DreINT0151528 @ danRer10
Intron Retention
Gene
ENSDARG00000013730 | slc4a4a
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 4a [Source:ZFIN;Acc:ZDB-GENE-060526-274]
Coordinates
chr5:45169553-45171498:-
Coord C1 exon
chr5:45171385-45171498
Coord A exon
chr5:45169715-45171384
Coord C2 exon
chr5:45169553-45169714
Length
1670 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
ATCTCTTTTCATGTTCTCAGCCA
3' ss Score
7.23
Exon sequences
Seq C1 exon
GTGAGGAAGCTCATAAGTGACTTTGCTATTATCCTGGCCATTTTGATCTTCTGTGGTGTCGATGCTCTGGTTGGGGTTGAAACACCAAAGCTCATAGTGCCAAGTGAATTTAAG
Seq A exon
GTAAGCATCTTTCCATAATGTCTGTTTTTTGTAAAATAAAATTCCTTCGGGTATATGATTTTAAATTAGGTTTAGTGCAGGTCTAACGTTTTTATTTTGTTTTTATTTAAAATTTGTTTTGTTTTGTTTTGCTTTGCTTTGCTTTGTTAATTTAATTTTTAATTTTTGAAATTAAATTAAATTAAATTAAATTTATATTTTTATTTTATTTTATTTTATTTTATTTTATTCATTTTCCATTGGCTTAGTTCCTTATTAATCTGGGGTCGCCACAGCAGACTGAACCGCCAATTTATTCAGCATATGTTTTATGCAGCAGATGCCCTTCTAGCTGCGACCCATCTCTGGGAAACATCCATACACACTCATTCACACACATACACTACGAACAATTTAAACTCTTTGGACTGTGGGGGAAACCGGAGCACTCAGAAGAAACCCACGCAAACACAGGGAGAACATGCAAACTCCACACAGAAACACCAACTGACCCAGCCGAGGCTTGAACCAGCGACCTTCTTTCTGTGATGCGACAGCATTACCTATTGCGCCACTGTGTTGCCTTTGTTTTATTTTATCGTATTATTTTTTGATAAATTTTCCTTCGACATAGTCCATTATTTATCAGAGGTGGAATGAACCACCAACTATTTTTATTACATTTTATTTTCAATAATTTTCCTTCAGCTTAGTTCCTATATTTATCAGGGGTCACCACAGTTGAATGAACCACCAACTAATTTATTTTATTTTATGCTCTATGGTGCATTTTCTTTATTTAAATTGTTGTTCACAAAAATTTATCACTTTTAATTTTAAGTGTAATTCTTGAATTTCCAACTGACATTACTAAAATTTATTTTATTTTATTTTTAATTTTAAAGTTTTAGAAAGTTGGTTGAGTTTTATCATATATATTACTAATACTGATTGCAATACTAAAACATGTCTATATAGTATTATACTTTTTATACTATTTTATTTTGTACTTTTTTTACTATTTTATAGTGTTTTATATATATTTAATTTTAGTTCGTTTTATTTAGTTTTGCAGTTTAAATGAACAAAAATTGCAACAAAATAAAGTTTAACAAAATGTAACATCTTATGGTTTAGTTTTAGTAAGTACAATTAAAGCATAAGGAAATGCATGTCAAATGATTTTCAGATGTAAGAACGACTTTACTGTAATGAATAGCTCTGATTAATTTACATGCCAAAACTGCATCCAATCATATGTGAGCTTACGAAGGCATAATGAGTTTTCCCGAGCTTTTCTGCTCTTTTATATTTTATCAGTATGTTTACTTAAAATAAGCATTGTTTACTGTGTAAATGATGAACAGCCAGTTTTGCATGAACTGCTCAGTATTTGTTGCTGTTTATGTATGCAGAGTTTCTTTTGGGACAGTGATCAGTGTTTGGGTCAAGCCACAAGGTGTTTTTGCTCAGGTGGCCTGATGCTCTGTTTAATAAAAATAGATTTTTCTCAGGAAGAGTTAACATCAGAGGGTGCACTGGGTGGCACACTGCATCTTACACTCAGACTCACAGTATGAGTCAATATCAGTCCAGTCAGATCATTTCTGTTTGTATCCTGTAAACATTTGCCAAGCGCCCTGACTGCAGACTTCTGTGATCCTCAAACTGATCTCTTTTCATGTTCTCAG
Seq C2 exon
CCAACAAGCCCAAACCGTGGCTGGTTTGTGCCACCGTTTGGTGGAAACCCCTGGTGGGTGTACCTGGGAGCGTCTGTGCCGGCCCTGCTGGTCACCATCCTGCTCTTCATGGATCAGCAGATCACCGCTGTCATTGTCAATCGCAAGGAGCACAAGCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013730:ENSDART00000124336:3
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:
PF0095516=HCO3_cotransp=FE(11.6=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(10.2=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:
TGAGGAAGCTCATAAGTGACTTTGC
R:
GCTTGTGCTCCTTGCGATTGA
Band lengths:
270-1940
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]