Joint Open Genome and Omics Platform (JoGo)

Search by Genic region

geneid	728395
ensemblid	ENSG00000233803.9
hgncid	37287
symbol	TSPY4
name	testis specific protein Y-linked 4
refseq_nuc	NM_001164471.2
refseq_prot	NP_001157943.1
ensembl_nuc	ENST00000426950.6
ensembl_prot	ENSP00000399668.2
mane_status	MANE Select
chr	chrY
start	9337464
end	9340278
strand	+
ver	v1.2
region	chrY:9337464-9340278
region5000	chrY:9332464-9345278
regionname0	TSPY4_chrY_9337464_9340278
regionname5000	TSPY4_chrY_9332464_9345278

ahapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	alen	total	AFR	AMR	EAS	EUR	SAS	JPT	regionname	genename	aa	chr	start	end
a0001	0/0	54	1	0	0	1	0	0	1	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
a0002	0/0	308	1	0	0	1	0	0	1	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
a0003	0/0	308	1	0	0	1	0	0	1	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278

chapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
c0001	0/0	930	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
c0002	0/0	927	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
c0003	0/0	927	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278

thapid	grch38 chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
t0001	0/0	235	2	0	0	2	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
t0002	0/0	235	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278

ghapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
g0001	0/0	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278
g0002	0/0	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278
g0003	0/0	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278

achapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
a0001c0001	0/0	930	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
a0002c0002	0/0	927	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
a0003c0003	0/0	927	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0002	0/0	1164	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
a0002c0002t0001	0/0	1161	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278
a0003c0003t0001	0/0	1161	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	copy fasta	chrY	9332464	9345278

actghapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
a0001c0001t0002g0001	0/0	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278
a0002c0002t0001g0002	0/0	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278
a0003c0003t0001g0003	0/0	1	0	0	1	0	0	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
NA18974	hp1	a0002	c0002	t0001	g0002	EAS	JPT	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278
NA18983	hp1	a0001	c0001	t0002	g0001	EAS	JPT	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278
NA18985	hp1	a0003	c0003	t0001	g0003	EAS	JPT	TSPY4_chrY_9332464_9345278	TSPY4	chrY	9332464	9345278

chr:pos	ref	alt	# # of ahapid:amino-acid(protein) level	ahapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:9337537	C C	CG CG	1	a0001 a0001	1	NA18983.hp1 NA18983.hp1	frameshift_variant	HIGH	c.31dupG c.31dupG	p.Val11fs p.Val11fs	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/6	78/1179	32/945	11/314		INFO_REALIGN_3_PRIME	chrY	9337537
chrY:9337537	C C	T T	1	a0003 a0003	1	NA18985.hp1 NA18985.hp1	missense_variant	MODERATE	c.28C>T c.28C>T	p.Arg10Trp p.Arg10Trp	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/6	74/1179	28/945	10/314			chrY	9337537
chrY:9337579	CG CG	C C	1	a0001 a0001	1	NA18983.hp1 NA18983.hp1	frameshift_variant	HIGH	c.73delG c.73delG	p.Ala25fs p.Ala25fs	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/6	119/1179	73/945	25/314		INFO_REALIGN_3_PRIME	chrY	9337579
chrY:9337649	A A	AG AG	1	a0001 a0001	1	NA18983.hp1 NA18983.hp1	frameshift_variant	HIGH	c.145dupG c.145dupG	p.Ala49fs p.Ala49fs	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/6	192/1179	146/945	49/314		INFO_REALIGN_3_PRIME	chrY	9337649
chrY:9337720	ATGGCGGA others(11): Show ATGGCGGAGGTGGAGGTGG	A A	3	a0001 a0002 a0003 a0001 a0002 a0003	3	NA18974.hp1 NA18983.hp1 NA18985.hp1 NA18974.hp1 NA18983.hp1 NA18985.hp1	disruptive_inframe_deletion	MODERATE	c.239_256delTGGAGGTG others(10): Show c.239_256delTGGAGGTGGTGGCGGAGG	p.Val80_Glu85del p.Val80_Glu85del	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/6	285/1179	239/945	80/314		INFO_REALIGN_3_PRIME	chrY	9337720
chrY:9339094	A A	AG AG	1	a0001 a0001	1	NA18983.hp1 NA18983.hp1	frameshift_variant	HIGH	c.751dupG c.751dupG	p.Ala251fs p.Ala251fs	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	4/6	798/1179	752/945	251/314		INFO_REALIGN_3_PRIME	chrY	9339094
chrY:9339155	C C	CA CA	1	a0001 a0001	1	NA18983.hp1 NA18983.hp1	frameshift_variant	HIGH	c.812dupA c.812dupA	p.Asn271fs p.Asn271fs	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	4/6	859/1179	813/945	271/314		INFO_REALIGN_3_PRIME	chrY	9339155

chr:pos	ref	alt	# # of chapid	chapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:9337644	A A	G G	1	a0001c0001 a0001c0001	1	NA18983.hp1 NA18983.hp1	synonymous_variant	LOW	c.135A>G c.135A>G	p.Val45Val p.Val45Val	TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/6	181/1179	135/945	45/314			chrY	9337644

chr:pos	ref	alt	# # of thapid:transcript level	thapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:9337480	TC TC	T T	1	a0001c0001t0002 a0001c0001t0002	1	NA18983.hp1 NA18983.hp1	5_prime_UTR_variant	MODIFIER	c.-27delC c.-27delC		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/6				27	INFO_REALIGN_3_PRIME	chrY	9337480
chrY:9340108	A A	AT AT	1	a0001c0001t0002 a0001c0001t0002	1	NA18983.hp1 NA18983.hp1	3_prime_UTR_variant	MODIFIER	c.22dupT c.22dupT		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	6/6				23	INFO_REALIGN_3_PRIME	chrY	9340108

chr:pos	ref	alt	# # of ghapid:genebody level	ghapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	genebody_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:9338082	TG TG	T T	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.504+72delG c.504+72delG		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/5					INFO_REALIGN_3_PRIME	chrY	9338082
chrY:9338140	G G	A A	2	a0002c0002t0001g0002 a0003c0003t0001g0003 a0002c0002t0001g0002 a0003c0003t0001g0003	2	NA18974.hp1 NA18985.hp1 NA18974.hp1 NA18985.hp1	intron_variant	MODIFIER	c.504+127G>A c.504+127G>A		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/5						chrY	9338140
chrY:9338163	A A	AG AG	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.504+152dupG c.504+152dupG		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/5					INFO_REALIGN_3_PRIME	chrY	9338163
chrY:9338475	C C	A A	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.505-146C>A c.505-146C>A		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/5						chrY	9338475
chrY:9338481	G G	C C	1	a0002c0002t0001g0002 a0002c0002t0001g0002	1	NA18974.hp1 NA18974.hp1	intron_variant	MODIFIER	c.505-140G>C c.505-140G>C		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/5						chrY	9338481
chrY:9338550	C C	T T	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.505-71C>T c.505-71C>T		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	1/5						chrY	9338550
chrY:9338722	A A	G G	1	a0002c0002t0001g0002 a0002c0002t0001g0002	1	NA18974.hp1 NA18974.hp1	intron_variant	MODIFIER	c.582+24A>G c.582+24A>G		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	2/5						chrY	9338722
chrY:9339221	A A	G G	2	a0002c0002t0001g0002 a0003c0003t0001g0003 a0002c0002t0001g0002 a0003c0003t0001g0003	2	NA18974.hp1 NA18985.hp1 NA18974.hp1 NA18985.hp1	intron_variant	MODIFIER	c.840+36A>G c.840+36A>G		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	4/5						chrY	9339221
chrY:9339592	G G	GGT GGT	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.922+220_922+221ins others(2): Show c.922+220_922+221insTG		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	5/5					INFO_REALIGN_3_PRIME	chrY	9339592
chrY:9339728	G G	A A	3	a0001c0001t0002g0001 a0002c0002t0001g0002 a0003c0003t0001g0003 a0001c0001t0002g0001 a0002c0002t0001g0002 a0003c0003t0001g0003	3	NA18974.hp1 NA18983.hp1 NA18985.hp1 NA18974.hp1 NA18983.hp1 NA18985.hp1	intron_variant	MODIFIER	c.923-340G>A c.923-340G>A		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	5/5						chrY	9339728
chrY:9339788	CA CA	C C	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.923-277delA c.923-277delA		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	5/5					INFO_REALIGN_3_PRIME	chrY	9339788
chrY:9339857	T T	C C	3	a0001c0001t0002g0001 a0002c0002t0001g0002 a0003c0003t0001g0003 a0001c0001t0002g0001 a0002c0002t0001g0002 a0003c0003t0001g0003	3	NA18974.hp1 NA18983.hp1 NA18985.hp1 NA18974.hp1 NA18983.hp1 NA18985.hp1	intron_variant	MODIFIER	c.923-211T>C c.923-211T>C		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	5/5						chrY	9339857
chrY:9339873	A A	AG AG	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.923-194dupG c.923-194dupG		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	5/5					INFO_REALIGN_3_PRIME	chrY	9339873
chrY:9339904	TG TG	T T	1	a0001c0001t0002g0001 a0001c0001t0002g0001	1	NA18983.hp1 NA18983.hp1	intron_variant	MODIFIER	c.923-160delG c.923-160delG		TSPY4	ENSG00000233803.9	transcript	ENST00000426950.6	protein_coding	5/5					INFO_REALIGN_3_PRIME	chrY	9339904