Research Article

An Exon-Based Comparative Variant Analysis Pipeline to Study the Scale and Role of Frameshift and Nonsense Mutation in the Human-Chimpanzee Divergence

Table 2

The occurrence patterns of exon-disrupting mutations on chromosome X of humans and chimpanzees.

FrameshiftPremature stop codonSubject peptide exon Alignment scoreFunction annotation

EXON_ID: HUMAN_X_792407 Testis-expressed sequence 13A protein

104351239-CHIMP_X_110562715.92Testis-expressed sequence 13A protein
--HUMAN_X_792407607.24Testis-expressed sequence 13A protein
--CHIMP_X_110628435.54Testis-expressed sequence 13A protein
--MONK_X_10782288.8Testis-expressed sequence 13B protein
--DOG_X_198644272.73

HUMAN_X_806072 Glypican-3 precursor (Intestinal protein OCI-5)

132662038-DOG_X_194924136.67Glypican-3 precursor
--HUMAN_X_806072117.76Glypican-3 precursor
--MONK_X_12252117.76Glypican-3 precursor
--MOUSE_X_2142643116.89Glypican-3 precursor

HUMAN_X_817906 Cancer/testis antigen 1B

153468119-HUMAN_X_818108231.77Cancer/testis antigen 2
--HUMAN_X_817906216.52Cancer/testis antigen 1B
--HUMAN_X_817908117.27Cancer/testis antigen 1B
--MONK_X_13842102.91
--MONK_X_1384584.38
--HUMAN_X_81811078.11Cancer/testis antigen 2
--CHIMP_X_16076578.02Cancer/testis antigen 2
--CHIMP_X_16069252.31

HUMAN_X_815259 Green-sensitive opsin

-153149508MONK_X_13549298.36
--HUMAN_X_815212223.34Green-sensitive opsin
--HUMAN_X_815259223.34Green-sensitive opsin
--CHIMP_X_157000204.73Red-sensitive opsin
--HUMAN_X_815154204.73Red-sensitive opsin
--DOG_X_197028201.64Red-sensitive opsin
--RAT_X_186855200.53opsin 1 (cone pigments)
--OPOSSUM_X_8729199.61

HUMAN_X_781680 Translationally-controlled tumor protein (TCTP) (p23)

--CHIMP_X_92139367.27TPT1-like protein
--HUMAN_X_781680367.27TPT1-like protein
71297119 & 71297149-MONK_1_81482343.44Translationally-controlled tumor protein (TCTP) (p23)
71297119 & 71297149-MONK_9_138306335.33
71297119 & 71297149-MOUSE_6_2214409326.93Tumor protein, translationally-controlled 1
71297119 & 71297149-MOUSE_9_2157034323.69
71297119 & 71297149-RAT_1_18606319.31
--OPOSSUM_1_184539318.51
--OPOSSUM_4_115959302.14
71297122 & 71297149-RAT_16_40873298.6
71297119 & 71297149-RAT_7_212305293.94
HUMAN_X_805870 Heparan-sulfate 6-O-sulfotransferase 2 (EC 2.8.2.-) (HS6ST-2)

131920284-MONK_X_12231316.46Heparan-sulfate 6-O-sulfotransferase 2
131920284-COW_Un_11290273.56
131920284-DOG_X_154771268.61
131920284-MOUSE_X_2142311125.07Heparan sulfate 6-O-sulfotransferase 2
131920284-RAT_X_171447125.07
--HUMAN_X_80587072.68Heparan-sulfate 6-O-sulfotransferase 2
--CHIMP_X_13664268.81Heparan-sulfate 6-O-sulfotransferase 2

HUMAN_1_851437 solute carrier family 26, member 9 isoform A

204150951-CHIMP_1_235519351.23Solute carrier family 26, member 9 isoform A
204150951-MONK_1_76747337.22Solute carrier family 26, member 9 isoform A
--HUMAN_1_851437252.06Solute carrier family 26, member 9 isoform A
--HUMAN_1_851439252.06Solute carrier family 26, member 9 isoform A

HUMAN_1_837766 calcium activated chloride channel 3 precursor

-86881166CHIMP_1_224547183.12Calcium activated chloride channel 3 precursor
--HUMAN_1_837766157.82Calcium activated chloride channel 3 precursor
-86881166COW_3_170345139.02Calcium activated chloride channel 3 precursor
-86881166COW_3_170045138.65Calcium activated chloride channel 3 precursor
-86881166DOG_6_162589128.97Calcium activated chloride channel 3 precursor
-86881166MOUSE_3_2282090123.94Calcium activated chloride channel 3 precursor
-86881166RAT_2_220515118.93Calcium activated chloride channel 3 precursor
-86881166MONK_1_36555103.72Calcium activated chloride channel 3 precursor

HUMAN_X_785548 Putative P2Y purinoceptor 10 (P2Y10) (P2Y-like receptor)

78227761-RAT_X_146932618.82
78227761-MOUSE_X_2200474617.25RIKEN cDNA A630033H20 gene [
--HUMAN_X_785548579.93
--CHIMP_X_98456563.37
78227761-OPOSSUM_X_50171459.83
78227761-MONK_X_9587432.12Putative P2Y purinoceptor 10 (P2Y10)
78227761-HUMAN_X_785541431.7Putative P2Y purinoceptor 10 (P2Y10)
78227761-DOG_X_165474419.31
78227761-COW_Un_11583417.2purinergic receptor P2Y, G—protein coupled, 10

CHIMP_X_29616 Putative ataxin-3-like protein (Machado-Joseph disease protein 1-like)

--CHIMP_X_29616432.13Putative ataxin-3-like protein
-13263802HUMAN_X_705429423.98Putative ataxin-3-like protein
-13263802HUMAN_X_705430394.12Putative ataxin-3-like protein
-13263802MONK_X_3550376.14Putative ataxin-3-like protein

CHIMP_X_144931 Melanoma-associated antigen C3 (MAGE-C3 antigen)

141392714-HUMAN_X_809214555.35Melanoma-associated antigen C3
141392714-HUMAN_X_809208365.01Melanoma-associated antigen C3
--CHIMP_X_144931125.45Melanoma-associated antigen C3
--COW_15_18518550.28
CHIMP_X_146199 AF4/FMR2 family member 2 (Fragile X mental retardation protein 2 homolog)

148435573-HUMAN_X_809667867.67AF4/FMR2 family member 2
148435573-MONK_X_12858854.06AF4/FMR2 family member 2
--CHIMP_X_146586844AF4/FMR2 family member 2
--CHIMP_X_146199840.35AF4/FMR2 family member 2
148435573-DOG_X_165267735.92AF4/FMR2 family member 2
148435573-MOUSE_X_2153947701.72AF4/FMR2 family, member 2
148435573-RAT_X_179540701.09
148435573-COW_X_46124690.64AF4/FMR2 family member 2
148435570-DANIO_14_239638274.31AF4/FMR2 family member 2

CHIMP_X_99308 Cylicin-1 (Cylicin I) (Multiple-band polypeptide I)

83230590-HUMAN_X_7862891347.4Cylicin-1 (Cylicin I)
83230590-MONK_X_97281143.6Cylicin-1 (Cylicin I)
--CHIMP_X_993081123.9Pan troglodytes cylicin, basic protein of sperm head cytoskeleton 1 (CYLC1), mRNA
--MONK_X_9731827.18Cylicin-1 (Cylicin I)
--MONK_X_9741375.4Cylicin-1 (Cylicin I)
--MONK_X_9742316.01Cylicin-1 (Cylicin I)
83230593-DOG_X_87481305.14Cylicin-1 (Cylicin I)
--DOG_X_87432214.85Cylicin-1 (Cylicin I)
--RAT_X_149412164.28

CHIMP_X_142174 HIV Tat-specific factor 1 (Tat-SF1)

135897343-MONK_X_12551108.9HIV Tat-specific factor 1 (Tat-SF1)
135897343 & 135897388 & 135897418-HUMAN_X_807829106.55HIV Tat-specific factor 1 (Tat-SF1)
135897343-DOG_X_18360394.43
135897343-COW_X_2991791.31Hypothetical protein (Fragment)
135897343-RAT_X_17462185.76HIV TAT specific factor 1
135897343-COW_12_9537182.45
135897343-MOUSE_X_214805277.47HIV TAT specific factor 1
--CHIMP_X_14217461.13HIV Tat-specific factor 1 (Tat-SF1)

Note: Numbers under the columns of frameshifts and premature stop codons are the chromosomal positions of the sequence mutations. “ ” presents no annotation available from Ensemble database.