HsaINT0153305 @ hg19
Intron Retention
Gene
ENSG00000004939 | SLC4A1
Description
solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group) [Source:HGNC Symbol;Acc:11027]
Coordinates
chr17:42325758-42328700:-
Coord C1 exon
chr17:42328527-42328700
Coord A exon
chr17:42327907-42328526
Coord C2 exon
chr17:42325758-42327906
Length
620 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
CTCCTGTCCCTCCCCTCCAGCTG
3' ss Score
11.02
Exon sequences
Seq C1 exon
GTGAAGACCTGGCGCATGCACTTATTCACGGGCATCCAGATCATCTGCCTGGCAGTGCTGTGGGTGGTGAAGTCCACGCCGGCCTCCCTGGCCCTGCCCTTCGTCCTCATCCTCACTGTGCCGCTGCGGCGCGTCCTGCTGCCGCTCATCTTCAGGAACGTGGAGCTTCAGTGT
Seq A exon
GTGAGTGGCTGCCTGGGCCTGGGGCACAAGAGCTGGGAGCATGCGAGGGGCGCGTCTCAGAACTAGGGCAGGCAGGACAGAGTCATGGGTAAAGTCTGGGGCTAGGGCTGGTGTCCAGGTTCTGGCCTGCTGTGTCCTAGCATATGATCTGGAGCACGGGGCCTTGTTTCTCTGTGTCTTCATTTTGCTCACCTGTAAAGGGGGAAATGATGGCACGACTGGGGAGAGCGTCAAGAGGCAGACAGGGTGTGCTGTGAGTGAGCTGGACCCCTAAGCAGCAAGTCCTGCCGTCTTCCGAGTCATTTGGGACAGAGTCACTCCTCTAATAGGATTCTTCCACAGGGTGACTCAGGTCACTGTGGGGCCGCCTTGGTGAAAAGGTCCCCTGCTCACCCTCTGCAGGCCCTCCCCTGCCAGGGTCCACATCCCCGGGGTTGCCTCTCACTTTGACAACGACTCATTTAGGCCAGTCCTAGCTGCTGGGGAGATAAAACAGGACTGGTCCAAGGTTCAAGACAGCCAGACCCTCTCCTAACTCCAGAGGTGCCTTTCGTGCCCGGGGAGGGCTCTTCTGGCCCCAGGGTCTCTCACCCTGTCTCTCTCCTGTCCCTCCCCTCCAG
Seq C2 exon
CTGGATGCTGATGATGCCAAGGCAACCTTTGATGAGGAGGAAGGTCGGGATGAATACGACGAAGTGGCCATGCCTGTGTGAGGGGCGGGCCCAGGCCCTAGACCCTCCCCCACCATTCCACATCCCCACCTTCCAAGGAAAAGCAGAAGTTCATGGGCACCTCATGGACTCCAGGATCCTCCTGGAGCAGCAGCTGAGGCCCCAGGGCTGTGGGTGGGGAAGGAAGGCGTGTCCAGGAGACCTTCCACAAAGGGTAGCCTGGCTTTTCTGGCTGGGGATGGCCGATGGGGCCCACATTAGGGGGTTTGTTGCACAGTCCCTCCTGTTGCCACACTTTCACTGGGGATCCCGTGCTGGAAGACTTAGATCTGAGCCCTCCCTCTTCCCAGCACAGGCAGGGGTAGAAGCAAAGGCAGGAGGTGGGTGAGCGGGTGGGGTGCTTGCTGTGTGACCTTGGGCAAGTCCCTTGACCTTTCCAGCCTATATTTCCTCTTCTGTAAAATGGGTATATTGATGATAATACCCACATTACAGGATGGTTACTGAGGACCAAAGATACATGTAAAATAGGGCTTTGTAAACTCCACAGGGACTGTTCTATAGCAGTCATCATTTGTCTTTGAACGTACCCAAGGTCACATAGCTGGGATTTGAACTGAGCCGTGCAGCTGGGATTTGAACCAGGCCTTCTGATTTCAAGGTCCGAGCTCTGTCCTCTGTCAGTCATGCGTCCACTTTCCCTTCCCCTGTGACTCCTCCCTTCCCCACTCTGCTCCCAGCCCCTACCTTGAGACCCTCTTCTCTGGGCCCAGAGAGAGGCGTCCTGGTGAGGACAAGGTACAGGCAAGGATGATCCAGGGATTGGGCCTGGGACTCAGGCCTCCTAAGTGTTTGGTTCCTCCCTCCAAACACTCATTAGTTCACTCATTCATTCATTCCACAAACATTTACTGAGGGCCCCGGAATCAGTGGACTCCGAGGGGACTGAGACAAGCCCTGCCCTGGGGTGGGGGTGGGGGGCAAGGTACAGTTGATTCTACATTTGGATAGGGAGTGGGGGAGGGTGGGAAGGTAGGGGCGGGAGAGTGAGGGGGTTTGTAATTTATTAATTGCGTATTTTCTAAGAGTTTTCAACATAGTTTGGCTTCACACACAACTTCAGGCCCCTCATTTGAGAGCCATTATCCTCAACTCCATCTAAACTGAATCTTGGGGAGAACCCAGATCTGACCAATTGGGGTAGGAGACAGCAGGCTCTCCAAGAACATGGGCAAATTTATTTTTTTATAAAACAAAAAGATAAAAAGAGTTGAAAGACGTGAAAGTGGTGAGAGATGGAGGAAACAGAATCAGGAAGTGGTAGAAAAGAGAGGAGGTGGCTGGGCGCAGTGGCTCACGTTTGTAATCCCAGCACTTTGGGAGGCCAAGTTGGGCGGATCATTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCCGTTACTACTAAAAATACAAAAATTAGCTGGGTGTCTCGTGGCAGGCACCTGTAATCCCAGCTACTTAGAAGGCTGAGGCAAGAGAATCACCTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCAAGATTGCACCACTGCACTCCAGCCTGGGCAACAGAGCGAGACCCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAACGGAAGGAAACATCAGCCTTGGGGGCCACAGACTCAACATGTGTGTGTGGTGGGGTTCCAGCCCAACATAGAGTAACATTATTTGTACCTCCCAGGCTAGCTCAGTCCATGGGAGGCTCTCCTGTCCCTGAAAGCTGACACCCACCTTTCACCACTTCGCCCATGCTACAGTTCAGTTTCCTCGTCTGTAAAATGGGGATGATAATGGTACCTACCTTGCAGTGTTGTTATAAGGATTAAAGGAGACAGTGCAAGAAAAGGCCTTGGTTGGTGAAGAGCCCAACCTCGGAGGGGAGCTGCTGGGATCCTCCTTATCTTGACTGGGATGTCCCTGTCTCCCCCTCCCCTTGCTCCTTGAACATGGCCAAGGAAAGTGAAAAACAAAAATTATTCACTCTGCTAGCACCCTTCCCCTTGATGCCTGGGAATAGGTTTTGCCAATAAACGTATCTGTGTTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000004939-SLC4A1:NM_000342:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0095516=HCO3_cotransp=PD(3.9=19.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTTCGTCCTCATCCTCACT
R:
AAAGCCAGGCTACCCTTTGTG
Band lengths:
344-964
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)