GgaINT0120021 @ galGal3
Intron Retention
Gene
ENSGALG00000016144 | F1NY88_CHICK
Description
NA
Coordinates
chr1:112394483-112396616:-
Coord C1 exon
chr1:112396442-112396616
Coord A exon
chr1:112394659-112396441
Coord C2 exon
chr1:112394483-112394658
Length
1783 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
ATTTGTTTTTTTTTCCATAGGCT
3' ss Score
11.62
Exon sequences
Seq C1 exon
AGTGCGGCCTGCCCACTAAAAGCACAGCTGTCATGAGCAGGATCGTGGGTGGCAGCATGGCGTCGCTGGGGCAGTGGCCGTGGCAGGTGAGCCTCCATGTGCAGGACACCCACGTCTGTGGAGGCTCCATCATCACCCGCGAGTGGCTGGTGACGGCGGCCCACTGTGTGGAGGG
Seq A exon
GTGAGTGTCTGTATTTCCTCATGTCTTCATGCTGCAGTGTAGTAAACCCCAAGCCAGTATTAACCGTAGATGTACATGTACCTACCCAGGGAACACTTTGTGTAGACATCAACGAGAAGGAAGGCTGGTATTTTGTCAATTTTTAACTTGGAAGCAGAAACTTAAAGCACAGTTAAGTGCATTTCTGTTTGAAGGCAGCTGCTTTTATTGGAGGGAAAACCCAGTAAGCAAAGACATTTTAACGGTTGGTTGAATCACAGTTTGAGGTTCAGCCAAGGGAAAATAACTTTGTCCTTAACCTTGAGAAAGGAATGTGAGCGTTTAGTTCTATGTGAAGATCTTATCCCTCCTGATTTCTAGTGTGTGCTCCATAATATGCAAAAGCTTTAGGAGTGGTGACCAAGGTGTGCCTGGGTTTTAAGATTCAGGTTAAATTGGTATTTTTGCAAAGTGGTTGTCAGTTCCAGGGGAGGGATTTTTAACACATGTAGAAAGTCCTTTACAGAGCATGTGGAAATTGTTCGGGAGCACAGAGACTGCTTAAATTACATCTAGTGAGTATGCCTAATGTTAAAAACTAACCAACCAGCCTCCTAGCATTTTCAAGATAAGGAAATTCCTTCACTAGATTATGTTTTTGCTAATTCTGGTTTCTGCTGCCCTCCCATGCTTTGGATAGCACACGAGTGGTAACACTGACATATGAGACTTCAGAAATTACACCTTGATCCCTCAGTTGCTGAAATCAATAAAGAGGCTTCAGTGTTCCAGTCTCAGGCTATAATTTGCAGTGCTGAGTGACTAAGGGGATAGACAGTGATACATAACTTACTTCAAATAATTTTGCATATTTATGAAACTAGAGTCAAGCTCTCCTGAAGTTAGATGGCCTGTACTTTGTCTTTCAGGAAGAAAAACACAAACAACTAAAAAACCTTGTGGTCAGTTTTTGATTAAATTAGCTCTCTTCTATACTATTTGTCCATTTCACTAGTTTTTATTTGTATGGGACACAGGTATCTGAACAATGATTTTTCCCTAGATTTTTTTTTTTTTGACATGTTAATACATTTGCATTACAGTAATTTCATGCTGCTGAAGTTGACTGGCGGAGGGAGGCTGGCCAAAAATAAAGAAGGCATGAGTTACTGTTTGCTTTTGCCTTCAGAAGCGGCAGTCAAATATGTATGCATTCTTGGTCATGGATAGTAAAGACAATTCTTTGAAGGTTGAGTACTGTACTCCAGGTGCAAGAGAGACAGGGATCTCCTGGAGAGTCCAGTGGAAGGCCACAAAGATGATAAAGGGCCTGGAGCATCTCCTGTATGAGGAAAGGCTGAGCGACCTGGGTCTGTTCAGCCTTGAGAAGGCTCAGAGGGGATCTGATCAATGTTTATAAATATCTTAAGTGTGGGAGTCAAAGAGGCATGGCCAAGCTCTTTTCAGCGGTCTGTGGGGACAGAACAAGGGGAAATGGCCATAAACTGGAGCATAGGAAGTTCCACACCTATATGCAAAGGAACTTCTTCACAGTAAGGGTGATGGAGCACTGGAAGAGGCTGCCCAGGGAGGGTGTGGATTCTCCTTCTCTGGAGATATTCAAGACCCACCTGGATGCCTACCTGTGCAGCCTGAGGCGGGGGGCCTGCTTTGCAGAGAGGCTGGACTTGATGATCTCTGGAGGTCCCTTCCAGCCCCTACAATTCTGTGATTCTGTGGCTCTTTAAGCTGAGTTTCTCTACCAGTGAAGCAAGCCTTCTAACATTTGTTTTTTTTTCCATAG
Seq C2 exon
GCTATTTTCTGACCCGTACATCTGGTCTGTTTATGCTGGGATTCTGAGTCAGAATGAGATGCACTCAAGGCCTGGATACAGAGTGCAAAAAATAATTTCCCATCCAAATTATGATACAGATTCTAAAGACAATGATGTCGCCCTTATGAAGTTAGAGACACCGCTGAGTTTTACTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016144:ENSGALT00000026003:8
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:
PF154941=SRCR_2=PD(5.2=8.5),PF0008921=Trypsin=PU(19.2=74.6)
A:
NA
C2:
PF0008921=Trypsin=FE(25.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCCACTAAAAGCACAGCT
R:
AGTAAAACTCAGCGGTGTCTCT
Band lengths:
342-2125
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]