DreINT0019520 @ danRer10
Intron Retention
Gene
ENSDARG00000104005 | SLC4A3
Description
solute carrier family 4 (anion exchanger), member 3 [Source:HGNC Symbol;Acc:HGNC:11029]
Coordinates
chr9:46864838-46866255:+
Coord C1 exon
chr9:46864838-46865060
Coord A exon
chr9:46865061-46865994
Coord C2 exon
chr9:46865995-46866255
Length
934 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAA
5' ss Score
4.51
3' ss Seq
GCCGAGGTTTTGTGTCACAGACG
3' ss Score
4.8
Exon sequences
Seq C1 exon
AATTTCCATGAGGTAGCGTACTTTGCTGATGACCGCCAGGATCTGCTTAATGGCATCAACGAGTTTTTAGACTGCAGTATTGTAATTCCACCATCGGACGTTGAAGGAAAAGACCTGCTGAAAACTGTGGCCTCCTTCCAGAAACAGATGCTACGTAAACGCAAAGAGAGGGAGCTCAAAAAATGTGCCAGTACTGTGACAGGAGCCGAGCTGGAGACCAAAG
Seq A exon
GTGAAATACATTTCTGTTTACATTTCCCCTTGACCTTATTCTTCACATAGTAGTGGGCAACAACTATTGGAATATTTTTGGCTCAAGACTTTGGGTCTCATCAGCCGATTCGAATGTTATCACTTGACTGAATGGGTGTTGTCAGTGGTTATCAGTTGATAGATATGGGCCAGTATGGGCATTCTGCACCTACTGGTAGGCTCTGAATGCAGTTATCATCCTTCCACATGGTTAATCAGATATAGATAACATACGGCTGCGGCTTAATTAACAAGAATTATTTATATTATTTATTAAATTTCCCTTTAATTGTATTTTAATTAATGTCTACCCCAACCCTAAATCCAACTATCACAGTAATTTAAAAATAAATCTTGATCTGTTGTCTTCTCTATTAGTATAGCTGATTAACCATGTGGATGGATGATAACAACCTTCTGAGCCTACTAGTAGGTGCAAAAGGCCCCTGCTAGCCCATATCTACCACTGATAATGCCCTTTCAATCGAGTGATAACATTTGAAGCGGGTGGTCTCATTCACTTCCATTGATTTTTAGTTGTTAAAAATGGCAAGATGTGCTGCTTGATGTTGCAAACATATGCTTTCTTATTACATTATTATACTTTTTATGTATAGTCAAAAACACATTTGTTTACAGAGCGTTTTTTTTTTTTTTTTTGCGATTGCTTTGGAACTTCTGATTTAGTTTCGTATGGGAGAAATGACTAGGAATAATTAAGGCAGAAAACGGTCCGTCTGAGACCCTCTTAAGCGCTCTGCTATTTAGTTTGACTGTTTTCAGCTGTTAATTATTCCTAGTCATTTCTCCCATAGGAAACTGAATCAGAAGATCTCAAACAATCGCAAAAGCGGCATTGAAGAATAAGGTCAATAGTCGGTCTGCTGTGTTAATGCCGAGGTTTTGTGTCACAG
Seq C2 exon
ACGTGAATATAGAAGAACAGGAGGAGGAGGATCAGTTTGATGTAGACCCTCTCAAGCGCTCTGGTATTCCCTTTGGAGGTCTGATTCACGATATTCGCCGCCGTTACCCACGCTACATAAGTGACCTGAAGGACGCCTTGGACACACAATGCATTGCTGCTGTTATTTTCATTTATTTTGCTGCTCTTTCGCCCACTATCACCTTCGGAGGTTTATTAGGCAAGTAAACCGATGAGAATTTCATACCTCTAATTTGAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104005:ENSDART00000160285:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.120
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PD(13.6=48.0)
A:
NA
C2:
PF0095516=HCO3_cotransp=WD(100=77.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCGTACTTTGCTGATGACCG
R:
AGGCGTCCTTCAGGTCACTTA
Band lengths:
347-1281
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]