GgaINT0050395 @ galGal4
Intron Retention
Gene
ENSGALG00000011052 | SLC38A11
Description
solute carrier family 38, member 11 [Source:HGNC Symbol;Acc:HGNC:26836]
Coordinates
chr7:19517220-19519167:+
Coord C1 exon
chr7:19517220-19517381
Coord A exon
chr7:19517382-19519054
Coord C2 exon
chr7:19519055-19519167
Length
1673 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
GATGTTTTGCTATACCTTAGGAG
3' ss Score
6.56
Exon sequences
Seq C1 exon
CATTCATCTGCCATCATAACAGCTTTTTAATATATGGCTCTCTGAAAGAACCCACATTAAACAACTGGTCTCGAATCACACATATGTCTGTTTTACTTGCTGTTGTTATCAGTGTACTATTTGCTGCATGTGGATACATGACTTTTACAGGATACACTGAAG
Seq A exon
GTAAACTGCTCAATCCCTCAATCTTCATGCTTCCTTACAGTCCTTACATTTCAAGTCCTGTTGTTAACAGCTTTGTATGATTTTGGCATACTTGCACTCATTATGGACCTAAATAGTTAGGACAGCTATTTCTCGTAGTTATCCATCAATCAAGGCCGGATACAAAGATGTTGGATAGATGCTAGTAGGTGTCAGATTCCAAGTGGAAGCCTCACTGGTGGAAAATGCCCTTTGAGTGCTTCCATGTCTAAATGAGGACTAAACATCCATAACTTAGCCATGTGGTTCTCTAACAAAGCGAGAAGGAAGAAGAAATTGTTGTCTTGCCTTTTGTATAAGGTGTCTAGTATACACTTCTGTACATTCTGCTATCTGTGCAAACATAGCATCCTAGCTCTGACTTAGGGACACTTCCTATCCTTACAACAGCCATCTGATATAACTAGTGATTCCATCATCTCTGTGTGTATATACAAATATATAAATGCATAAAACAATAAATATATAATGCTATTTGACATGATTTTGTTAAAAAGAAAATGGAGAAGTGCTTTCAAAAGAAAAGGCATAATACTGGTCAGTGCATTAGTTCTTTGAGGTAAAATACATGTTGCAGTTAACTCTTCTGGTATTTAATAGTGCCATACCAAATCATAGGAGAAGGTGTCCAAGCTTTGTGATGAGAGGCAATGTATAGCTGAGAACAGGAATTGTGGGATGGGGGTTACTGGTTTACCTGTCCTTTTTTCCTACTTCCTGTGCTGTTTATGCAGAATAATTTACTGTCCTAGACACAGCTATAGGTAGAGTAAGTGCAAACTGGCTTGACATTTCAAACAAGAAAGCTCTGACTGCAACTATCCCTCAGCTTATGGCTGTATTGCTGATGGGCTCTACCTTGCCTTCTGCATCTCCTGTCAAAATCTTTCAGATGTTTTTCTCTAAAGCACACTTTATTCCTTCTTTAGTGCTGTTGTGATCCTGAAAGTAGTAAATAGTAGAACAGTATGATAACCAGGTAGAAAGGATGCAGTATGTTGTCTAATTGTGGTCTGGTGGTTTTTCTTAAGTCTCATGGATTGTTATTCCAGATCCATTGTTGTAGCCACTAAGCAAGATGATGATTTGAATTCTGTAGCAATGTTTTTGTTGTTAGATGTAAAAGATGTACTGGTTAATAATCCATATATATATATATATAATGGGCATTCAGGGTCGGAATACTTGAAATTCTTCACTGCAGCTTACCAGCTATGATTAGATACTGCAAGGGAAGTGCAGTTATGCAGAGGTAACGTCCTGGTCTCCTTGTATAATTGTTCTTGTTCTGTGACTTACATTCTTAAATGAAATATGTTTTTCATATGCAAGCTTTTTCTGTTTCCTATCAAGGTAAACACCAGCATTTCAAACAAAACTGATACTAAGGGGAAGATGACAGATGACACTCTGATATGCATATATTAAAATATTTCTGTAAGATATATGCTGCTCCAAGTTTTAAAAAAAAAAAAAACTGCTAATTGGTTAAGATGAAGATTTTTTTTCTTGATGCAAGAGGAAAGGGGATTAGGAAGTCTCAATTATTCCAGTGATTCTATTAACTTATTCTTCAATTTACAAATAAGTAAATGAGGTGACTTCAATCTAATTGATGTTTTGCTATACCTTAG
Seq C2 exon
GAGATATATTTGAAAACTACTGTAGAGATGACAACCTTGCTACATTTGGAAGGTTTTGTTATGGAGTTACTGTAATTCTGACCTTTCCTCTTGAATGTTTTGTCACCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011052:ENSGALT00000018002:9
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=0.000
Domain overlap (PFAM):
C1:
PF0149013=Aa_trans=FE(13.9=100)
A:
NA
C2:
PF0149013=Aa_trans=FE(9.5=100)
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:
TTCATCTGCCATCATAACAGCT
R:
TCTGGTGACAAAACATTCAAGAGGA
Band lengths:
270-1943
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]