GgaINT0083965 @ galGal3
Intron Retention
Gene
ENSGALG00000016332 | MCPH1
Description
NA
Coordinates
chr3:91479046-91480867:-
Coord C1 exon
chr3:91480727-91480867
Coord A exon
chr3:91479139-91480726
Coord C2 exon
chr3:91479046-91479138
Length
1588 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
TATCATTTGCAAATTCCTAGCTT
3' ss Score
3.22
Exon sequences
Seq C1 exon
AAACTGATATACCAGTTTTACTGTTTGAAGATGATGGTTCACTTGTGTATAGCCCTGTTTCTAAAATAAGAGATCAATGCAGTGAAATGGAAAGAAGAATAAATGAGATGAAGGAGAAAAGAGAAAATCTTTCTCCTACTG
Seq A exon
GTAAGCAGTTAAGCTTTATTTATTCATGAGCAAGCACAAATGGCGACCATTTTTATTGCTGCTTTTTTTGCCATGTTTTTTTGCTGTCTCTCAGAATTACTCTTACCGTGCTTTTCTTGAAGTATTTAATTACCTAGACTCAAAATGAAAATATCTGATTAGAAATGTGTGAGATAGTACCACTGGAATTAGTTAGCCTTAATCGTTATGTGGGTAGCATTTTGCAAGACATCAATCCATTTAGCCCATAACTCATTTGAAATGAATGCTGACTGTTCAGAGCTTTGAATCCCACTGAAATACGAAGGGATACTGGTCTAAATGGTGCATGCAGAAAGGGTGGGCCCTGTTTCTTTTACAGTCTGGAATTAGAGCTGTGGCTATGCCTATTTTGTACTTAATGCTTTGTTTTATGATTTGCTCTGAATGGCTCTTAAGTATGATGACTGAACCTAAAAGTTGAGTAGATTTTTTTCTTCTAAATCATTTGGATTTGAACTGAGCCTAGAATCTCTAAGTTCTTAAAACTCATCTCTTGAGTATAGTCCGTGCCTCTGACCACCATAGCTGAAGGGTCACTGCACAAAACTTCCTTCGTCACAAGTTTTGAGTAGGTATGACTGCTTTTTAGCTTTTCATTTCTGTATTGAAAGTGACATGAGGAGGAAGACGATTTTAACAAAATGAAATTTCTTAATCGTCATACATTCTGGGAATAATAACTGAAATAGACTTTTAAGTTTGTAATTTGCTATTATAACTTGGTTGAACTTTACAACAAGATTCTAAATCATATTTCCTATTAAATTCTAATGTGAATCCCATAGTTGACAAAGATTGTAATGTTATTACTTCCTCGCCAACAGTTTAAAAAGGAGTTTCAAAATGCTCAGGCACCTGTTCAAGTACTGAAGAATGGGGTTTAAGTAACAACAAAAGACCTAAATGAATAAAACCAATTGACTTGAAAATGCAGATTCTGGTGATTTAAATCTGGACTTGAGATTTCAAATAATTTATCAGCACTTGTGTTATCTCACGTTATCTCATCCGTAGTGTTTGAAGTTTCAAGAAATCTGTCAAATAAACTGTCACTTTATGCCTCCAAATAAAATTGTGAAAGGAAATTATAGATAGAGTTATACATTGATGAAAAATTAAATCTTATGTATTTTAGCATGGCTTGTATTTGTTTAATTTTGCGGTTTTAAGGTAATACTTCCAAAGGTCTTGAAAAGCATTTCTGCTGTATGGAGGCATTTCTACTAGCTGCAGAAGTTACCTGATTCTTTAGTTAAAAGATCTCGACTGTCTTAGAAGTGTCCATATTTCATCGATGGTTTTCTTTCGTTCTTTCATTTCAGAAAAATACGGTGCTGAGTTTTCTAGAAGAAATTTGATTCATTTGTAAAATCTAATACATTTTTTTGAGTAAATAAGTTTGAGATACTTTTAAGCAGTCTATAGTTAGTTGTCAAAGCAACCACATATCTCTTAAAATTGAACTGTTCTGAGATATGAGTAGATGCTGTAGAAACTTGTATGTCTGCACATAGAGCTGACTAATTTATCATTTGCAAATTCCTAG
Seq C2 exon
CTTCCCAAATGTTTCAAGCATCTCCACGTTGCTCACAAGGAGACTGCCCTCTCTCTACCTCTTTAACTAATTCAGAAGACGCAGTATTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016332:ENSGALT00000036955:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.417 A=NA C2=0.188
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACCAGTTTTACTGTTTGAAGATGAT
R:
GCAATACTGCGTCTTCTGAATT
Band lengths:
222-1810
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]