BtaINT0136098 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002348 | SLC4A4
Description
Bos taurus solute carrier family 4, sodium bicarbonate cotransporter, member 4 (SLC4A4), mRNA. [Source:RefSeq mRNA;Acc:NM_174605]
Coordinates
chr6:88517152-88518555:+
Coord C1 exon
chr6:88517152-88517330
Coord A exon
chr6:88517331-88518482
Coord C2 exon
chr6:88518483-88518555
Length
1152 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
ATCTTTTGATTTGGTTTCAGGGA
3' ss Score
8.33
Exon sequences
Seq C1 exon
AAAGGAGCTGGATATCACCTGGATCTCTTTTGGGTGGCCATCCTCATGGTGGTGTGCTCCTTCATGGCCCTTCCATGGTATGTGGCTGCTACTGTCATCTCCATCGCTCACATCGACAGTTTGAAGATGGAGACAGAGACTTCTGCACCTGGAGAACAGCCCAAGTTCCTAGGAGTGAG
Seq A exon
GTATGTTAAATCAGAAAAAAAAAAATGGCTCTACAAACCATGCCATTCACACATCTATGTGTCAGGCAGGAGATGGGCCAATGTGGAGGAGAAAGGACTGGTGATGAATGATTTATTCTGGACTTGCTATTCTAGAAAGGACTAAGTTTTCATTTGAAAGAGAGTCTTCAACAATTTCTTGAGTTCACTTCTCATGTTACATACATTTCCTTTGATTAGCAAAGAGCTAAAGGGTGCAGAGTAAAAACTCAAACAGGTCATTCAGTTTCTTCAACATGCAGGTAATTTTGGAGCTGTGGTGTGTACCATATCACAATCATAACTAAAGGCTAAAGCCTTTCATTTTTCAGCTCTGTTGAGACTTTCTAAAACTCTTGAGTCTGCTTATGACTTTCAAGATTCTATGAAAGGAAAGGAATTCTTATTTTCCACTTAATTTTCTGTCTCATAAGCACTGAGAAACCTTGACCTCCAGCTGTTCAATCTGGGTAGCCATGAAGGGCTTTTATGAGACCTTTATACTCTACTGTGTATTTTTCACAATGGACTCTGCTCCTAAGTGCTCGAGTGACTAGCTCACATGACCGGGCCAGCAGTTCCCACGCCACAACAGTGGGTGATTCTTTTTTGGGAGCTGGGGGAGGGGGTTGTTGTATGGGAATCATATTTGTTAAAAATTACTTTTGTTGTTGGTTGATTTGGAAATGAGACTGATGGGATTTATTGCATTTGGGAAATTCCCTGAGCTGATGTTAATTAGAATGTGGGGCAATGTAATAACTGTCTCCTGTGAAGGAAGGTGTAATTATATAATGGTACAACTTGTTTTAAAAATAAGGGTTTCATATGGTCAGTAACTGACCAAGAGCAAGTGATTTTTAAACCCTGATTCTAAAAAGACAAAGGATTTAGCAGAATTACTTTTTTCCCTTGATGAATTCAGATCACACACTGCACTAGTTTTAAGAGAATTTTATAGTTCTATTGAGCCTATAAGCTGTCCTTGAGGTGTTAATTGCATATGATATCCACACCTTTGTGAAATATCGATTTGGTCAATGTAGAGTCTTTTTTTTTTTTTTGAAGGTGAAAAGACAAGAGCATGTTTATGAAAACAAGAGGTAGATTGGTAATCTTTTGATTTGGTTTCAG
Seq C2 exon
GGAACAAAGAGTCACTGGAACCCTTGTGTTTATTCTGACTGGTCTGTCAGTCTTTATGGCTCCCATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002348:ENSBTAT00000003032:19
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(11.3=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(4.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGAGCTGGATATCACCTGGA
R:
AGATGGGAGCCATAAAGACTGAC
Band lengths:
246-1398
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]