Resequencing analysis for Gene: ARID1A
There are 3 sections to this alignment:
- resequencing alignment (unspliced, by construction)
- Ensembl alignments (spliced for coding sequence)
- Alignments of ref. [1] (spliced for coding sequence)
Note that:
- these alignments should be taken in context with whole protein alignment. Spliced alignments may be interrupted by splicing events.
- Putative signal of positive selection is shown in blue.
.... ....|1... ....|2... ....|3... ....|4... ....|5... ....|6... ....|7... ....|8... ....|9... ....|10.. ....|11.. ....|12.. ....|13.. ....|14.. ....|
reseq__B7_humanF91 ------------------GGAGATGTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_humanF7 --------------------------ACAG--CGAGGCCATTACAGCACTAGGGCAG-GGGCAGCCTCAGCAGCAGCAGTTAGCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_humanF67 -------------------TATGGTTACAG--CGAGGCCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_humanF55 ------------------GGAGATGTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_humanF43 ------------------GGAGATGTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_humanF31 ------------------GGAGATGTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_humanF19 -------------------AGTATGTACAG--CGAGGCCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_chimpF91 AGACGGACACGAAAAGGA-AATTGTAACAAGCCGTTGCCATAACAGCACTTGGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCTCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_chimpF79 --GCGG-CACGAAGGGGGTAGATGGAACAG--CGTGGCCATA-CAGCACTTGGGCAGAGGGCAGCCTCAGCAGCAGCAGTTCGCCTCCC-------AGCCCAGCCT-AGCC-----CGCCA--GCCAGCAACAAGTTGCCCAGCCTTCTC
reseq__B7_chimpF7 ---------------AGGGTAGATGTACAG--CGTG-CCATTACAGCACTAGGGCAG-GGGCAGCCTCAGCAGCAGCAGTTAGCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_chimpF67 ------------------GGAGATGTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_chimpF55 -------------------AGATGGTACAG--CGAGGCCAT-ACAGCACA-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_chimpF43 ------------------GGAGATGTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_chimpF31 -------------------AGATGTTACAG--CGTGGCCAT-ACAGCACA-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
reseq__B7_chimpF19 ------------------GGAGATGTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGCTGCCCAGCCTTCCC
# Ensembl (v52) alignments (spliced for proteins)
human_dna_not_in_bw ------------------------GTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGC--------------
chimp_dna_not_in_bw ------------------------GTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGC--------------
macaque_dna_not_in_ ------------------------GTACAG--CGTG-CCAT-ACAGCACT-GGGCAG-GGGCAACCTCAGCAGCAGCAGTT-GCCCCC--------AGCCCAGCCCCAGCC-----TGCCA--GCCAGCAACAAGC--------------
# Ref.[1] alignments (spliced for proteins)
ENSP00000337170 -----------------------------------------------ACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGTTGCCCCCACAGTTTGCAACCAATGCCCAGCAAAACATGCCACCACAAATGATGGGCGGCCCCATACAGGC
ENSPTRP00000000684 -----------------------------------------------ACT-GGGCAG-GGGCAGCCTCAGCAGCAGCAGCCCCCAAATCAGTTTGCAACCAATGCCCAGCAAAACATGCCACCACAAATGATGGGCGGCCCCATACAGGC
ENSMMUP00000016675 -----------------------------------------------ACT-GGGCAG-GGGCAACCTCAGCAGCAGCAGTTGCCCCCACAGTTTGCAACCAATGCCCAGCAAAACATGCCACCGCAAATGATGGGCGGCCCCATACAGGC
15.. ....|16.. ....|17.. ....|18.. ....|19.. ....
reseq__B7_humanF91 CTCAGCAAGATGTATACAACCAGTATGGCAATGCCCAACC---------
reseq__B7_humanF7 CTCAGCAAGATGTATACAACCAGAATGGCAATGCCAAACTGGTT-----
reseq__B7_humanF67 CTCAGCAAGATGTATACAACCAGAATGGCAATGCCCAACT---------
reseq__B7_humanF55 CTCAGCAAGATGTATACAACCAGTATGGCAATGCCCAACT---------
reseq__B7_humanF43 CTCAGCAAGATGTATACAACCA-TATGGCAATGCCCAACTG--------
reseq__B7_humanF31 CTCAGCAAGATGTATACAACCAGTATGGCAATGCCCAAAG---------
reseq__B7_humanF19 CTCAGCAAGATGTATACAACCAGAATGGCAATGCCAAAAT---------
reseq__B7_chimpF91 CTCAGCAAGATGTATACA-------------------------------
reseq__B7_chimpF79 -TCAGCAAGATGTATACAACCA---------------------------
reseq__B7_chimpF7 CTCAGCAAGATGTATACAACCAGAGTGGCAATGC---------------
reseq__B7_chimpF67 CTCAGCAAGATGTATACAACCAGTATGGCAATGCCCAACT---------
reseq__B7_chimpF55 CTCAGCAAGATGTATACAACCATAATGGCAATGCCCAACA---------
reseq__B7_chimpF43 CTCAGCAAGATGTATACAACCAGTATGGCAATGCCCAACT---------
reseq__B7_chimpF31 CTCAGCAAGATGTATACAACCAGAATGGCAATGCCAAAC----------
reseq__B7_chimpF19 CTCAGCAAGATGTATACAACCAGTATGGCAATGCCCAACA---------
# Ensembl (v52) alignments (spliced for proteins)
human_dna_not_in_bw -------------------------------------------------
chimp_dna_not_in_bw -------------------------------------------------
macaque_dna_not_in_ -------------------------------------------------
# Ref.[1] alignments (spliced for proteins)
ENSP00000337170 ATCAGCTGAGGTTGCTCAGCAAGGCACCATGTGGCAGGGGCGTAATGAC
ENSPTRP00000000684 ATCAGCTGAGGTTGCTCAGCAAGGCACCATGTGGCAGGGGCGTAATGAC
ENSMMUP00000016675 ATCAGCTGAGGTTGCTCAGCAAGGCACCATGTGGCAGGGGCGTAATGAC