BtaINT0136115 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004884 | SLC4A5
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 5 [Source:HGNC Symbol;Acc:HGNC:18168]
Coordinates
chr11:10372099-10374120:+
Coord C1 exon
chr11:10372099-10372287
Coord A exon
chr11:10372288-10373945
Coord C2 exon
chr11:10373946-10374120
Length
1658 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCC
5' ss Score
5.96
3' ss Seq
CCTGGGCCTGTCTTGAGCAGGTT
3' ss Score
6.54
Exon sequences
Seq C1 exon
GAAGTCTGTGTTCTCCCTGACTGAATTAGGCCAGATGAACGGCTCCGTGGCGGGAGGCGGCGGCGGGGCTGCTGGAGGCGGCGCTGCAGGCGGCGGAGGGGGCGGCGGGGCCGGCGGAGGGAGCGGCGCGGCTGATGGAGAGATGCCAACAGCGCATGAAATCGGGGAAGAGCTGATCTGGACAGGAAG
Seq A exon
GTGCCCACTCCAGGCCTGCCGGCCACTCCAGCTGTCCTAGATTTCTCTGCTCCTTTTAGGAATCTTCTCCTCCTCAGTCTCCAGCACCCACTCCAGGCCTTGCGGTATCTGAGCGCTGCACGCTTTTCCTCCCCCGCCTGCAAAGCTCCTCCGGGACAAGACAGGAAAAGGGGAAGTGCGCATAAAGTGAAGGAACCCAGACTTTTCTTAGCACACCCTCTGTTAACTGTATTCATTTTCTAGGGCTGCGGAAACACATATCACAGACTAGGTGGCTTAAACAATAGAAATTGATTCTCTCGAAGTTCTAGAGTCTAGAAGTTCCAAATCAAGGTGCCAGCAGGGCCAGGCTGCCTCTGAGATTCTGGGCGGACTCCTTCCCTGACTGTCGCTAGCTTCTGGCGGCAGCCAGCGGTCATTGCTGCTGCTTGCCACTCATCCTGCCTGTGTCCTTGCATGATGCTCTGCCTGTGTTTCTGTCTTCATATGGCATTTTCCTTTTCTTGTGAAGATACCAGTCATATTGGATTAGGGTCTGCCTAATGACTTCATCTTAACTTGATTTCATGTGCAAAGACTCTGCTTCCAAATGAGGTCACATCTACAGGTTAGAATTTTGATACATCTTTTTGGGGGACACAATTCAGTCCATAACAGTACCTTTTGCATTTTTTAACCTTGTTACCTAGTCAAAAAACTTGTTTTAAAAGAAAACAATAGATTTTCCTGGCTTGTTTGGGTTTCTTTGCAAGCTTTTAGAATAACTTCGGTTGATCTGAATTTAGGAAAGGACAGAATCAGTCCTGCAAAGCTATGACTTTGAGAAGGGAGTCATGCTTTATATGCCTTTGGCTGTCTGCCAGCCAGTGTTTCCCAGGTTTACCCACTCCCTACCCTGATCCTTACCCAGGGGACATTCGGCAATTTTCAGAGACATTTTTTGTTTGTCCCAATTGAAGGGGAGATGATACTGTTATCCAGCAGATAGAGACCAAGGATGCTGCTCAATGTCCTCTGATGCACAGTACTGCCCACCCCCACGCGCCCCCCCCCCCCCCCCCCCCCGCCATTAACAAAGGATTATCCAGTGGTTCTACTGTATGCTAAACCCTGCTGTATGCTAAACCCTGCTCACTGTGTTCAGAGCTTTGGAGAATAGCGTCCCCAGTAAACACTCTCCCCAAACCTTAAATTTCCCACTTGTTTGTTCCACGAAGTAAATAAAACAGTTTTAAGGTTCAGGATCTGCCCTTGATGAATCTGCTATAAACCAGGATCTCTCCATCTCCTAACGCTGGACACACGTTTACCAAGCACCGAAATCCTGCAGATAATCAGGGACACGAGGAAGATAGCCATCACTGGACCCCAGGATTTTCATTCCCTGTAGAATGTTAGGTCTGCCCCCAAGACATGATCCCATAAGGCCTTCCTTCTCCCGCTCGGGCTGTCTGTGACCACCCTTCCCAGTGGAGATAGTGGGTCTAAGGAGAGAATTCTTCCCTGATGTGAAATGTTCTAGTGAAAAGATCCCTTCCTCCATCCATCCCTAGTCAAGTTCCCTTCCTTGCCACAAGCCCTGCAGGCTCCTGGGAATAGCTCTGCCCCTACACTGGTGTTTGTGGTGAGAAAGCAATCCCTGGGCCTGTCTTGAGCAG
Seq C2 exon
GTTCTTCGGTGGCCTGTGTCTTGATGTCAAGAGGAAGCTGCCCTGGTTCCCCAGTGACTTCTACGACGGCTTCCACATTCAGTCCGTCTCTGCCATCCTGTTCATCTACCTCGGCTGCATCACCAACGCGATCACCTTTGGTGGGCTTCTGGGAGATGCCACTGACAATTATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004884:ENSBTAT00000006425:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.359 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PU(1.1=9.4)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(10.8=100)
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:
TCCCTGACTGAATTAGGCCAGA
R:
TGTCAGTGGCATCTCCCAGAA
Band lengths:
343-2001
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development