Joint Open Genome and Omics Platform (JoGo)

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Item	Value
geneid	100289087
ensemblid	ENSG00000236424.7
hgncid	37473
symbol	TSPY10
name	testis specific protein Y-linked 10
refseq_nuc	NM_001282469.3
refseq_prot	NP_001269398.1
ensembl_nuc	ENST00000428845.6
ensembl_prot	ENSP00000406407.2
mane_status	MANE Select
chr	chrY
start	9527880
end	9530676
strand	+
ver	v1.2
region	chrY:9527880-9530676
region5000	chrY:9522880-9535676
regionname0	TSPY10_chrY_9527880_9530676
regionname5000	TSPY10_chrY_9522880_9535676

ahapid	grch38/ chm13v2	alen	total	AFR	AMR	EAS	EUR	SAS	JPT	regionname	genename	aa	chr	start	end
a0001	0/0	308	1	0	0	1	0	0	1	TSPY10_chrY_9522880_9535676	TSPY10	MRPEG others(303): Show MRPEGSLTYRVPERLRQGFCGVGRAAQALVCASAKEGTAFRMEAVQEGAA GVESEQAALGEEAVLLLDDIMAEVEVVAEEEGLVERREEAQRAQQAVPGP GPMTPESALEELLAVQVELEPVNAQARKAFSRQREKMERRRKPHLDRRGA VIQSVPGFWANVIANHPQMSALITDEDEDMLSYMVSLEVEEEKHPVHLCK IMLFFRSNPYFQNKVITKEYLVNITEYRASHSTPIEWYPDYEVEAYRRRH HNSSLNFFNWFSDHNFAGSNKIAEILCKDLWRNPLQYYKRMKPPEEGTET SGDSQLLS	chrY	9522880	9535676

achapid	grch38/ chm13v2	alen	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	aseq	cseq	chr	start	end
a0001c0001	0/0		924	1	0	0	1	0	0	TSPY10_chrY_9522880_9535676	TSPY10		ATGCG others(919): Show ATGCGCCCTGAGGGCTCGCTGACCTACCGGGTGCCAGAGAGGCTGCGGCA GGGTTTCTGTGGCGTGGGTCGGGCAGCACAGGCCTTGGTGTGTGCGAGTG CCAAGGAGGGCACCGCCTTCAGGATGGAGGCTGTACAGGAGGGGGCGGCC GGGGTGGAGAGTGAGCAGGCGGCTTTGGGGGAGGAGGCGGTGCTGCTGTT GGATGACATAATGGCGGAGGTGGAGGTGGTGGCGGAGGAGGAGGGCCTCG TGGAGCGGCGGGAGGAGGCCCAGCGGGCACAGCAGGCTGTGCCTGGCCCT GGGCCCATGACCCCAGAGTCTGCACTGGAGGAGCTGCTGGCCGTTCAGGT GGAGCTGGAGCCGGTTAATGCCCAAGCCAGGAAGGCCTTTTCTCGGCAGC GGGAAAAGATGGAGCGGAGGCGCAAGCCCCACCTAGACCGCAGAGGCGCC GTCATCCAGAGCGTCCCTGGCTTCTGGGCCAATGTTATTGCAAACCACCC CCAGATGTCAGCCCTGATCACTGACGAAGATGAAGACATGCTGAGCTACA TGGTCAGCCTGGAGGTGGAAGAAGAGAAGCATCCTGTTCATCTCTGCAAG ATCATGTTGTTCTTTCGGAGTAACCCCTACTTCCAGAATAAAGTGATTAC CAAGGAATATCTGGTGAACATCACAGAATACAGGGCTTCTCATTCCACTC CAATTGAGTGGTATCCGGATTATGAAGTGGAGGCCTATCGCCGCAGACAC CACAACAGCAGCCTTAACTTCTTCAACTGGTTCTCTGACCACAACTTCGC AGGATCTAACAAGATTGCTGAGATCCTATGTAAGGACCTGTGGCGCAATC CCCTGCAATACTACAAGAGGATGAAGCCACCTGAAGAGGGAACAGAGACA TCAGGGGACTCCCAGTTGTTGAGT	chrY	9522880	9535676

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1162	1	0	0	1	0	0	TSPY10_chrY_9522880_9535676	TSPY10	GGCCC others(1157): Show GGCCCTTCGCGCGCAGTCCCTTAGGGGGCGCCTGGAAGCCCGGCGCATGC GCCCTGAGGGCTCGCTGACCTACCGGGTGCCAGAGAGGCTGCGGCAGGGT TTCTGTGGCGTGGGTCGGGCAGCACAGGCCTTGGTGTGTGCGAGTGCCAA GGAGGGCACCGCCTTCAGGATGGAGGCTGTACAGGAGGGGGCGGCCGGGG TGGAGAGTGAGCAGGCGGCTTTGGGGGAGGAGGCGGTGCTGCTGTTGGAT GACATAATGGCGGAGGTGGAGGTGGTGGCGGAGGAGGAGGGCCTCGTGGA GCGGCGGGAGGAGGCCCAGCGGGCACAGCAGGCTGTGCCTGGCCCTGGGC CCATGACCCCAGAGTCTGCACTGGAGGAGCTGCTGGCCGTTCAGGTGGAG CTGGAGCCGGTTAATGCCCAAGCCAGGAAGGCCTTTTCTCGGCAGCGGGA AAAGATGGAGCGGAGGCGCAAGCCCCACCTAGACCGCAGAGGCGCCGTCA TCCAGAGCGTCCCTGGCTTCTGGGCCAATGTTATTGCAAACCACCCCCAG ATGTCAGCCCTGATCACTGACGAAGATGAAGACATGCTGAGCTACATGGT CAGCCTGGAGGTGGAAGAAGAGAAGCATCCTGTTCATCTCTGCAAGATCA TGTTGTTCTTTCGGAGTAACCCCTACTTCCAGAATAAAGTGATTACCAAG GAATATCTGGTGAACATCACAGAATACAGGGCTTCTCATTCCACTCCAAT TGAGTGGTATCCGGATTATGAAGTGGAGGCCTATCGCCGCAGACACCACA ACAGCAGCCTTAACTTCTTCAACTGGTTCTCTGACCACAACTTCGCAGGA TCTAACAAGATTGCTGAGATCCTATGTAAGGACCTGTGGCGCAATCCCCT GCAATACTACAAGAGGATGAAGCCACCTGAAGAGGGAACAGAGACATCAG GGGACTCCCAGTTGTTGAGTTGAATATGATGGAGCATCAGATTTTACCTA ATACAGCAGAACTCCTAAAAAGTTACAGCCATATGCAGGACGGCAGTACT CAGCATGGTCTTTATGCACAGGAACTAAAGGAAAAAGAGATCGAGTCACA AAAATTCAGGAAGAGGGGGTAAATGTGGATTGTATGGAATGAAAAATAAA CATTCTCAAGGA	chrY	9522880	9535676

actghapid	grch38/ chm13v2	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
a0001c0001t0001g0001	0/0	1	0	0	1	0	0	TSPY10_chrY_9522880_9535676	TSPY10	chrY	9522880	9535676

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
NA19089	hp2	a0001	c0001	t0001	g0001	EAS	JPT	TSPY10_chrY_9522880_9535676	TSPY10	chrY	9522880	9535676

view	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

view	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:9529767	G G	A A	1	a0001c0001 a0001c0001	1	NA19089.hp2 NA19089.hp2	synonymous_variant	LOW	c.900G>A c.900G>A	p.Thr300Thr p.Thr300Thr	TSPY10	ENSG00000236424.7	transcript	ENST00000428845.6	protein_coding	5/6	946/1161	900/927	300/308			chrY	9529767

view	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:9530575	C C	CT CT	1	a0001c0001t0001 a0001c0001t0001	1	NA19089.hp2 NA19089.hp2	3_prime_UTR_variant	MODIFIER	c.89dupT c.89dupT		TSPY10	ENSG00000236424.7	transcript	ENST00000428845.6	protein_coding	6/6				90	INFO_REALIGN_3_PRIME	chrY	9530575
	chrY:9530601	C C	G G	1	a0001c0001t0001 a0001c0001t0001	1	NA19089.hp2 NA19089.hp2	3_prime_UTR_variant	MODIFIER	c.113C>G c.113C>G		TSPY10	ENSG00000236424.7	transcript	ENST00000428845.6	protein_coding	6/6				113		chrY	9530601

view	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:9530052	G G	C C	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA19089.hp2 NA19089.hp2	intron_variant	MODIFIER	c.904+281G>C c.904+281G>C		TSPY10	ENSG00000236424.7	transcript	ENST00000428845.6	protein_coding	5/5						chrY	9530052
	chrY:9530126	G G	A A	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA19089.hp2 NA19089.hp2	intron_variant	MODIFIER	c.905-340G>A c.905-340G>A		TSPY10	ENSG00000236424.7	transcript	ENST00000428845.6	protein_coding	5/5						chrY	9530126