GgaINT0094722 @ galGal3
Intron Retention
Gene
ENSGALG00000017398 | F1NHU4_CHICK
Description
NA
Coordinates
chr2:109232784-109233454:+
Coord C1 exon
chr2:109232784-109232918
Coord A exon
chr2:109232919-109233268
Coord C2 exon
chr2:109233269-109233454
Length
350 bp
Sequences
Splice sites
5' ss Seq
TCCGTAAGT
5' ss Score
10.27
3' ss Seq
GTATTTATCTGTCATTCCAGTTT
3' ss Score
6.53
Exon sequences
Seq C1 exon
CAACACAGTAGTTACACTTTGGTTGTGAAGGCATCAGACCGGGATGGAGCAGCAGATGGAATTTCATCCCTTTGTAACTGTCATGTGAAAGTTATTGATGTCAATGACAACTTCCCAACTCTTGCTCAAAGCTCC
Seq A exon
GTAAGTTTTTAAAACCAAAAGCATCATGATCAGAAAGCAGCTTAGCAGAAATCCATTTCTGCTAAGCTGCCTCTGCAAATGTTTGGAGTGACACAGCTCTTTATACCTGCAATCAAAATCACAGTTTACACAGAACACACAGTTCTGTTCTGTTTTTGGTTTTTTTTTTTTTTTTTTTTTGTTTGTTTGTTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTTCGGTTTTTTTGTTTTTAATTAAATTTTAATTAATTTATTTATTCAATATTGACTGTGGACAGGACATTCTTAAATAAAATCTTCTGTGGTCAGCTGTGTTTGCTAATAAGTATTTATCTGTCATTCCAG
Seq C2 exon
TTTTCAGCAAGTATTTCAGAAAACTCACTCAGTTCAGAAATTCTACGAATACAAGCTCTGGATGCTGATGAAGAGTTTAGTGACAATTGGTTGGCAGAATTTTTCTTTATATCTGGTAATGAAGATAACTACTTTGAAATTGTTACAGATCCAGCTACAAATCAAGGAATCCTCAGAGTAATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000017398:ENSGALT00000036805:9
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=0.000
Domain overlap (PFAM):
C1:
PF0002812=Cadherin=PD(31.6=68.9)
A:
NA
C2:
PF0002812=Cadherin=PU(58.7=98.4)
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:
CAACACAGTAGTTACACTTTGGTTGT
R:
TGAGGATTCCTTGATTTGTAGCTGG
Band lengths:
310-660
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]