RetrogeneDB ID: retro_hsap_145

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:43368902..43369580(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000225099
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP6V1E1
• Ensembl ID: ENSG00000131100
• Aliases: ATP6V1E1, ATP6E, ATP6E2, ATP6V1E, P31, Vma4
• Description: ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E1 [Source:HGNC Symbol;Acc:857]

Sequence

>retro_hsap_145
ATGGCTGTCAGTGATGCTGACATGCGAAAGCAGATAAAGCATATGATGGCTTTCATTGAATAAGAAGCCAATGAGAAAGC
AGAAGAAATAGATGCAAAGGCAGAAGAAGAGTTCAACATAGAGAAAGGTCAGCTTGTGGAAACCCAAAGACTAAAGATTA
TGGAATATCATGAGAAGAAAGAGAAACAGATTGAGTAGCAGAAGAAAATTCAGATATCCAATTTGATGAATCAAGCAAGG
CTCAAAGTCCTCAGAGCGAGAGATGACCTTATCACAGACCTACTAAATGAAGCAAAACAGAGACTCAGCAAGGTGGTAAA
AGATACAACCAGGTACCAAGTGCTGCTAGATGGACTGGTTCTCCAGGGTTTGTACCAGTTGCTGGAGCACCGAATGATTG
TTCGTTGCAGGAAACAAGACCTTCCTCTGGTAAAGGCTGCGGTGCAAAAGGCAATCCCTATGTACAAAATTGCCACCAAA
AACAATGTTGATGTCCAAATCGACCAGGAGTCCTACCTGCCTGAGGACATAGCTGGTGGAGTTGAGATCTATAATGGTAA
TCATAAAATAAAGGTTTCCAAAACCCCAGAAAGCCAGCTGGATCTCATAGCCCAGCAGATGATGCTAGAAGTCCAGGGAG
CCTTCTTTGGTGCAAAAGCCAACAGGAAATTTTTGGAC

Alignment

ORF - retro_hsap_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKI
          MA.SDAD..KQIKHMMAFIE.EANEKAEEIDAKAEEEFNIEKG.LV.TQRLKIMEY.EKKEKQIE.QKKI
Retrocopy MAVSDADMRKQIKHMMAFIE*EANEKAEEIDAKAEEEFNIEKGQLVETQRLKIMEYHEKKEKQIE*QKKI

Parental  QMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQD
          Q.SNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLE.RMIVRCRKQD
Retrocopy QISNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEHRMIVRCRKQD

Parental  FPLVKAAVQKAIPMYKIATKNDVDVQIDQESYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPE
          .PLVKAAVQKAIPMYKIATKN.VDVQIDQESYLPEDIAGGVEIYNG..KIKVS.T.ES.LDLIAQQMM.E
Retrocopy LPLVKAAVQKAIPMYKIATKNNVDVQIDQESYLPEDIAGGVEIYNGNHKIKVSKTPESQLDLIAQQMMLE

Parental  VRGALFGANANRKFLD
          V.GA.FGA.ANRKFLD
Retrocopy VQGAFFGAKANRKFLD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.08 RPM	85.75 RPM
bodymap2_adrenal	0.02 RPM	95.63 RPM
bodymap2_brain	0.00 RPM	275.30 RPM
bodymap2_breast	0.00 RPM	76.62 RPM
bodymap2_colon	0.00 RPM	110.33 RPM
bodymap2_heart	0.00 RPM	130.46 RPM
bodymap2_kidney	0.00 RPM	191.87 RPM
bodymap2_liver	0.00 RPM	52.15 RPM
bodymap2_lung	0.00 RPM	95.48 RPM
bodymap2_lymph_node	0.00 RPM	78.59 RPM
bodymap2_ovary	0.02 RPM	77.09 RPM
bodymap2_prostate	0.00 RPM	139.39 RPM
bodymap2_skeletal_muscle	0.00 RPM	94.19 RPM
bodymap2_testis	0.00 RPM	95.98 RPM
bodymap2_thyroid	0.00 RPM	107.70 RPM
bodymap2_white_blood_cells	0.00 RPM	127.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_145 was not detected

EST

No EST(s) were mapped for retro_hsap_145 retrocopy.

TSS

No TSS is located nearby retro_hsap_145 retrocopy 5' end.

Lab

retro_hsap_145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_145 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_235

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017489	2 retrocopies	retro_amel_116, retro_amel_1502,
Bos taurus	ENSBTAG00000014238	1 retrocopy	retro_btau_244,
Canis familiaris	ENSCAFG00000016151	7 retrocopies	retro_cfam_1050, retro_cfam_1260, retro_cfam_1354, retro_cfam_1379, retro_cfam_1446, retro_cfam_1997, retro_cfam_73,
Callithrix jacchus	ENSCJAG00000017277	1 retrocopy	retro_cjac_1160,
Cavia porcellus	ENSCPOG00000024559	3 retrocopies	retro_cpor_172, retro_cpor_580, retro_cpor_76,
Equus caballus	ENSECAG00000016487	2 retrocopies	retro_ecab_165, retro_ecab_84,
Echinops telfairi	ENSETEG00000019283	2 retrocopies	retro_etel_1384, retro_etel_6,
Felis catus	ENSFCAG00000008081	4 retrocopies	retro_fcat_153, retro_fcat_602, retro_fcat_61, retro_fcat_654,
Homo sapiens	ENSG00000131100	3 retrocopies	retro_hsap_1126, retro_hsap_145 , retro_hsap_21,
Gorilla gorilla	ENSGGOG00000015027	2 retrocopies	retro_ggor_105, retro_ggor_235,
Loxodonta africana	ENSLAFG00000003802	4 retrocopies	retro_lafr_1220, retro_lafr_123, retro_lafr_134, retro_lafr_742,
Microcebus murinus	ENSMICG00000010643	6 retrocopies	retro_mmur_1214, retro_mmur_1234, retro_mmur_813, retro_mmur_886, retro_mmur_971, retro_mmur_978,
Myotis lucifugus	ENSMLUG00000014876	2 retrocopies	retro_mluc_312, retro_mluc_57,
Macaca mulatta	ENSMMUG00000021477	4 retrocopies	retro_mmul_1102, retro_mmul_139, retro_mmul_370, retro_mmul_873,
Monodelphis domestica	ENSMODG00000018452	4 retrocopies	retro_mdom_1456, retro_mdom_1853, retro_mdom_248, retro_mdom_489,
Mustela putorius furo	ENSMPUG00000018109	2 retrocopies	retro_mputfur_23, retro_mputfur_4,
Mus musculus	ENSMUSG00000019210	1 retrocopy	retro_mmus_122,
Nomascus leucogenys	ENSNLEG00000007839	1 retrocopy	retro_nleu_18,
Otolemur garnettii	ENSOGAG00000013886	5 retrocopies	retro_ogar_1255, retro_ogar_1401, retro_ogar_2930, retro_ogar_6, retro_ogar_839,