GgaINT0101877 @ galGal3
Intron Retention
Gene
ENSGALG00000015140 | F1NJD7_CHICK
Description
NA
Coordinates
chr2:109114400-109116177:-
Coord C1 exon
chr2:109116035-109116177
Coord A exon
chr2:109114616-109116034
Coord C2 exon
chr2:109114400-109114615
Length
1419 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
CAATTATTTTTATCTCGTAGATG
3' ss Score
8.55
Exon sequences
Seq C1 exon
CTACAAAATACCACCTGGACAGTGTAACTGGGTCAATATTGATGAAAAATCAGGTGAAGTCAGAACTGTTAGAGTCTTGGACCGAGATCTAGGAGAAGTGAAACGAGGTCAATGCAATATCACAGTCCTCGCAATAGACAGAA
Seq A exon
GTGAGTACTAAATGCCGTCATCTTCATTTGTAGTTTGTAGAAGAATTTCTCATGCAAATTAACATAGCTACAGCTACATTGATTCAGACCAGATGTGCACTTAGTTTGTTTTCTTACTTTTGGGATGACTCTATCAAATGCTTAGGTAATATTATTACCCTTACACATCCAGTGGCAGGATTTATTTTTAGCCTTTCTGTGCTAAAACATCAGCTGGAATAAAAAGCATACCTTGAAGTTGCTTTACAGCTAGGTATCATGACTCTCTCCAAGGCTTGGATATTAAAATTACAGGTAAACCACACCAGTTTAAATTGCTTAGAGATTCTGTTGTATATAAAATAAGCATGCTATATTTCTACAATTCAGTATGTCCAGTGACACTTTTAAGAGGTAAATTTGATATAATTTCTCTGTAACACTTGTACAAGCATTGACTGTTCTTAGATTATAAAAAAAAAAAATCAGGTTAGGATAGATAGATACAGTTCTAACATGTAGGCTTTGGTGATAAAGTGCGCTTTACGGCTGAAAGAAGCATACCGTATCGGAAAACATTCGTGTATCCAGGGGAGGGAGAAATGTGTTGTAGGGAAGCATATTTTTCTTCCAGGAGCAAAAATACCAGAAGCCTTCCCTTTCTGCTTTTGTCTCTCAGTTTGTCATAGCCTCCTTTACCTTGTTTCTTTTACCCTTCTTTTCTCATCCTCCTGTTAGAGCAGTATATGTACGCACGTAAGATGCCCATGAACAACAAAATAAACTGTCCACACACAAAACATGGAACTTTGGGACATCTTAATTTGGTAGTACTCTTTCTGTTTGTACCAGTACACATTGGCGCAATTAACGATGACCAGATTTCACAGCTGAAAAGAAATATTTTCAAAGCAAGTCAAGGAATTTCTGTATGGCACCCTGAACTACATAAAAAGATGCACTTCATCTTAAAGGAGTTGATAATTCAGATTTTTATTTTTATATTTTTCCAGTGCGGACTTGAGAAATTGTCCTGTCTCACCCATCAGAGGGGACGAACTTGCAGTTGCAGACTTTCTTCTATCTGTTCCATCTTTCCTGTTTCTTTTCTCCCCTTTACCCACTTGAGGATAGCACATGAATGACACTGACTGTGGCAATTTTTTCTCTGTCACCAGAAAATAGAAGTTCCTTACCAATTCATTTACTCCTTACAAAGTTGTAAGTTGTATGATCAGCCAAGCAAAGACGGGAAGTGGCCAAAAAAAAATCTATGAGAAGGCCCTCTCTGCTTTAGGCCAAATCCATAGCTGCTTTTCACCTTACTTCCTAGCTTGGCTGTTACAGTTAATGATACTTCATTATGCAAATTAGGACTAGATATAAAGAAATGGATGAATATTACTATTAAATGATAAAACAATTATTTTTATCTCGTAG
Seq C2 exon
ATGGCAAAACAGGCACTGGAACCCTTCAAGTTGTCATCCAGCGTTGCGACAGGAATTATCTACGGATTCCTACAACTCAGTATACAATGTGCAGAGACAGAAAACCGATCTGTCTCAGTGTAGGGGATGGTGATGACACTTCTTACAGCATGCCCTTAGTCTATCGCGTGACTGACCGTAGCCTGGGTTCCATGTGGAAGATAACACAGCACAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015140:ENSGALT00000024430:10
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=FE(51.6=100)
A:
NA
C2:
PF0002812=Cadherin=PD(14.0=17.8)
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:
ACCACCTGGACAGTGTAACTG
R:
TGCTGTGTTATCTTCCACATGGA
Band lengths:
345-1764
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]