GgaINT0125443 @ galGal3
Intron Retention
Gene
ENSGALG00000003534 | F1NM06_CHICK
Description
NA
Coordinates
chr17:7253555-7255494:-
Coord C1 exon
chr17:7255444-7255494
Coord A exon
chr17:7253695-7255443
Coord C2 exon
chr17:7253555-7253694
Length
1749 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CTCATGTTCCCTTTTTGAAGTAT
3' ss Score
5.57
Exon sequences
Seq C1 exon
GATGTCGCAGCACGTGGACTAGACCTGCCTCAAGTCACGTGGATTGTGCAG
Seq A exon
GTAGGTTCGCTGTGTGTGTATGTGTGTGCATGTATTAAATGCAGTCCTGCTTGGATGAACTGCCTTTCCAGTCTGGACCCTCTTTCTGCAGTTGGCTTGTCTTTGTGCTGATGCCTCAGGTGTAGGAGATGCATGTATTCCTGACTGCATCTGTGCAGTTATCTGAATGCTTCAGGCTGGTCTTTGCTGGACTGGGACTGGGGCTGGGTTAGCTGTAAGCATTCAGCTTTCAGTAGAACTGCATAGTTCAGATTTCTCCTTTAAAACAAACAAAAGCCCACACCAGCACTGCATTGCTGTTGACAGAAATACTGTCTTTAAAAAAAAAACAACTGAAACTAAGAGAGATGGATTGAACCTTAAAAATAGCAGCCTGTCACTTCAAAGTGGAATCTGGGGGCGTGAAGCAGATTTCATTTTTGTAAAAGATTGATAATTAAAAGGAAGGTTAGTTGAATTGGGGAAAACTGATTTAGAGATTCTCATATATCAAGTGACACATGGGTAAAAAGAACAGGGCACAAAGCATTGGTGAAACAACCTTTTAATTTCTACCTCATCCCCTCAGGTAACAAATTTGATTTTAATTTAGTGTTTTTAAAAATGAAAGATTTTGTGGCAGCTAGCTGGTCAGAGAAGGCTGGGGAAGTAAAGTCTTTAATTCCCAGATCTGTATATTAATAAAATTTACCAAAGATATAGTTGCCAGTGCTAGAACGCAGTGCAAATTACCTCAAGCCCTAGGAGACTTCTGTGTGTCCAGAAGGCGAAATCTCAGCTGTCCTGAGAGCTGTGTCCAAGAGCAAGGACCTGCAGGGAGCAATTAGATTGCTCACAGCATCTTACTCACACCTCTAGCCAGTAGAAACTTTGCCAGAGGGCACAGGTATAAACACTAGAGTGGGCTTTGGTTGTTGGTTTTTTTCCAGTTAAACTGCTGAGGGCTCGTTTCTAAGCAGTATCTCTATGCATGTTCATTTTTCTAGGAAAGGAGGGGGGAAGGAATGGGGGGAGGCTAAAGGGAGGGAAATATGTCACCCTTTATCAGATCTTGCAAATAGCTGGGCATTTTCTCAGTCAAATAAATGAGAGGCACTGCTATACTGGAGTTGGGTGGGGGCCTTTAAGCAACATCTCAGTTCAGTCTCACAGTCATAGATGGAAAGACAACTGCTACCTGTATCATGTGCTGCCCAAAGGACTTAATATCACGTCTCTCTTAGGTTTTCTCTATCCAATAACTACCTATGATTTGCTTTAATCACAACAAAAACATAGCCAAATTTAGATTTGCCATATTTAATTGCATGGCTTTTCTCCTAAATGCGGCGCAGGTGGCGTCCCGCTCTGTATGGGTACTGCTGGGCTTTGGTTGGTTGGAGGATTTAGTGAGAATTTTTTTTTTTTGAGAGGAAGAAGCAAACAGATTCCTGACGTGCCTGTATAGAAATAAAATGTAAAAGGCAAAGAGAGACACCGAGATGGGGAAAACTGTCCTATTATCTGAAAGTTGGCCAATGTGTCACATTCACATGTCAAGAAACTGCTGTGGCTGAGGGGGTTGAGTGATGGTTACAGCGATGAGTCCGATGGGCTCTTGATAAACAGACTGATTCCGAGGGAGGTACAGCAGGTGGGTTTTGCTGAGATCCCCTTTGTTTCAGACGAGCAGACTGAGTGTCTCGTTTATAATTAACATGCTGTGTTCTGTTAATTCCTCCCTTCCCTTCTCATGTTCCCTTTTTGAAG
Seq C2 exon
TATAACGCTCCAGCTTCACCTGCGGAATACATCCACCGGATCGGGAGGACGGCTCGGATTGGCTGTCACGGGAACAGCCTGCTTGTCCTGGCGCCTTCGGAGGCAGAATATGTCAGCTTGCTGGCTTCTCACAAGATTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003534:ENSGALT00000005588:14
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:
PF0027126=Helicase_C=FE(21.3=100)
A:
NA
C2:
PF0027126=Helicase_C=PD(26.7=42.6)
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:
GATGTCGCAGCACGTGGACTA
R:
TAATCTTGTGAGAAGCCAGCAAGC
Band lengths:
190-1939
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]