BtaINT0136102 @ 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
chr6:88531380-88533675:+
Coord C1 exon
chr6:88531380-88531553
Coord A exon
chr6:88531554-88533513
Coord C2 exon
chr6:88533514-88533675
Length
1960 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGG
5' ss Score
5.88
3' ss Seq
CTTTGTATCTGTCCTTCCAGATC
3' ss Score
11.44
Exon sequences
Seq C1 exon
TTCATGGATCGTCTGAAGCTGCTCCTGATGCCTCTGAAGCATCAGCCTGACTTTATCTACCTGCGCCACGTCCCGCTGCGGCGAGTGCACCTGTTCACTTTCCTGCAGGTGCTCTGTCTAGCCTTGCTCTGGATCCTCAAGTCCACCGTGGCTGCTATCATTTTTCCAGTCATG
Seq A exon
GTAGGGATTGTTCTGATTGAACCTACTCATGAGATCACACCAGCATCATGTAGTTATTGTAATATTGATGACACATGTATCTTTTATGGATAGTTCCATTTTTTTTTTTTTGAGTTTTGACCTAATCAGTTTGGTGGGTTATAACTTAGGGTTCCCGGGTCTCTGGTTGTCTAGGCTGGACCTTGTAGTCCAACAGCTGAGTTCAGGTACTGGCTCTGGTTCATGCTGACCCGTGAACTTCCCTGAGCCCCCATTAACTCATCAGTAAAATGAGAATGGCATCTTTGTTTTATTCTGTGCGTCAACAATGAATATAAAGGGGATAGCATAATGCCTGACACATGGTAGACACAAGTACACATGACATTAGTTATTTTTGAAATATTGCTACATTGGAGTCAATCAGAATACACTTCAGGCACACTTCAGGTCAAATAATAGAGGGCCAGTGTGGCAGCTTATAAGAGGTCAATGAGTGAATTAGAAGAAACGGAGATCTAAGCTTAGTTTTTGAAGTTCTTCAAATTTGTATCATGCTAAGTGTTAGGGTAAGTCTGGGCTCGCCTTGCCATGTTATGATGTGAAGGAAGGTGAAACAGCTAATGTTCAACTCTGAATCACAAATGAAGAAGGACATAAGGAAATGCTAGCTCTGTATTTGACTTCATCATTGAATTTGTGTGTATGGGAAATAATGCTATTGTAGCTTTACCTTTTTTTTTTTTTTGCTTTTTTTTTTTCTTTTTAATTAAGTTATTATTTCTCTAAGAGATGCAGAGGCTGACATAGAGCATAATCTAAAGACAACTGTTACTTTGAAGCAGAGTCAGGACTTCCAGGTCCTACTGCATATTAATTTTGCTGTTGAGCAAAAGCATCTTTAATATACCTTCAAGAGCAGTTCATAAAATCAAAGATACAGAGCTCAAGAGTCCTGGGGTTCAAGTTAGAAAACTGGACCTTTTGTATTCTCCCTTTATCTGGCTTTGTGATCTTGGATAACCTTCATATGTCCCTAAGCTTCAGTTTTCTCTCCTTTTGGATTAGAGATACTAACATCTACCTTTTGGGTTGTTCGTCATGGCAATAAATGAGAAAATATTGTCTAAGAGTTTACCACAGTGTCTGACTAAGGGTAAATATTCAGTTAAAGGTGGTGATTAAAGTCACCCCATTGGAATAAATGGTCTGAGTAAACTAAATCAGTTCAGTTCAGTTAAGTCGCTCAGTCGTGTCTGACTCTTTGTGACCCCATGAATTGCAGCACGCCAGGCCTCCCTGTCCATCACCATCTCCTGGAGTTCACTCAAACTCACGTCCATCGAGTCGGTGATGCCATCCAGCCATTTCATCCTCTGTCGTCCCCTTCTCCTCCTGCCTCCAATCCCTCCCAGCATCAGAGTCTTTTCCAATGAGTCAACTCTTCGCATGAGGTGGCCAAAGTACTAGAGTTTCACCTTTAGCATCATTCCTTCCAAAGAACACCCAGGGATGACCTCCTTTAGAATACTCCCCCATTATTAATATTTTGGAGATGCCTCTGTGAACTGTGCATTGTACACATTTTTTGACTTTCAAAAACCTGTATAATGGCTTAATTTTGAACAATTAGCAATCATATGCAAGCTGTTTTTCCTTTGAAACTTTAGTTATTTTATTAGAAATCTGACATGGAAGAAAATGCTTTAAAAAATAATGCTTTCACACAGAAATTCCAAATGGGGGGATCATACATTACAGTGAACAAAATTAAGTCAGCCAAAGACTTCTGTAAACCAACTTTCCCTGTGAAGAAAATGTTTATGGTCCACTTAATATAAATCCATACAAGCCAGACAAGTTCTGTCATACTTCAGCCTTGTACAAAAACGTTTCTACTGATTTTGGTAGAGCAATATTAATACTCACTCAGACTTCTCTGACATGCATTCTTTCCTACCCTTTGTATCTGTCCTTCCAG
Seq C2 exon
ATCTTGGCACTTGTAGCTGTCAGAAAAGGCATGGACTACCTCTTCTCCCAGCACGACCTCAGCTTCCTTGATGATGTCATTCCAGAAAAGGACAAGAAAAAGAAGGAGGATGAGAAGAAAAAGAAAAAGAAGAAAGGAAGTCTGGACAGTGACAATGATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002348:ENSBTAT00000003032:22
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=0.407
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PD(6.5=58.6),PF103594=Fmp27_WPPW=PU(0.1=0.0)
A:
NA
C2:
PF103594=Fmp27_WPPW=FE(63.1=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:
TCATGGATCGTCTGAAGCTGC
R:
TCATCATTGTCACTGTCCAGACT
Band lengths:
334-2294
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]