BtaINT0136096 @ 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
chr6:88506178-88508006:+
Coord C1 exon
chr6:88506178-88506291
Coord A exon
chr6:88506292-88507844
Coord C2 exon
chr6:88507845-88508006
Length
1553 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TGTCTTCTCTCTTCTTCAAGCCA
3' ss Score
7.88
Exon sequences
Seq C1 exon
GCAAGAAAGCTCATCAGTGACTTTGCCATTATCTTGTCCATTCTCATCTTTTGTGTAATAGATGCTCTAGTAGGTGTGGACACTCCGAAACTAATTGTGCCAAGTGAGTTCAAG
Seq A exon
GTAGGTGAATTTCTGTCTTTTGGTCATTCCCTGATTTTGTTTCTTTTCCCTTATTCTATTTTGTCTTATCTCCGAGTTAGTTTTGTATAGTTACCCATTTCTTTATGTTATAAATGGTCTCTTGGTACATTTATAACCAATGTACATTTTATCTATTTTTTCACTAAAATTAAATGCCTGACTAGAACTAAATGCAAGGTTCACATTATACTGATTTTGATTGAAAATACACAATTATAAAATCTGTTTTATCTAGAGGATTTAAAATATCCCAAACATTTTAAAACAACTTGTAACCTTGATGCATATAATAGTTCTAGGATGTAATGTAACTATTATCATCCTGATTTTGTGAAGTTGAGATTGAAGCTTATAAAAATTAAACTATCCAAGGTTACACTACTAATTCAGTGCTGTTTTCCTGCTACCAAACGACTTGCTATAACACACATGTTTCTATACAAAGAAGATGTGAGAATTATTCATTTTATAAACTTGTTGGTATGTGAAGACCTAACGGGTAAAATTTACGTTTCAGCCATTCTTGAATATCCCTGTCTAAATTTTCCATTTTAAGTCTTTCACTTATTTTCTAGAACACCCCTAATGTTTCTCTTCATCCCTGATAACCATATATTTGCTAAGAAAAATTAAACTAACAGCAGTTTTAGCTTCATGACTACCTAATGAGAAAGGAATATCAGTGTTATAGCAAACAAATTTTTTTTTTTTTGCATTTTCTCTGCCATTAGCAAAGATAAGTTCTCATTTATTCAGTTATTTAAGTCAGCATTTATTGAATGTTTGCTTTAAGTCAAGCCTGGTACTAGGGATTTGAAATACATTGAAGGGCAAGACATAGTTCCTTTCTTTCTAAGCTCACAGCCTGGTAAATGTAGTAAAATGTGTATAGGTTCAGTGATGGGATTATGAGCCAAGCGAAACAGAAATATCTTTAGGAGAAGTGAGGATTTCTCAATAGTAAATGTGGAAAAAATAATTCATAGATAGGATTCTATTTTAGTTTATTTGTATCGTTTAAAATTTGGAAAAGAATAGGAAAATATGAAAATAAGAAATATTTAATATAACTTTAAATATTTGTAGCTTTTAAATGAAACCATTTCAATTTGGCAGTAGTAGACATAACTTCAGTGCAGTTGCTAAAACTTATGGACAAAATTCAAGGTCACTTTGTAGTTTCTTGCCTCCTTCATTACTGAATATTGCATTTGGGTTTTTCTTATGGCTGTCCCTTAGATCACTTTCTTCCCTCCTGAGTCTTATCTTCGATCATCCTGATCATGCAAAATGACATTTACTTCTTTTCCATCACCCTATATTCTTAGTTTTCCTTCATTTAAAACATTGCCTAAAAAATAACCTCCTTTAGGAACTTTTTGGTGAATAATCTTTGTCTAACCTATCAGTAAAACTGTTTCTGTTTTTTTAACACGCTGACTCTCCAAATACAAAACTGTCATCCCCACTTATTTTTCGTCATGGAGTATGTATTAATATTGTTTCAAATAATGTCTTCTCTCTTCTTCAAG
Seq C2 exon
CCAACGAGTCCAAACCGAGGTTGGTTTGTTGCACCGTTCGGTGGAAACCCCTGGTGGGTGTACCTTGCAGCTGCCATACCTGCTTTGTTGGTCACCATCCTGATCTTCATGGACCAGCAAATCACAGCTGTGATTGTAAACAGGAAGGAACACAAACTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002348:ENSBTAT00000003032:17
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(7.1=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(10.2=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:
AAGCTCATCAGTGACTTTGCCA
R:
CTTGAGTTTGTGTTCCTTCCTGT
Band lengths:
270-1823
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]