GgaINT0047789 @ galGal3
Intron Retention
Gene
ENSGALG00000009362 | ITA6_CHICK
Description
NA
Coordinates
chr7:19094350-19095983:-
Coord C1 exon
chr7:19095858-19095983
Coord A exon
chr7:19094480-19095857
Coord C2 exon
chr7:19094350-19094479
Length
1378 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
AATACCTTGCTTCCTTGTAGTGT
3' ss Score
7.39
Exon sequences
Seq C1 exon
GTGCGCGTTACTGTCTTTCCTGCAAAACCAGTAGCCCTTTATACAGGAGTGCCTTGGTGGATCATCGCAGTGGCTATTTTTGCTGGAGTACTGATGCTTGCACTCCTGGTATTCTTGTTATGGAAG
Seq A exon
GTAAGTTTTTACTTATTTCATTATTTCGTATTTCCTGGCATACAGGTGACAAGGTAGCAAACAATTAAGTATTTTTGCTTTGCATTTGGAACTGAAAACACAACAAAACAGCCCAAACTGTACATTACCTGCATCAGTTGCTCAATTTTGGAACGTTTGGCATGAAAATGGTCATAGAAGAAAACTCATTTCTATCCTTGATAGGAAATATTTCTGTTTCTAGATCCTCGAAAGGAAATGTTTGAAGCTTTGGCCAAAGCTCAAAACAGCTAGCCAGAGACTGTAGTTTACTTCATTACAGATGGATAATAACTGGGGCTGCTGCAGTTAGGTGTGAGACTTTGTGAACCTGTTCACAGATGTTTTAGCAGGGGTTTGTTTTCATGGTATTTCTAATGCTATTAAACTCAAGAGTAGATGGAAAAAAATACAACAAAAATAGCATTTTACCTGTGTGTTCAATTTCTTTTGTATGGGCTCCTTGTCTTAGAAACCCTGAAGGAGTAAATTCATATTTAAAAGCAAAAGTTAAGCATTTGCAAAAGAAAAAAAAAACAAGTACTTTTTAAAATGCCTTTGGTATTTTCGCAATTAACTGGTTCCAAGTAGAATAGGGTAGTTATTTTATTCTTATTACTTACTGGCTTCAGCAGTTAGTATAAGTTGATGGGGAGAGAAGACACTCATTTAGAAAGAGTGGGTGAAGAGGAATATCCTGTCACTTCCCTCAGAAGAAACTGGAGCAGGTGGCATTGTTGGACTTGCTGCTTGCTACAGATGACTTCTCATAGGACACTTGATTTCCTCCTTCTGATGAATTATCATTAACGTTTTGGATGGGCTGTTAGTTTACAACTGTTAGTCGTCTACTGCACATGAAAATGCTCTCATACACACTGTGAACTCCTCCTTCTGATGACAAAAAAATCATCTTATGAAAGACAAATGCTGTACATCATAGGCAATTAGGTGGCTGGGGATGAGACGTGCTCCTGTTGAACAGGTCAAAGCATTTACCATGTGCATAAATTGGTTTTTGTATAGAGATCTTGCTGCTCTTTACAGACAGCTTTAGTTGCTACAGACATGCTGTTTAAGTAGCTTTTCTTCAAAAAACAATGCATTAAAATTTTATCACAAAGCCTCTAAAATAATAATATTCCTTACACCCCAGGTTATTTTGCTCTTGCACAGAGTAAGTTAGTCCCAGAAGTTCTCAAATCTAGTAACAGCAGCTGACTTTTCTTGTGAAAACTTCCTAAAACTTCAGGCAACCAGCCTGTGAAGGGATTACGGAAAGGTTATTCTAGTCGGTTCTGATAGGTTTAACTCTTCTTCCGGTCCACTGAAATTGACTAAATACCTTGCTTCCTTGTAG
Seq C2 exon
TGTGGTTTCTTCAAAAGAAGTAAGAAAGATCATTACGATGCCACATATCACAAGGCTGAGATCCATGCTCAGCCATCTGATAAAGAGAGGCTTACTTCTGATGCGTAGTATTGATCTACTTCTGTAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009362:ENSGALT00000015247:23
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=0.114
Domain overlap (PFAM):
C1:
PF151761=LRR19-TM=PU(50.0=81.0),PF0035715=Integrin_alpha=PU(0.1=0.0)
A:
NA
C2:
PF151761=LRR19-TM=PD(47.1=88.9),PF0035715=Integrin_alpha=PD(86.7=36.1)
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:
CGCGTTACTGTCTTTCCTGCA
R:
ACAGAAGTAGATCAATACTACGCA
Band lengths:
248-1626
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]