GgaINT0077111 @ galGal4
Intron Retention
Gene
ENSGALG00000011604 | SLC4A4
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 4 [Source:HGNC Symbol;Acc:HGNC:11030]
Coordinates
chr4:49775927-49777857:+
Coord C1 exon
chr4:49775927-49775995
Coord A exon
chr4:49775996-49777683
Coord C2 exon
chr4:49777684-49777857
Length
1688 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CTTTTCCATTTTCCATCCAGTTC
3' ss Score
8.9
Exon sequences
Seq C1 exon
TTCATTCCTATGCCTGTGCTCTATGGTGTCTTCCTGTACATGGGTGTTGCATCCCTCAATGGCGTGCAG
Seq A exon
GTAAGCTTCCGCAGCGCCCAGGGCTGCTCTGGCAGCTGTGAGCAGACTCCCCGCAGGACCTTGCCCAGAAGATGGTAATCATTAATTATTACAAGGCTTCTCTTAGGACTTTCTGGCCTTCCTCTTCTCCTCCGCCGCCTCATTTATGTTTCCAAAGAAACCCAGGCAGGGCAGCAACTGTTTACAAATATTGCCACACACTGGCTGTTCTTGAGAATGACACTAAAGGAAAGAAATTTGCTCAGCAGGAAAGCAGCCAAGTCTTGGCCCCGTAAGCAATGAGGGGGGTCTATGTGAAGACCCGGGATCCTTCTTCACCCCCACCATACTGATACAGAGAAGAGCATGTGCTTACAAAGGCTCTAGGCTCACTTCTGGGATAGATTGGGTCCTCTGCTGGGACATGTGTTACAGACTGAAGAAAAACAAGAGAACATGATTTATGGTGGTGGCATTATTCCGCAGTGTTAACAAGTGGGAACATTGCTGTTTGCTATGGAAGGGAAGCCAAGCCCCCTTTCTTTGTCACTGAGGAAATATTACGTAAGGAGCCTTTCTCACAGTGCACTATCTTTAATTGGTGCTAGGAAGCTGGAAGTGTTTTTGTTGCTTTCTGGCACCCTATTAATTGTAGCCTTTCTTTTTAGTGCTTAGTGGTGCTCTAATGGGGAAAGACTCTGTGTTCTGTGAGCACCATGAGAGTTTATTTGGGTATTCTTTAAAAAGGCCTGGGCTTTCATTCACTGGTTTGCGATAAATCTGGTCTCAGAAGTGGGCAGTAAGCCCAAGTTCTGGCAAGAGACAAGGGGGGATTGTAATATTCACCCTTGGGCTGGTTGAATCCCTGGAGGGGATTTCCCCTGCTTTCTGGCACAGGTGGTCACAGAACTGTGCGCTTACTTATTTTCCCCGATCAAAGATGTTTTTCAGTCAGTGAGAACTCTCCAGTTTGGTTTAACTCCAAGTCCACCCAGTCCAGCATGGGCAAGGGACACTGCCTGAAAAGCTGTCCATCTTCCTCGCTCTTCAGTTAGGTGCATTCTATACTCTGATAACACGATGTCTGCCCTCACCTCTGCTGACCTCTGCTTGCAGTTAATTTGATAAAGGCACTACTTTTAAATGCCGAATGTCTTTATAGCGTTCCCTGGCAGGTACAGGGAAGTTAACAGAACTAACCCAAGCATTGATGCTGACCACAGTCAGGACATTCATCTTTTTTCTCTGTCTCGTGGGTGATAAACTGCTTTCTTCAACAGAAAATCTCCTGTCTCCAGCTACAGCAGATCAGCCTAATTGTTTTGAAGCCAGCAGAGCTGTTTCCACAGACACCTAAGTTTTTTGGTTTAAATATTAATCATCAGATTACATGGAGCCCTGCTCCCTAAAATAAAGGCACCTCAAGGCCTTGCTTTGAGAAATGCTCGATTCCTGTGTCTGTGTAGGTGCCAAATGTAGGTGTGGAAGCTTAACTTCCGATAACTCAGTTAAAATATTTAGCCCATTGCATTAAGCAATAGTTACTCAAGATAGAGGAACCATGCTGCGTTCCCTGCTGTGCTTCCTTTATGGAAGGAAAACAAGTTGATTCAAGGTCTCACTTTATAGTTTAATTATGCAATTGTCTCACTTTGTTGTTTACCCTGTGTTTCATTTATATGTATGTTGCTTTTCCATTTTCCATCCAG
Seq C2 exon
TTCATGGATCGTCTGAAGCTGCTCTTGATGCCTCTAAAGCACCAGCCTGATTTTATCTATCTGCGTCATGTCCCGCTGCGCAGGGTCCATCTGTTCACGTTTCTGCAGGTGGTTTGCTTAGCCCTACTCTGGATTCTCAAGTCAACTGTGGCCGCTATCATATTCCCTGTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011604:ENSGALT00000018948:21
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(4.2=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=PD(6.5=58.6)
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:
TCATTCCTATGCCTGTGCTCT
R:
ACAGGGAATATGATAGCGGCC
Band lengths:
238-1926
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]