GgaINT0048437 @ galGal3
Intron Retention
Gene
ENSGALG00000012444 | AVR2A_CHICK
Description
NA
Coordinates
chr7:36161712-36163285:+
Coord C1 exon
chr7:36161712-36161821
Coord A exon
chr7:36161822-36163130
Coord C2 exon
chr7:36163131-36163285
Length
1309 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGT
5' ss Score
10.07
3' ss Seq
TTTTTTTTTATTCCCTTCAGCAA
3' ss Score
9.28
Exon sequences
Seq C1 exon
GAATGATTGCATAGAGAAAAAAGACAGCCCTGAAGTGTTCTTCTGTTGTTGTGAAGGCAACATGTGTAATGAACGCTTCTTCTATTTTCCAGAAATGGAGGTCACACAGC
Seq A exon
GTAAGTTGGTCTAACACATTGATAAAGAAACCATATAGCAGAGTTCAGAAATGCCTGATATTGTGCATGTATAGGAGATGAGGCTTTCCAAAATGTTACAGTCAGTTTTTCTATGCCAGAAGGTTTCTGTTTCTCTAAGTGATATAGAGCTGTATGCATTCACATAACAAACCTAGAAAGTTACCAGTTCTTTCCTTCAATTTTAAAAGCTACTAAAAAATAGTAATTTAAATGGATGAAATGCACTCAGCTCTTTTCTGAAGAAAGAATAATATGAAATAATTGGAATAATTGGCCATTTTAATATACTGGCTCTACTGTCAAATCTTACCTTAATTGTGTAGGTAAGCTTCTGTAAGCATTTATAAATTATTAGACTATAAGCAGTATCATCTTCATATGCACTTACCAGGCTAGGAATGCTCCTCTTCATGAAAAAATGTTAGCAGTATTTCTTTAAACTGATTGACACAGTAACGTTTAAAAATTTCAGGAGGATTTCTTCCTAAGTTACAGAGCACATCAGATAACCACACTTAACAAATTGTTTTAAGAAAACAGTAGCTAGAAGATTATTAGGCTATTCTTGAGTATCTTCTTCCAGCCAAGAATCTCATAATCTTTGTTGGAAGACTATCAGTGTTAATAAGTGAATTGAAAACAGCAAATGTCTTGTGCGCTGCATAGCCAGAGGAAGTTGTGATATTAAATAACATATATGTGAGATTGAAGTAATCTTTGGTGACCCAAGAGATGCTCCTGTCACTTTTGTCAGTGGTATTGCTAACACAATAATGGGCATTCTTCCTCGCTCTCTTTTGCCCCAGAAGTTCCTCTGGGGTCCTCCCTGAGACACTTAGGTAAGGTTCTTCAGCTAGAGGATTTTTACTTCCAGCAAATGAGCAGAGCCTCAATACGTTGGCAGATTATTTCTGGCCAGCACTACTTACTAATGATATCTTATTATTTACATTCCAAAGATTAAACGTCTGTATCGATTCTTTTTTCATTCATTTAGTGATGGCATTCTTACAGTCTTTTAAAATAAAAACATCTCTTACACAATGTAGATAGAGCAAGCATAGAAGCACAAAGCAGTTGGGTACACTAGCATGTAAGTCTGGGGGTCTGGGTTATCTCCACGTTTTCTGAAGTGCTGCCTTTCAAGTACACACATGTTTAATTATTAGACTATGCTACTTGATCAAGTGTTGTTAGCCTGTTGCACTGATTGCATGAAGTTTAGATCAGGATGATAGATTTTTCCATCAATGAATGAATGATGTACTTTTTTTTTTATTCCCTTCAG
Seq C2 exon
CAACTTCCAATCCAGTCACACCGAAGCCACCTCTATTCAATACCTTGCTTTATTCATTGGTGCCTATAATGGGAATTGCAGTGATTGTGCTCTTTTCATTTTGGATGTACAGACATCACAAGCTAGCATATCCTCCAGTACTTGTTCCAACCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012444:ENSGALT00000020344:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.048
Domain overlap (PFAM):
C1:
PF0106418=Activin_recp=PD(33.0=78.9)
A:
NA
C2:
NO
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:
AGACAGCCCTGAAGTGTTCTT
R:
TGGAACAAGTACTGGAGGATATGC
Band lengths:
238-1547
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]