GgaINT0108089 @ galGal3
Intron Retention
Gene
ENSGALG00000016727 | PHF16
Description
NA
Coordinates
chr1:134255777-134258296:-
Coord C1 exon
chr1:134257823-134258296
Coord A exon
chr1:134255895-134257822
Coord C2 exon
chr1:134255777-134255894
Length
1928 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
CTCCTGTTATTTCTCTGTAGGTA
3' ss Score
10.89
Exon sequences
Seq C1 exon
TGTTCGGTGAAAAGCTGCATCACTGCCTTTCACGTCACCTGTGCCTTTGAGCATAGCTTAGAGATGAAGACTATCCTGGATGATGGGGATGAGGTCAAATTCAAGTCATACTGTCTAAAGCACAGCAAGAACAAACAGAATTCCCTGCCTGATGTTGATGAACACCCCAAAAGCATATCAGATCAGAAGCAAACTGAGAGTGAGAAAACCAGTTTGCGAGCCCAGAAACTCCGAGAGCTGGAAGAAGAGTTTTACTCACTGGTTAAAGTGGAGGATGTTGCAGCAGAACTGGGCCTCCCTAAACTTGCTGTAGACTTCATCTACAATTACTGGAAACTAAAGCGGAAAAGTAATTTTAACAAACCTTTGTTTCCTCCCAAGGAGGATGAAGAAAATGGCTTGGTGCAGCCAAAAGAAGATAGCATTCATACTCGCATGAGGATGTTCATGCATTTGAGGCAGGACCTAGAGAGG
Seq A exon
GTAAGAGTTTTAACTGGTGAAAATGATGTGAAAGTTAGAAGCAGCTTTGTCTGCAGCAGGGTGAAGCACAGAGAGATGATTGATGAAATAATGATAATAAAAAGGTAAGGCCTTGAACTCCATTCTGGTGGTACGCTGCATGTTGCAGAGACTTTCAGGAGCTGTCCCTTTTCAGTTCAGTGTTGAGATCCACTGTGAACACCGTGCTGAGAGGTTTCTCCTTTATATGACGTAACACGTCTTTCCGTGCACAATGGGCATACTTGAGTACTGACTCTTTGATTTCAATGTAAATTGAATTTGCCTTGGTAAAGCACTAAGTATTCTTTGGTGAGTGTGATTTAACATTTTAGGATTCTGCAAAAACTTGAAACAGACCTTCTCACCCTCATAGTTAGAGGGCAATTAGTGAAGTCGTGGGTTAACTACTACAGAGGCTTTTTGGTTCCACACCCGAAGAAGGATGCTGGCTTATGCTCAGACAGCTTCCCGTGACACCTGATTCAGGCCCCTTACTCACCTCCCTTCTTTGACAGTGTGCTGTTGTCAGCTAGCCCTAGGTAAGGGAAGGCTGAATCACATCTCATGCTCTTGAACTGGACACTTTCCCAGCACGTAGCTGCCCAGGGTGCTACAGTTGGTTAGCTGTTGGAAAACAACCCACCAGGCCTAGCCCTGCCTGCAGCTTTGCTGAGTAGAGTAAAAAGGAAATGATCTTTTTACCAGTATCCAGCTTGGCTCTTTACCGGATTATCAGCTAGCCAGCATTTGGAAAAGATGGAGTCCTTGAGCAAAATCCAGAGCAGGAATTTGGTCCCTACCTAAATATGCTTTGTATGTATGTTTTATACATGCATAACATGCGTTGAATGGAAGGTTTTCTTTTTTGTTTGCTTTCTCAAGAAAGCATTTCAAGCTTTTCCTTTTTGTTCGAAGAGTGGTTGGTTTACATCTGACTGTGTTGAAACGGATGCACTTACTTTGAGTGGAGGGACTTGGTAGTTTGAAACATCTATCTCAAAGTTTCCGAATTTCCCACACCATAAGATTTCCAACTGACATATGTCTTGGGGTGAAAATTAATTTGGGAATCTTGGAATTTCCTTTCTGGGGAGAGAAGCTTCAGTTTCTGAACAGCTCAAGTTAAGTGCTGGGAGGGAAGTACACGTGGCAAATATCTTTCAGCCAGCCCCTGCGCTGCTTCTATGTTCTGCAGGCTCTTTCAGGTCTGTATCACAACTTTCTTCGCCTCTTCCTGTTTTCGTTATGTGAGGTGGAAATATGGCTATTAACTCAAACAGTGAAAGCAGAAATATGTGGAACTGCAATGGAGTCTGAAAATAAACTGCTGAATGAGTCAACAGAAATGTGTAAAATGCACAAGAAGCTACAGTGTTCTTTTAGGGGTCATTTACATGTTAATTCCAGTCCAAACATGCCCTCTCTATTGAGTAGCTTTCCTAAAAGTATTACTTTCTAATGTAGCAATAATCCTAGAAGAAACGAACAAATTAACTGTTAAAAATCATTCTGTGAAACATTTTGCAAGGAAATTCTGGGAGGACTGAGTACTGATTGCAGTAAGATCCCCAGCAAAATTGTGTGGTGGAAGTAGGCTATCAGACAAGCTGTACAGATCACGTGCTTTTCCTCTGACTGGAATTTTGTGTTCCCTTTCTGTTCTTATAGATGCAAATACATTCTGCTGTCTCATGAAACATACTCAAGGCATTCAGTAAACTGGCAATAAAAAAAAAATGCAGGATTTGTTTTATATTCATAGTTACATACGTTCAGTAACATCCATGAGCTGTTTGCCAAGGGATTTTGCTCGCAGTGTTTCTGTTATTCTGTTGTTGATACAGTATTTTTCCTAAGTCAGGATTTTTTTTTAATTTTATACTAAGTCTCCTGTTATTTCTCTGTAG
Seq C2 exon
GTAAGGAATCTCTGCTACATGGTAAGCAGGAGAGAGAAACTGAAGCTGTCTCACAGTAAAGTACATGAACAGGTCTTCAATTTGCAAGTTCAGCTCATTAATCAGGAAATTGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016727:ENSGALT00000026992:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.285 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138321=zf-HC5HC2H_2=PD(35.4=25.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGATGTTGATGAACACCCCA
R:
TCCTGCTTACCATGTAGCAGAGA
Band lengths:
358-2286
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]