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