BtaINT0136129 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004884 | SLC4A5
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 5 [Source:HGNC Symbol;Acc:HGNC:18168]
Coordinates
chr11:10399399-10401291:+
Coord C1 exon
chr11:10399399-10399551
Coord A exon
chr11:10399552-10401213
Coord C2 exon
chr11:10401214-10401291
Length
1662 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGG
5' ss Score
4.41
3' ss Seq
TTCCCACTGTTGCTCTCCAGCCC
3' ss Score
8.23
Exon sequences
Seq C1 exon
ATCCTGGGTCTCATCATTGTTCGAAGGCTTCTGGACCTCATCTTTTCCCAGCATGACCTGGCCTGGATTGACAACATCCTCCCAGAGAAGGAGAAAAAGGAGGCAGATAAGAAGAAGAGAAGGAAAGGGGCCCATGAAGACAGTGACGAGGAG
Seq A exon
GTGGGGAGGATGGGAGGCCTCAGCTGACGGGAGGGATCAAGACCCTCCCTCCACCTCTGCCATGGCCAGGGAGGGGTGGCTTCTCAGGTATCCAGGGGGCACTGCCCGGGCCCAGCCTTGGTCTGATGTGCTGAGATCACGTCTGTTTCTGTGAATACCATTATCGTAGGCCAGAATGTATGAGCCCCCTCACCCAGGGAAAAGGTTGGCCAGGCCCACTGTCTCCAATTTCTGTGGGCCCCTGGGCTCATTGTAACAGCAGTATAGGCCCCAGAGGGGACAGTGCAGAAGCCTCGGCTCCATCATCAAGGTTATGACAACTGACCTCCAAAGGACAGAGCAGGCCTGGCGGGGAGGGTGCTAATGGGGACTCACTAGTAGACTGGATTCCTGGACAAGTGGGAAGATTGGGGCCGAGTCTTGCTTGGAGCTGTCCCTAGGGTCCTGGGGAGGGAGGTGGGGGAAGAGGCACAGGTCCTCACTGAAAGAGTGACCAATTCCCCAAATGTCTGGGACCTCTCAGTTGCCCCATCAGCCCCTCCCTTCTCCCATGTTCCTCCCCATCTCACCCTAAAACAGGGAGTCAACAGACAAGAAGCCAGTCCCGAATTTATAGTAAATTACAAAATATTTGTGGATAAGATTGTCTACTTCAAGTTTTCATTACAAATGATGAAACTGTCCCCAAAATGGAAGTGATTCACCCAAAATGGTCATGTCTAGGAGGGAATAAGAAAACCATTCCCCACTTTGGATCTGATCATTTCCCATATACTGAGCTGCCCATGCCATTCCTAATAACCATGTCTGGCTCCCATCCTTCCCAGTCTGACCCAAACCCATATCCCTGCCTCCACCATCAACTATTCTAGCAATCTTGCCTTTTGCAGATCAAAGTTGCTCACAGGCAAGCCCTTGCTGACTGACTAATGACAATCAAACCGCCTTCTGATGATAGTGATAGGCCCAAACTCCCCTGGTCCTTGATTACTGTCCTCTTCCAGGAAGGTAAGAGGCCCACAATCCCTGTCCACATGTTTTTCATTGATTTCCCGCCCCCCTCCAAAGGGCTGTGCTGCACAGCTTACAGGGCCTCGGCTCCCCGACCAGGGAATTGAACCCGGGTCACAGCAGTGAAAGCTCAGAATCCTAACCACTAGGCCACCAAGGAACTCCCCTTTGTGAATGAGTTAGATGATTTGAAAGTTAGGTTCTGCAAACAAAGAAGCCGAGAGTCTAAGTGCCTTTTAAAGACAAATATTCTTTCATTGATTCATTCAATAAATATTTGAGTGCCTACCACATGCCAGGAACTATTTCAGGGGAGGGAAAAAAGCTTCCTTTATATATGCAAAGGAAAACTGGGATCCAATTTACATAAATTCATTTTACACACATCTTCACAATTGGTGTGAGGTTCACTCCCAAATGACTGTTATCATGACAGTTGAAACAGTTCTAATGAGTAACATTCCTGCAAGAGTAGTGTCCTCTCCAGTGTCCTCAGTGGGCCCCAGGGTATTTGCAGTACCCACCACCTGTCTGGGTGTGAAGAGGATGGTGATTTGCACACTGCGGATGCATGTGTTTTCCATCCTGGCAAGAAAGCCAACACTGTTGTACTGGTGGTGTTTATCAGCTCTTCCCACTGTTGCTCTCCAG
Seq C2 exon
CCCCAGTTCCCTCCTCCCTCAGTTATAAAGATTCCCATGGAAAGTGTCCAATCAGATCCCCAAAACAGTATCCACTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004884:ENSBTAT00000006425:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.373 A=NA C2=0.154
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCTGGGTCTCATCATTGTTCGA
R:
AGTGGATACTGTTTTGGGGATCTG
Band lengths:
227-1889
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development