GgaINT0103077 @ galGal3
Intron Retention
Gene
ENSGALG00000019640 | F1NE14_CHICK
Description
NA
Coordinates
chr2:32579695-32581500:-
Coord C1 exon
chr2:32580912-32581500
Coord A exon
chr2:32579955-32580911
Coord C2 exon
chr2:32579695-32579954
Length
957 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TCCTCTCGCTCCCCCCGCAGATA
3' ss Score
13.04
Exon sequences
Seq C1 exon
CAGCCCCGAATTGCGGCGGGTCGGGCGCCCGCGCCGCGCCGCGCCATGTCGGCCCCCGGGACCCTCAGCAACTACTACGTGGACTCCTTCCTGGTGCCGGAGGGGGACGAGCTGGCGGCCCCCCGCTACGCCCCCGCGCCGCTGGGGCCGCCGCCGCGCCCGGCGCTGGCCGAGCACCCCGAGCTGACCCCCTGCAGCTTCCAGCCCAAGGCGCCCGTCTTCGGCCCCCCCTGGAGCCCCGCGCACCCCGCCGGCGCCAGCGGCGTCCCCGCCGTGTACCACCCCTACGCGCACCACCAGGCGCCCGTGGCACCGCCCGACGGCAGGTACATGCGTTCGTGGCTCGAGCCTGTGCCGGGCTCCTTGTCCTTCCCCGGGTTACCTACCAGCAGGCATTACGGCATTAAACCTGAACCGCTGGCGGCCAGAAGGGGTGACTGTACCACGTTTGACACTCACACTTTGTCTCTGTCTGATTATGCTTGTGGTTCTCCTCCAGTTGATAGGGATAAGCAAAGCCACGAAGGCGCATTCTCTGAAAACAATGGAGAAAGTGAGGCAAACGGAGAGAAACCACACATTGATCCAA
Seq A exon
GTAAGTGGGGCTGCGGGGCGGCGCGTTTGGGGCCGGGGAGGAGGCGCGGTGCGGGGCTTCGCGCTGCCCGGGCACCGGGGACTGAGAGCCGCGCTGCCCCTCGCGGGCTCTGCCGGGATCCGGGACGGCTGCGGCTCTGCGGGCCGAGGGGAGAACAAAACCCCTCTCCGCGGCTGCGACTTAAAATAAAATAAAATAAAATAATCGGGGGAAAAAAAAAATCCCACCCCTCCCTCCCTCTCCTCCCCGCCCTCCCCTCCCCCACCACCCCCCCCCCCGGCCACCCCAGCCAACTTCGCAGGACGTACTCGCATCCTCCCGCAGCACTCACGGAGCGGGTGCCCGAGAAGCATTGGAGGTGAATGTGAGCTGTGAGGCCGGGGGGGGCAGCTCAGGGCCGGCAGCCGGAACCTCGCCGTTGCGCGGTGCCCTCCTCCCCCTCCGCCTCCCGGCGGAAATGCCCGCGCTGGGAGCCGCGGGGCCGCGGAGCGGAGCTGCTCCTGCTAATAACGCCATTGCTAATAAGGGCCCTGAGCTGCCGGGGCTGTAACGACGGCGGCCTCGGGCTGGCTCGTCAGTTCCCCGGGTCCTGCCAGAGATGACACGGGAGAAGGGCGAATTGTAACAGGGAACCGATTCAGACGAGCTGCCCCTCCGGCCGAGCTGGCACTCGGAGGGGCTGCGGGGAGGGCAGGAAGGAAGGAGGCAGCCGGCAGAGAGCAGGCGGACGGCTGTTTTCAAACTGCATCCTACAAACAATAAAAAAAGAAAAGCGGAGGGAGGCGGGGGCGGCGTGGCTCTGCCGCTCACGGGTCTCCGTGACCCCCCCTCCGTGCGTGGGGATGCGGGCGCTCCGTGCTCACAGCGGAGACGAGGGGCACCCCGACGCCAGGACCCCCTCCCTCCCCCTCCAGACACCCCCCTGAGCCTCAACTTCTCCTCTCGCTCCCCCCGCAG
Seq C2 exon
ATAACCCCGCTGCTAACTGGCTCCACGCGAGGTCCACCCGGAAAAAGCGCTGCCCTTACACCAAGCACCAGACGCTGGAACTGGAGAAGGAGTTTCTGTTCAATATGTATCTCACCAGGGACCGCAGGTACGAGGTGGCCAGGCTCCTCAACCTCACCGAGAGACAAGTGAAAATCTGGTTTCAGAACAGGAGGATGAAAATGAAGAAAATCAACAAAGACCGAGCGAAGGACGAATGATGGGGATACGGGGGTTAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000019640:ENSGALT00000018035:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.639 A=NA C2=0.304
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=98.9)
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTTGTGGTTCTCCTCCAGT
R:
GTCCTTCGCTCGGTCTTTGTT
Band lengths:
343-1300
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]