GgaINT0057642 @ galGal3
Intron Retention
Gene
ENSGALG00000009474 | ACTN1_CHICK
Description
NA
Coordinates
chr5:30572314-30573735:+
Coord C1 exon
chr5:30572314-30572406
Coord A exon
chr5:30572407-30573504
Coord C2 exon
chr5:30573505-30573735
Length
1098 bp
Sequences
Splice sites
5' ss Seq
GATGTAGGT
5' ss Score
4.9
3' ss Seq
TCTTGTCATTGCTTTTTCAGCTG
3' ss Score
9.63
Exon sequences
Seq C1 exon
GCGGAGACAGCAGCAAATCGTATTTGCAAGGTTCTGGCAGTCAACCAAGAGAATGAACAGCTCATGGAAGACTATGAAAAACTGGCCAGTGAT
Seq A exon
GTAGGTGTCCGTGGTGCTGTTGGTTTCTGGGTGGTGGTGTGTAGAAAGGAATTGCATTTAACACTTACAGCTAATCCTGGGCAGTGCTACTGGCCTGTGTTTTCCTAGAATCTTCTTTCTTTCTCTTCTAGCTTTAGAAAAATGAAAGGAGAGAGAACTTGGCTTTTAAGTAGAAAACTCCCATGTAGCAGTTTTAAGTTTCTCAGTTTATTAGGAGCAGCCACAACAATAATAAAACTTAAAGAAAAATCAAGCTGTTTTGACTTGTCTTGCTCAGGACTATGTATATGTCTAATGATATCTTTCATACAAATTGTATGCCAATATAGTGCAGAAGTCAGGAATTGGATCTAAGAAAATGGAAGTTAAGAGGTAGATAACTGAGGAAAGAAATATACGTTTGCTGATAACTGGAAAGAATTTGTGTACAGTACAGTCTGAGGCTTCGTTGGTTAATGGAGAATGCTGACAGACTGACATCTGTGAAACTCTAGAAGTGACCAAATGTGGTCTGGAGTATGTCTGTGGAAGATAAGTAGAGAGGAAAAGATGGAAAACAAAAGGTCAAACAGCCAACAGGCCTGTTTTCAGCCTGGTTTGAAAAGTGTAGGACACTGCTTCACTCATGCGACAAACTGCAAATTGCTGCCTTGCCACCTCTGCAACTCAAAGGGTGATGCTGACTTCTAAGCAGCTAGAGTGAGAAAAGCATAACTGGAGGAAACAACTTGCTTTCTCCTTCCAGACACCTCTGGAGCTAATATGACTTAGAGCATCCTCTAGTTGTGCAACAGCTCAGCAAAATTCTCAGGCTGTAGTGTAATCTAAGGACGTTGTTTGGTCTTGATTGTGTGAAAGCTATGACTTAAGCACGTTGTACTGGCAGTGCTGCAACAAGCAGTGTGGTAAGGGATGAGCTGCTTATAAGGAAAAAAATAGGTAGTTCCAAAAAGGCTGGCAAGGTTTTCTTTACTAGCCCTGCTGTAGGCAGAACCTTTCTGACAGCAAAGAGAAATAAGTAGTCTCTAGTAAGATCAGACCAACACCTGTAGTTTTAACACAGTTTCAATTCAAGGCTTCTTGTCATTGCTTTTTCAG
Seq C2 exon
CTGCTGGAGTGGATCCGTCGCACCATCCCCTGGCTGGAGAACCGGGCACCAGAGAACACCATGCAAGCCATGCAGCAGAAACTGGAGGACTTCCGGGACTACCGCCGCCTGCATAAGCCCCCCAAAGTCCAAGAGAAGTGCCAACTTGAGATCAATTTCAACACCTTGCAGACCAAGCTACGGCTCAGCAACAGGCCGGCCTTCATGCCTTCAGAAGGGAAAATGGTTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009474:ENSGALT00000015425:9
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=0.143
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PU(9.9=35.5)
A:
NA
C2:
PF0043516=Spectrin=FE(68.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGACAGCAGCAAATCGTA
R:
TGAAACCATTTTCCCTTCTGAAG
Band lengths:
323-1421
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]