GgaINT0056653 @ galGal4
Intron Retention
Gene
ENSGALG00000012339 | ATL1
Description
atlastin GTPase 1 [Source:HGNC Symbol;Acc:HGNC:11231]
Coordinates
chr5:57779209-57781024:+
Coord C1 exon
chr5:57779209-57779280
Coord A exon
chr5:57779281-57780592
Coord C2 exon
chr5:57780593-57781024
Length
1312 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
AGGCTGTGCTTTCCGTGCAGGTC
3' ss Score
8.84
Exon sequences
Seq C1 exon
GCCACGGCAGAAGCCAACAATTTAGCAGCAGTTGCCACTGCCAAAGACACCTACAGCAGGAGAATGGAAGAG
Seq A exon
GTAGGTGTGCTCAGCACCCTATTTCACAGGCTCTCCCGTCCTGGGGAAACCTCCCTGCCTGGTTTCCTGATGGAAAACATCCTGCAAGGACTCGGCCAAGATTTATGGCCGCATCCGTGCAGGTGCAGCGTGTTCAGGTTCCCAGTGAGACACTCTGCCATGTTCGTGGTGGAAAGGGGCCAAAGGAAAGCGATGTCTGGTCAGGATTCCGTGGCAGGGCATGGGAAGACAGTTGACAAATGGTTGCTCTTCTATCTGATGGCAGCTTTTTGCAGAGCGCTGTGACTCCAGCTGAATTTACATCCTCTTCCCAGTGTTCCCTCAGCTGCAAAGTGTAATGGAAAGGGGCAGCGCTGCTGTGTGACCATGCAACCCCTGACGGTCAGAACATGAGGTGATGGCACAAAGGTGTACCAGGGGAGGGTCAGACAGGGCATGAAACATTTCTCTATCACGAGAGTGGTCAGACACCAGAGCAGGCTTCCTAGCAAGTTGGTTGGTGCCCCGTGGCTGTCAGCATTCAAAGGGCATTTGGGCAACGCCCTCAGTGATGTGCTTTAACTTTTGGTTAGCCTTGAAGTGCGGTGGGACTGAATGGTCTTCGTGGGTCCCTTCCAAGTGAATATCCTGTCCTATCCTAATCCTGTCCTATCCTTTAACCCGTGCCACGTCTGGTGCTAATTAGGGGATAAAGTCATTATATATCATTAAATTAAAGTCACTAAATATCATTATAACTGGCATTTCGCCTCTGCCCTGCCCTACCAGCCCGTCTCAGCTCAGGCATGAGATGATTGTGATGTTTTAAGGTGAAGCTCAGACCTTAGCCTGTCTCCTGCCACTTCCAGCTCTGTTCTGCAGTACTGGAGGTTGCTGTGCTTTGGCACGGAGGGCGTGCAGAGCTGCATGGCCAAATTACTGTGCGCTGCCCTGGGTCTGTGTTTGTGCTTATGCCTTAAAACCCGAAGTGCTGATCTTCTGTAGCAGGAGGAGAACAGTGCTGCTGGAGCCGGTTAGTTGAGGGTGGGCCTTTGAGTCTCCAGGTTCAAGTCCTGAGCAATAGCGGCTGGAAGACACGGTCCCAAGAGGAGGGCAGGGTCTTGTGATAGGATGGGAGCCAGGGTATTAGGACCAATTTATTAGGCTAAGAGGAGGGTGAGAGGGACTGGTTCCTAAGACCCTGGTGAGCAGTCACAGAGTGTGGACATACACAGTGCCAAAGAGGAGCGCGTGGAGCTGCCGTTCCGGTGGTTTGCATGGCAGAACACGGGAGCTGAGGGTGCCGAGTGAGCAGGCTGTGCTTTCCGTGCAG
Seq C2 exon
GTCTGTGGTGGGGACAAACCCTTCCTTGCACCCAGTGACCTGCAGACCAAACACGTGGAGCTGAAGGACGAAGCCGTGAGGCTGTTCCGTGGGGTGAAGAAGATGGGCGGGGAGGAGTTCAGCCGCCGCTACCTCCAGCAGCTGGAGAACGAGATCGATGAGCTCTACATCCAGTACATCAAGCACAACGACAGCAAGAACATCTTCCACGCCGCCCGCACCCCCGCCACGCTCTTCGTCGTCATCTTCATCACTTACGTCATCGCCGGAGTGACCGGCTTCATTGGCTTGGACATCATAGCCAGTCTGTGCAACATGATCATGGGCTTGACACTTATCACACTGTGTACCTGGGCGTACATCAGATACTCTGGGGAGTACAGAGAACTGGGCGCAGTAATAGACCAAGTGGCGGCGGCGTTGTGGGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012339:ENSGALT00000020162:10
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:
PF028419=GBP_C=FE(17.8=100)
A:
NA
C2:
PF028419=GBP_C=PD(53.5=47.9),PF096855=Tic20=WD(100=55.6)
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:
ACTGCCAAAGACACCTACAGC
R:
ATCATGTTGCACAGACTGGCT
Band lengths:
356-1668
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]