GgaINT0040807 @ galGal3
Intron Retention
Gene
ENSGALG00000004222 | F1NEI1_CHICK
Description
NA
Coordinates
chr6:12000893-12002943:+
Coord C1 exon
chr6:12000893-12001076
Coord A exon
chr6:12001077-12002787
Coord C2 exon
chr6:12002788-12002943
Length
1711 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
GCTGCTGTCTTTCCTTGCAGGTA
3' ss Score
12.85
Exon sequences
Seq C1 exon
GAACTGGCAGCAATGCCTGTTACATGGAGGAGATGAGAAACATAGAGATGGTGGATGGTGAGCAAGGACGGATGTGTGTGAACATGGAGTGGGGAGCTTTCGGGGATAATGGATGCCTGGACGATATCAGGACAATATATGACAAAGCAGTTGATGACTATTCACTAAATGCTGGAAAGCAAAG
Seq A exon
GTACTGTGGGATAAATGCTGTGCTGAGAATAAGCCAGGCTGCCTCAAATGCTTTTAAGGGAGAACTGGATTTCTCCCACGTCTCAGAAAGGAGAGGTTAAGAGTGGAGGATGACTGCAGCCCTTCTGTCCTGTGTGATTTCCCCCTTCTCTGCTTCTCTTTTTCTGGCCTCCAAGAGGGCAAACATCTCTCATCTTCTAATGTCTTCTATATTGACAATTGAGGTCCTAATCGTTGCCAAGCTGTTCTGCAGCAGCATCTCTGTGTCTTCTTTACAAAGCCCTAAGTTCATTTAACTACTATCAAATTCCTCTGCCAGCCCTTTGGGTGGGCAGAGCCCTTATGTCCACTGAGCATCTGCCCAGAGCTTGTTTGCTGCCATGGAACTGTGGTGCAGGGTTTTTGCTGAGAGCCTCAGGAGTCTTCTCATTACTGAGACACCCTGTTTCTCATCCCATGTTGTATGCAGGGTTTTAAGATGGCTTGTCATTCTTGTGCTCTTGGTCTCATCTCTTTTAGCTGAACTCTCTCTGTAGGGAGCTCTGCCTCTTGGAATCGTAGAATCAAAGGATGGCTTGGGTAGGTACAGACCTCAAAATCATCCAGTTCCAACTTCTTTTCCATAGGGCTGAAATCTCAGCCTAAACCCGCTGGCATGGTTTGGAGCTTGAAGCTGATCACTGTAATGCAGTTATGAGCTCTGTATCAGTTGCAGCCAATTCTTATTCGAGGCAATTTTCTGGGTAATGTGGTGCATTAGAGCACCTGCCTTTCTTGGCCCCGTTTTGGGGACCCAGCTCGTGTGAGCAAATGTTTCCCTGTGCCCTGCAAGAAAGGGCTGACAAGGAGGTGCACCCAGCACGGCATTACTGTGCTGACACACGTGCTGCCTCATGCCCAGGCTGCTCTTTTTCATTTCTCTGCGGCAATGCATAAGAAAATTGTGCAAATAAAGTAGATCTGCCTAGGAACCTCGGGGATGTGGGCAAGTAGGCAGGTCCCTTGGGAAGCTTTTGGGAGGTTAGGGCACAAATGGACGCAGAGGGGCGGACACTGAGTGAGGCTGATGCAGCGGTGGAGCTGGCATAAAGTAAGCAGCCATACGTGGGAGGCTGCCAGGGGGAATAATTGATTCCAGAAAGAGTTGGGCACTCAGGAGGAGGGCGCTTACTGGGTACAAGCCTGGGAGAGCTCCTGGTATTAAATGGACTGCGTGGCCTGCTTCCAGGTGGCTGCTCCGCTGGGCTCAGTTCCTTCCAGGGCAGAAACCCTGCTTAGAGCTTCAGGAGATGAAATAAAGGATGCATCACTGAAAGCACTTTTCACTAAATGAAAAAGTGTTCAGTTCTCATTGCTAAGGGCACAGCTTGGTTACAGAGCACAGAATGCTCCTTTCACACCAGAATGATGCTGGAAGGGAAGGAGAGCCAAGCAGACTCCTGTCTTCAGCACAGGGCTGCCCACGGCCACATAGAGCACCACTACTTGGTGTGTGCTGTCATTAACAACTGCCTGGCTGGGGGAAAATGGACACAAGGAATATGTGAGGTACTTTTAGACGGACTCACAAGGTTTCCCACTGAGCGTTTGTGCTTTTCCTTGCCATAATAAATGACTGTTCTTTTTCAATTGGTTTGTGTGTTCCGTGCCCTATCTGCATGTGTCCCTCTGTCAGGTGTCCCCCTGAGCCATGCTGCTGTCTTTCCTTGCAG
Seq C2 exon
GTATGAGAAGATGATCAGTGGGATGTACCTGGGGGAAATAGTCCGCAATATTTTGATTGACTTCACCAAACGAGGGTTCCTGTTCAGAGGACAGATCTCAGAGACTCTGAAAACCAGGCATATCTTTGAAACCAAGTTCCTTTCACAGATTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004222:ENSGALT00000006719:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0372711=Hexokinase_2=FE(25.4=100)
A:
NA
C2:
PF0372711=Hexokinase_2=FE(21.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCAATGCCTGTTACATGG
R:
AGGAACTTGGTTTCAAAGATATGCCT
Band lengths:
319-2030
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]