DreINT0151524 @ danRer10
Intron Retention
Gene
ENSDARG00000013730 | slc4a4a
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 4a [Source:ZFIN;Acc:ZDB-GENE-060526-274]
Coordinates
chr5:45171702-45173623:-
Coord C1 exon
chr5:45173549-45173623
Coord A exon
chr5:45171888-45173548
Coord C2 exon
chr5:45171702-45171887
Length
1661 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TTTTTGTCTCATTTGTGCAGCGC
3' ss Score
9.09
Exon sequences
Seq C1 exon
GCCAATTCTTCAGATGTGTACACTGATCCACTTGATTCAACGTTTGTCTGGACTGTAAATTATACAACAGATCCA
Seq A exon
GTAAGTTTTACCAAAACATCACGGATTTGAAACTTCACACAGGATAAACTCTTTTTTTTTACAGTTCCTACAATTATTGGTGGAAGTAGCTACTTTTTGTTATGTTTGCACTGCATAACGTGGGGATGATTTTAGCTCTAGGAACACCATTTGGTGGAACTAAATCAGCTCATACTTTAGAGCAGGGGATAATCCAGCACAATAGGAACTACAGTGACATTATTATGTGCTGATCGTTTGAATGCATGCCGTGCAAAACTCTGACACAGTTTTTTACAAGCCATATACATTCGAATAGCTCCTATTAGTGTTAGTGTTGCTGCAGAGTTGCATTGCATTACTAGTAACAGGTAGCTTTTGATCCAGTAAAGTGATGGCAGTTGTTGTCTTGTATTTTATGAATCATTAAGTGCAATTTTTTTGTAAAGATGACCTATTATACCCCTCTTCACAAGATGTAAAATAAGTCTCTAATGTCCCTAGAGTGTGCATGTGAAGTTTCAGCTCAAAGTACAGCACAGATAATGTTTTATAGCTCTTTGAAGCTGCCTGGCTTTGATCCAAATTGTGCCATTTCGGTTACTGTTGCTTTAAATTCAAATGAGATTATGCTCTCAGAAATATTCTTAATAGAGGGTGGAGCTACAAATGCCTATGTGTTAGCATAGTGGCAGATTTAAAAACAAGACTAACTTCCTATGCTAATGAGGGAGAGATCTTCACTAATGGGTGGGGCTTTTCCCCTCTGATGACCTGCACAAAGGGTGAATGTCAATCAAATTGTTTCTGCGGACTGTTTTTATTAAGTGTGATTATAAAAAAATTCATTCATATTCATTAATATTTTTTTTTTTATTAACATTAAAAGCATTTTTACCTTTAGAAGCTGGTTATATTATTGCACTGTTGTCACACAACTGTGTTTAAACTTCTAATGAAAGGGATTTTTGCATAATAGCTCCCCTTTAAAAATATATATGTTGTACTGAAGAAAGTCATCTACGTCTTGGATGGGTTCCAGATGAGTAATTAAAAAGTAAAAAAAATACATAAATTATACATTTTTAGTAAGTTGACAAACCTTTGAGAAAATGTGCCCGATTAAGTTCAGAAAAAGCAATAGATTAAAATAAACTTAAATTGTTTTTGGTCTTCTAAAATCATTTTGTTCAGACCCGGCTGATGTTGTTTTCAGCTTCTGCCACCCAAACTCCAAGCTGCAAATAATAGAGAAAGGTCTCTATGACAATAAATTCATTCAGATAGTCCTCTGTTTGAGATCATGAATGCTGAAATCCCTGCCAACATCTTTGTGACTCAATGTGCCGTTTCTCATGTGTTGCACCTTTTGTGCAAACCTGAACAGCAACAGAGTCATTGTGCAACTTCAGAGAATCTGGAGAGAACCAGGCATCTGCCTTCAAAGAGAAACTAAAAGCTTTAATGTTTTGCATTTGTCTTTGTTTAAAACTCCACTTTAAATGGATGGTCTGGGTTCAGGTCAAGCTGAGGGAAAACATTTGAACTCTTCATTAATGTGTTATATGGAATGTATAATGTGTTATAAGGGGTGTTATATGGAATTTAGTTTTAAATGTTTGATTTAATCCCCTGATGATTAGATATTCTGATCAAGTGTTTTTTTTGTCTCATTTGTGCAG
Seq C2 exon
CGCATGAATGCCACCTGGTCCTCCTTATCAAAGAAGGAATGCCTGAAATATGGAGGAGAGCTGGTGGGTAAAGCCTGTGAATTTGTGCCCGACATCACCCTCATGTCCTTCATCCTTTTCTTTGGCACCTACACCTGCTCCATGTGTCTGAAGAAATTCAAGACCAGTCCCTTCTTCCCTACTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013730:ENSDART00000124336:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PU(6.9=88.0)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(11.7=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:
GCCAATTCTTCAGATGTGTACACTG
R:
AGGGAAGAAGGGACTGGTCTT
Band lengths:
255-1916
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]