGCACAAACTAAACAAGGTGTAAGGTCCCGTGACGTGCTGGGTTTCAAAACAAATTTGGCGAAAGGGATAAAATGAGGCAGATGTATCTTAAACCCAGCGTGCTGCCGGGACTTCCAGGCAGCCCCCTGCACAGAGCTTGCTGAGCTCACGGCACGCTCCCTCACCTCTTCCTGCCTCTGTTTGCCCGCAG
Seq C2 exon
GGAATGGCGATGCTCTGTGAAACCATCGAGGAGTGCTGGGATCACGACGCAGAAGCCAGGCTGTCGGCGGGGTGCGTAGAAGAACGCATTATTCAGATGCAAAAATTAACTAACATTATAACAACAGAGGACATTGTGACTGTGGTCACGATGGTGACAAACGTTGACTTTCCTCCCAAAGAATCCAGTCTATGATAGTTGCACTGGTCACGTAACTGACCAACGGGACTCTTCACTGGAGCTGCTAAAGCTAACGGGACTGCTGTCGTCGTTGTGTTCTGTGTGAAGCGACCGCGGGGTCTCTGGGAGCATCGTCAGGAGGTGTTTCCCTTTCTGCTCCCCCTCCTCCTCCCACACACGAATCCATGAGACTTTCTGCATTCCCTGCTTACGCCGGAAGGCCGCGTGCTGAGAGGTGGCAGTGGGCCGTTCAGGGCCTGAAGCGAAGAGCGGACCTGGACGGGCTAACGGAGCGTTTTAAAAACTGACATCAGATTTCTTAATAGCCGTCAGAAGAGACTAATTCCTTAAATGAACTACTGTTATTTTTTTTAAATCAAACATTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012444:ENSGALT00000020344:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.029
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(14.9=100)
A:
NA
C2:
PF0006920=Pkinase=PD(10.4=46.2)
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:
AAATTGGCCAGCATCCTTCCC
R:
GCAGTCCCGTTAGCTTTAGCA
Band lengths:
358-1364
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]