GgaINT0083965 @ galGal4
Intron Retention
Gene
ENSGALG00000016332 | MCPH1
Description
microcephalin [Source:RefSeq peptide;Acc:NP_001098789]
Coordinates
chr3:88076935-88078756:-
Coord C1 exon
chr3:88078616-88078756
Coord A exon
chr3:88077028-88078615
Coord C2 exon
chr3:88076935-88077027
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:ENSGALT00000031627:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.438 A=NA C2=0.281
Domain overlap (PFAM):
C1:
PF070836=DUF1351=FE(54.7=100)
A:
NA
C2:
PF070836=DUF1351=PD(1.2=3.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
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]