Line 1 is the reference ensembl human protein sequence for the gene. Lines 2-4 show the translations of our own DNA alignments for human, chimpanzee and macaque respectively, shown in lines 5-7. Lines 8-10 show the corresponding alignment published in ref [1]). Line 11 shows codon position of alignments of ref [1] Line 12-14 show protein translation of ref [1]. Positions within the protein alignment which do not match the protein consensus are highlighted).
n |
gene_id |
msa_link |
1 |
ALPK3 |
msa.html |
2 |
ANKRD11 |
msa.html |
3 |
ARID1A |
msa.html |
4 |
BVES |
msa.html |
5 |
CDC5L |
msa.html |
6 |
CR025 |
msa.html |
7 |
CSF2RB |
msa.html |
8 |
CTTNBP2 |
msa.html |
9 |
DRP2 |
msa.html |
10 |
EML5 |
msa.html |
11 |
GLCCI1 |
msa.html |
12 |
GRPR |
msa.html |
13 |
HECW1 |
msa.html |
14 |
HELZ |
msa.html |
15 |
IPO9 |
msa.html |
16 |
JOSD3 |
msa.html |
17 |
K1434 |
msa.html |
18 |
KRTHA6 |
msa.html |
19 |
LANCL3 |
msa.html |
20 |
LSM14A |
msa.html |
21 |
MARK1 |
msa.html |
22 |
MCF2L2 |
msa.html |
23 |
MYH9 |
msa.html |
24 |
NP_060227.1 |
msa.html |
25 |
NP_078947.2 |
msa.html |
26 |
NP_115923.1 |
msa.html |
27 |
NP_955806.1 |
msa.html |
28 |
NRIP1 |
msa.html |
29 |
NT5DC4 |
msa.html |
30 |
PADI6 |
msa.html |
31 |
PALLD |
msa.html |
32 |
PCNT |
msa.html |
33 |
PGBD4 |
msa.html |
34 |
PLEKHG3 |
msa.html |
35 |
POLR3B |
msa.html |
36 |
Q9NSI3 |
msa.html |
37 |
RNF130 |
msa.html |
38 |
SORBS1 |
msa.html |
39 |
SUV39H2 |
msa.html |
40 |
TAIP2 |
msa.html |
41 |
TARBP1 |
msa.html |
42 |
TEC |
msa.html |
43 |
TRERF1 |
msa.html |
44 |
TTC21B |
msa.html |
45 |
UCHL5 |
msa.html |
46 |
USP44 |
msa.html |
47 |
XPO7 |
msa.html |
48 |
XRCC1 |
msa.html |
49 |
XRCC4 |
msa.html |
Genomic alignments for primates are also available at Ensembl [4]. Here we make a 3-way comparison between i) our alignments, ii) those of ref.[1], and iii) Ensembl. In all cases, the positive selection indicated in ref.[1] is present neither in our own alignments, nor in the Ensembl alignments.
gene_id |
msa_link |
HELZ |
msa.html |
NP_115923.1 |
msa.html |
POLR3B |
msa.html |
TEC |
msa.html |
Line 1 is the reference ensembl human protein sequence for the gene. Lines 2-4 show the translations of our own DNA alignments for human, chimpanzee and macaque respectively, shown in lines 5-7. Lines 8-10 show the corresponding alignment published in ref [1]). Line 11 shows codon position of alignments of ref [1] Line 12-14 show protein translation of ref [1]. Positions within the protein alignment which do not match the protein consensus are highlighted).
n |
gene_id |
msa_link |
1 |
PRM1 |
msa.html |
2 |
IRF7 |
msa.html |
3 |
BCDIN3 |
msa.html |
4 |
KRT36 |
msa.html |
5 |
TMCO5 |
msa.html |
6 |
DLEC1 |
msa.html |
7 |
C14orf121 |
msa.html |
8 |
NPFFR2 |
msa.html |
9 |
FLJ46210 |
msa.html |
10 |
PARD3-007 |
msa.html |
genome |
availability |
coverage |
total contig length |
N50 contig length |
n_contigs |
notes |
chimp (panTro2) |
public |
6x |
2.97 Gb (no gaps) |
29 kb |
265882 |
- |
chimp (constructed) |
on request |
7.26x |
2.83 Gb (no gaps) |
43.5 kb |
145414 |
- |
macaque (rheMac2) |
public |
5.1x |
2.87 Gb (no gaps), 3.01 Gb (with gaps) |
25.7 kb |
- |
20.1e6 used in assembly |
macaque (ours) |
on request |
6.17 x |
2.92 Gb (no gaps) |
34.9 kb |
179250 |
- |
- Higher coverage in principle yields more accurate local assemblies, and a higher quality consensus. This is ideal for scans of positive selection. - full assemblies for both chimpanzee and macaque are available on request.
Genomic alignments for primates are also available at Ensembl [4]. Here we make a 3-way comparison between i) our alignments, ii) those of ref.[1], and iii) Ensembl. For C14orf121, our alignments show a signal of positive selection which we filter out due to its proximity to the end of a genomic alignment (indicated by the splice site), where misalignments may occur. Ensembl alignments indicate that this is the correct thing to do. Ref 2 shows the false signal of positive selection here, due to misalignment. For IRF7, the same situation occurs. Here, however, the filtering is over-aggressive.
gene_id |
msa_link |
C14orf121 |
msa.html |
IRF7 |
msa.html |
Chimpanzee: Clara Clint Gina Masuku NA03448 NA03450 Noemie Yvonne ./Clara: B0_chimpF61 B2_chimpF63 B5_chimpF65 B7_chimpF67 B11_chimpF69 G0_chimpF71 B1_chimpF62 B3_chimpF64 B6_chimpF66 B8_chimpF68 B13_chimpF70 G1_chimpF72 ./Clint: B0_chimpF49 B2_chimpF51 B5_chimpF53 B7_chimpF55 B11_chimpF57 G0_chimpF59 B1_chimpF50 B3_chimpF52 B6_chimpF54 B8_chimpF56 B13_chimpF58 G1_chimpF60 ./Gina: B0_chimpF37 B2_chimpF39 B5_chimpF41 B7_chimpF43 B11_chimpF45 G0_chimpF47 B1_chimpF38 B3_chimpF40 B6_chimpF42 B8_chimpF44 B13_chimpF46 G1_chimpF48 ./Masuku: B0_chimpF73 B2_chimpF75 B5_chimpF77 B7_chimpF79 B11_chimpF81 G0_chimpF83 B1_chimpF74 B3_chimpF76 B6_chimpF78 B8_chimpF80 B13_chimpF82 G1_chimpF84 ./NA03448: B0_chimpF1 B2_chimpF3 B5_chimpF5 B7_chimpF7 B11_chimpF9 G0_chimpF11 B1_chimpF2 B3_chimpF4 B6_chimpF6 B8_chimpF8 B13_chimpF10 G1_chimpF12 ./NA03450: B0_chimpF25 B2_chimpF27 B5_chimpF29 B7_chimpF31 B11_chimpF33 G0_chimpF35 B1_chimpF26 B3_chimpF28 B6_chimpF30 B8_chimpF32 B13_chimpF34 G1_chimpF36 ./Noemie: B0_chimpF13 B2_chimpF15 B5_chimpF17 B7_chimpF19 B11_chimpF21 G0_chimpF23 B1_chimpF14 B3_chimpF16 B6_chimpF18 B8_chimpF20 B13_chimpF22 G1_chimpF24 ./Yvonne: B0_chimpF85 B2_chimpF87 B5_chimpF89 B7_chimpF91 B11_chimpF93 G0_chimpF95 B1_chimpF86 B3_chimpF88 B6_chimpF90 B8_chimpF92 B13_chimpF94 G1_chimpF96
Chimpanzee: Clara Clint Gina Masuku NA03448 NA03450 Noemie Yvonne ./Clara: B0_chimpR61 B2_chimpR63 B5_chimpR65 B7_chimpR67 B11_chimpR69 G0_chimpR71 B1_chimpR62 B3_chimpR64 B6_chimpR66 B8_chimpR68 B13_chimpR70 G1_chimpR72 ./Clint: B0_chimpR49 B2_chimpR51 B5_chimpR53 B7_chimpR55 B11_chimpR57 G0_chimpR59 B1_chimpR50 B3_chimpR52 B6_chimpR54 B8_chimpR56 B13_chimpR58 G1_chimpR60 ./Gina: B0_chimpR37 B2_chimpR39 B5_chimpR41 B7_chimpR43 B11_chimpR45 G0_chimpR47 B1_chimpR38 B3_chimpR40 B6_chimpR42 B8_chimpR44 B13_chimpR46 G1_chimpR48 ./Masuku: B0_chimpR73 B2_chimpR75 B5_chimpR77 B7_chimpR79 B11_chimpR81 G0_chimpR83 B1_chimpR74 B3_chimpR76 B6_chimpR78 B8_chimpR80 B13_chimpR82 G1_chimpR84 ./NA03448: B0_chimpR1 B2_chimpR3 B5_chimpR5 B7_chimpR7 B11_chimpR9 G0_chimpR11 B1_chimpR2 B3_chimpR4 B6_chimpR6 B8_chimpR8 B13_chimpR10 G1_chimpR12 ./NA03450: B0_chimpR25 B2_chimpR27 B5_chimpR29 B7_chimpR31 B11_chimpR33 G0_chimpR35 B1_chimpR26 B3_chimpR28 B6_chimpR30 B8_chimpR32 B13_chimpR34 G1_chimpR36 ./Noemie: B0_chimpR13 B2_chimpR15 B5_chimpR17 B7_chimpR19 B11_chimpR21 G0_chimpR23 B1_chimpR14 B3_chimpR16 B6_chimpR18 B8_chimpR20 B13_chimpR22 G1_chimpR24 ./Yvonne: B0_chimpR85 B2_chimpR87 B5_chimpR89 B7_chimpR91 B11_chimpR93 G0_chimpR95 B1_chimpR86 B3_chimpR88 B6_chimpR90 B8_chimpR92 B13_chimpR94 G1_chimpR96
Humans: NA07348 NA10831 NA10863 NA12753 NA18502 NA18870 NA19201 NA19238 ./NA07348: B0_humanF73 B2_humanF75 B5_humanF77 B7_humanF79 B11_humanF81 G0_humanF83 B1_humanF74 B3_humanF76 B6_humanF78 B8_humanF80 B13_humanF82 G1_humanF84 ./NA10831: 945625_humanF95 B1_humanF86 B3_humanF88 B6_humanF90 B8_humanF92 B13_humanF94 B0_humanF85 B2_humanF87 B5_humanF89 B7_humanF91 B11_humanF93 G1_humanF96 ./NA10863: B0_humanF49 B2_humanF51 B5_humanF53 B7_humanF55 B11_humanF57 G0_humanF59 B1_humanF50 B3_humanF52 B6_humanF54 B8_humanF56 B13_humanF58 G1_humanF60 ./NA12753: 945601_humanF71 B1_humanF62 B3_humanF64 B6_humanF66 B8_humanF68 B13_humanF70 B0_humanF61 B2_humanF63 B5_humanF65 B7_humanF67 B11_humanF69 G1_humanF72 ./NA18502: B0_humanF1 B2_humanF3 B5_humanF5 B7_humanF7 B11_humanF9 G0_humanF11 B1_humanF2 B3_humanF4 B6_humanF6 B8_humanF8 B13_humanF10 G1_humanF12 ./NA18870: B0_humanF37 B2_humanF39 B5_humanF41 B7_humanF43 B11_humanF45 G0_humanF47 B1_humanF38 B3_humanF40 B6_humanF42 B8_humanF44 B13_humanF46 G1_humanF48 ./NA19201: B0_humanF25 B2_humanF27 B5_humanF29 B7_humanF31 B11_humanF33 G0_humanF35 B1_humanF26 B3_humanF28 B6_humanF30 B8_humanF32 B13_humanF34 G1_humanF36 ./NA19238: B0_humanF13 B2_humanF15 B5_humanF17 B7_humanF19 B11_humanF21 G0_humanF23 B1_humanF14 B3_humanF16 B6_humanF18 B8_humanF20 B13_humanF22 G1_humanF24
Humans: NA07348 NA10831 NA10863 NA12753 NA18502 NA18870 NA19201 NA19238 ./NA07348: B0_humanR73 B2_humanR75 B5_humanR77 B7_humanR79 B11_humanR81 G0_humanR83 B1_humanR74 B3_humanR76 B6_humanR78 B8_humanR80 B13_humanR82 G1_humanR84 ./NA10831: B0_humanR85 B2_humanR87 B5_humanR89 B7_humanR91 B11_humanR93 G0_humanR95 B1_humanR86 B3_humanR88 B6_humanR90 B8_humanR92 B13_humanR94 G1_humanR96 ./NA10863: B0_humanR49 B2_humanR51 B5_humanR53 B7_humanR55 B11_humanR57 G0_humanR59 B1_humanR50 B3_humanR52 B6_humanR54 B8_humanR56 B13_humanR58 G1_humanR60 ./NA12753: B0_humanR61 B2_humanR63 B5_humanR65 B7_humanR67 B11_humanR69 G0_humanR71 B1_humanR62 B3_humanR64 B6_humanR66 B8_humanR68 B13_humanR70 G1_humanR72 ./NA18502: B0_humanR1 B2_humanR3 B5_humanR5 B7_humanR7 B11_humanR9 G0_humanR11 B1_humanR2 B3_humanR4 B6_humanR6 B8_humanR8 B13_humanR10 G1_humanR12 ./NA18870: B0_humanR37 B2_humanR39 B5_humanR41 B7_humanR43 B11_humanR45 G0_humanR47 B1_humanR38 B3_humanR40 B6_humanR42 B8_humanR44 B13_humanR46 G1_humanR48 ./NA19201: B0_humanR25 B2_humanR27 B5_humanR29 B7_humanR31 B11_humanR33 G0_humanR35 B1_humanR26 B3_humanR28 B6_humanR30 B8_humanR32 B13_humanR34 G1_humanR36 ./NA19238: B0_humanR13 B2_humanR15 B5_humanR17 B7_humanR19 B11_humanR21 G0_humanR23 B1_humanR14 B3_humanR16 B6_humanR18 B8_humanR20 B13_humanR22 G1_humanR24
[1]Bakewell M., Shi P., Zhang J. (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104: 7489-94. [2]Rhesus macaque genome sequencing and analysis consortium (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234. [3]Rice,P. Longden,I. and Bleasby,A. (2000) EMBOSS: The European Molecular Biology Open Software Suite.Trends in Genetics 16, (6) 276277. [4] Ensembl: www.ensembl.org
source |
gene |
protein alignment |
resequencing alignment |
Bakewell 0 |
HELZ |
msa |
msa |
Bakewell 1 |
NP_115923.1 |
msa |
msa |
Bakewell 2 |
POLR3B |
msa |
msa |
Bakewell 3 |
TEC |
msa |
msa |
Bakewell 5 |
C18orf25 (CR025) |
msa |
msa |
Bakewell 6 |
HECW1 |
msa |
msa |
Bakewell 7 |
ARID1A |
msa |
msa |
Bakewell 8 |
EML5 |
msa |
msa |
Bakewell 11 |
GLCCI1 |
msa |
msa |
Bakewell 13 |
BVES |
msa |
msa |
Gibbs 0 |
IRF7 |
msa |
msa |
Gibbs 1 |
LRRC16B (C14orf121) |
msa |
msa |