DreINT0019542 @ danRer10
Intron Retention
Gene
ENSDARG00000002771 | SLC4A5 (1 of 2)
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 5 [Source:HGNC Symbol;Acc:HGNC:18168]
Coordinates
chr5:27488946-27489398:-
Coord C1 exon
chr5:27489238-27489398
Coord A exon
chr5:27489099-27489237
Coord C2 exon
chr5:27488946-27489098
Length
139 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGC
5' ss Score
9.86
3' ss Seq
TTTGCTTTTATTCCATGTAGATG
3' ss Score
8.34
Exon sequences
Seq C1 exon
GTGGGTGAAGTTTGAGGAAAAAGTTGAGGAGGGTGGAGAAAGATGGAGCAAACCACACGTTTCCACACTGTCCCTGCACAGCCTGTTTGAACTGCGGACATGCCTGCAGACCGGCACCGTGCTGCTGGACCTGGAGGGATACTCGCTCCCACAGATCGTCG
Seq A exon
GTAAGCTTCTGGACATAAAACAGAAATTGTCTAGCATACTGAAGTGTGCATTCGAATGTGTTTATTTTTATGATAATGCCTATTGTGTCATCCAGCTGAACATATAAAGGTAAACTAACTTTGCTTTTATTCCATGTAG
Seq C2 exon
ATGACATCATCGATCGTCAGGTAGAGGAAGGGTTGATCGGTCCTGAATTGAGAGACAAAATCAGCTTTGTACTGCTGAGAAAGCACAGACACCAGACCAAAAAGCCCATCCATCGCTCCCTTGCGGATTTGGGCAAGTCTGGTTCAGGAGGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002771:ENSDART00000138140:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.078 A=NA C2=0.320
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PU(17.5=85.5)
A:
NA
C2:
PF075658=Band_3_cyto=FE(19.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCACACGTTTCCACACTGTC
R:
AACCAGACTTGCCCAAATCCG
Band lengths:
254-393
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]