GgaINT0078874 @ galGal4
Intron Retention
Gene
ENSGALG00000009896 | TRERF1
Description
transcriptional regulating factor 1 [Source:HGNC Symbol;Acc:HGNC:18273]
Coordinates
chr3:22224809-22227073:-
Coord C1 exon
chr3:22225443-22227073
Coord A exon
chr3:22224856-22225442
Coord C2 exon
chr3:22224809-22224855
Length
587 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CTCTCTTCCTATAATGGCAGGTG
3' ss Score
8.63
Exon sequences
Seq C1 exon
ATGCCTGGCACACTGAACCTATTAGCGTAAGATTTGCGCTGCAGTCCATTTTTTGAAGATGTGAAGCAACATTGAGTCTGATTGGAATTACTGACAGACTGGAGGAAATCTTAGTCCTTCTGTTGCACACGCACATGCTGAATTATAAGTAATCCTAGCTTCTCTTCCCGCCCCTCCCTCTCCCTCACTCAGCTATCTCAGGGTTCATAGAGATTTCAATGGTTCGCGTGCCTGTAAGATTGGAACGGAAGTGACCAAAAATGGGGGACCAGCAATTGTATAAAACTAACCATACTGCCAACAGCAATGAGAACTTATACTACCAACACCAAATGAACTCCCTTCCATCTCTAAATCACAGTTATGGGACATCTGTTATAGATGCTCCCCAGGCGTCCCCTCTCTCCCCCCAGTTTCCCCAAGATTCAAGAGATAGTATAGCTTTGCCTGTAGGTTCAAAAAGTCTTGGATCAATGGATACACTTAGACAAACATGGACGCATTCTGGCTCAGGAAACCACATCCCAGTGCGGAACAATTTGAGTAATCAAAGCTCAATGTGGAGCCCCCTTGGGCAGGGGGAATCTCACGATGGATACCAATATTCTTATTCTCAACCCAGCGAAAATCGATCACAAAAAATTACCAGTGGGGTCCTGCATAAATTGGACTCTTTTACACAAGTATTTGCTAACCAAAATCTGAGAATTCAAGTCAACAACATGGCTCAGGTTTTACACACTGAGACTTCGATGGCGGATAATTCTGGTGACAGTGCGCTCAGGCAGCTGCTGTCCCAGAAGCCAGCAGTTGAGCAACAGCCTGTAACTTCCAGCGTACAAAGATATCAACCAGTGCCACAGCAGACACACCAGAATTTTGCAAGCACACAGCAAAAGCAACAAATGCAAGTCATGCAGCACCAACAGTTGTACTATGACTACCAGCAGCATTTGTCACAAATGCAGATTCATTCTGCGTTTCAGCAAGGACAGACGCACGTTCAACAAATGCAGTCCCAGCAGCTCTTACCGCAACAGATGCAGCACTTGCAGCAGGCTCAGTACTATGCTCAGCCGCAGCAGGGACATCAGCGACTCTCAATACATGAGATCCAACAGCAGCAGCAACAGCCAACTCGGCAGCAGCAGCAGAGGCAGTGTCCGATGCAAATAGCTCAGTATTACCAAACGCAACCTGTCATGCAGCTACAGCAACAACAGCAGCAAATGCAACTGCAGCTTCCTCCGTATCACAGGGAACCCGATCCAAAGACTGTGCATGAACCCCACCAGTACCCCCAGGATCCGAGTCATCCTGTGCAGCTCATCCAGTTGGGAGCGGCGCCTCCGTATTGCTACCAGGATCCCCACGAACAGTACAGGCATTTGTACCCCCAGGGTTTGCTGCAGCAGCACGACCAGCAGAAGCAATACACAAGTGAGGGTAGAGCTCCATCTCTGAACTCCCACGTCGGCCTCACTCCACCGGGGACAGCAGAGGATCCTGCGCGGTCGGAGGTCAATTCTGTGGGTAACAATGTACCTCATCGAACTCTTTTGCCACCCTCAGGAGCACATCTGAACAACAAAAGCTCTCAGCAGGACTCTCCTGGCCCTGGGTGGCCTCAG
Seq A exon
GTAGGTGACATTTTGCATCCCTGCTCCAACTTGTTTAGTGGAAAAGCAGCCAGGTATGGAAATGAAATGCTATGGTTGAGCCGCGTCAAGATGCGTCAAGATATGAGCAGTGGGCATTGCTGGGATGTTTTGGGGAACTGTGTTAACAGAGTTCTACATCGCTGCTTTGGCTTTGGGCCAGCTGGGCAGTAGCATGAAGCTGCTGCTGTGAGGCTACTGGTTCCCTTATGAGAGGGTTTGGGGAGCTCGGAGTCGAGGTGCTCCTGCTCATTTTTCAGCACTCAAATGCCTGAATGTGCATAAAGATTTAGCTCCTTGTTTCCAAAAGTAATACTGCCGCGGCAGAGGGAAACCTTTGAACAGGAGGTGAGTGTAAGAAAGCTTGCATCAGCTGTGCTCATGGAGGCACTGATTTGCTGGATAAATGTAAGGCTCTCAATTCAGAGGCATGCAGTATTGCAGTAAGTAGAAGCATATGCAAAATGCAAGAATAAAGCTGTGAGAACCTTCATTTATATATCAGTATTTCCTGAAAAATTCTTTTTGCTTTTTTCCCCCTCTTTTCCCCTCTCTTCCTATAATGGCAG
Seq C2 exon
GTGCAATTGTCAGATGGCAGACTGCAACCACTGTCCCCAGAACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009896:ENSGALT00000016090:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.832 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GTCATCCTGTGCAGCTCATCC
R:
GTTGCAGTCTGCCATCTGACA
Band lengths:
348-935
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]