GgaINT0048442 @ galGal3
Intron Retention
Gene
ENSGALG00000012444 | AVR2A_CHICK
Description
NA
Coordinates
chr7:36177346-36178856:+
Coord C1 exon
chr7:36177346-36177460
Coord A exon
chr7:36177461-36178717
Coord C2 exon
chr7:36178718-36178856
Length
1257 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TTATGTTTGTGTCTCTCCAGGTT
3' ss Score
11.56
Exon sequences
Seq C1 exon
GGACATCAAAAGCAAGAATGTGCTGCTGAAAAACAACCTTACAGCTTGCATTGCTGATTTTGGTCTAGCTTTAAAGTTTGAGGCTGGAAAATCTGCAGGAGATACACATGGACAG
Seq A exon
GTAAAGACAGATTGTTTACCGAACAACGCAACTGTTACTGTGTGTGAACAGAAATTGATAGTTTGTACATTCTTCATGCAAAGGATGCTGTATTACCAACCCTATTTTTTGACCTTTAAGAGAGATGGCAACTCTGACCTTCTTCTCACAGAATGAACTGATATTGCTCAATTCTGTAAATAATTAAAGATCACAGCTTTTTGTCCTCTGCCCGTCTCACTGCTCGCCCCTTTCCTCCCATTTCACACTGATGGGCAGCTCAGCTCCACCTCACCACCCTCTCACTTCCCCGCTTCAAAAGTACAGGGGGAGAAAATACCACAGATAAAGGCCCATGGGTTGAGATAAGCACAGGGAGATCCCTCACCAACTCCCACCATGGGCAAAACAGACGCAGCACATGGAGATGAGTTTATTGCCTGTCCCTCTGCTGTGAATTCAGTGCTCACCATGCAACAGGGAACTGGCTTTGTATCGTGTACTTCTTAAATAACAAGCTTGAGCCTGGAGCGTTGTGGTTTCTGGAAAGCTAGATTTATTTCATTTGAGGCAGAATTTCAGGTTAGGGACAAAAATAAAATCCTTATGTTAGGATTAAAAAAACCTCAATGGCACTGTTTAAGAGAAGCATATCTATTATCGTGGGGGCTCAATGTTCAGACATTGTGTGAGCTCTGATTTATTCACGTTACATAATTGCATCGTTGGTTGTGGTCAGAATGAAGGGGTAGCCCCAGAGTTTCCATTTAACATCCAGATTTGCCTAAGTGTCTTCATATAACTTTCTAGGTTTCAGTTGGTTTCTCTCTGGTATCATTACTTCTCCTGTCAGGGGGAGAGGCATAAGCCAGTTCTACATCTTTACGTGCAACTGTAATAATTCCCAAAAAATATATCAAAAATATCAGAAAATAAGACGAGTGGCCTTCCTGTAAGCTGGAAGGGAATAAGGAACAGAGGTGACAACTGCATTGAGTTATTTGTAGAGATTGTATTTCCTGATTTCCTGATTCATAAATATCCTTTGTAGGGCCAAGTGTAAAAGAGAAGCACAAAACCATTTCCTCTTATTCTAGAAGAATACAAGACACTTTCAAGATTTAGTTGTAAGCCAGGGTAGCCATAGCTGAGTTTCATCTTTGACAAAAGTTAGTGCTACTCTGCACTGTTTTTATCATAAGCACCATCTCAATAGAATGGTTACAGTGGGCATATTGGTTCCCAGTGTGCAATTTCGTTATGTTTGTGTCTCTCCAG
Seq C2 exon
GTTGGCACACGAAGGTACATGGCTCCTGAGGTACTAGAAGGTGCTATAAACTTCCAAAGGGATGCGTTTTTGAGAATAGACATGTATGCCATGGGCTTGGTCCTCTGGGAGCTGGCATCGCGCTGCACTGCCTCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012444:ENSGALT00000020344:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(13.1=100)
A:
NA
C2:
PF0006920=Pkinase=FE(15.9=100)
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:
GGACATCAAAAGCAAGAATGTGC
R:
CATCTGAGGCAGTGCAGCG
Band lengths:
254-1511
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]