RetrogeneDB ID: retro_hsap_21

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:46739169..46739850(-)
• Located in intron of: ENSG00000250565

Retrocopy information

• Ensembl ID: ENSG00000250565
• Aliases: ATP6V1E2, ATP6E1, ATP6EL2, ATP6V1EL2, VMA4
• Status: KNOWN_PROTEIN_CODING

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_21
ATGGCCCTGAGTGATGTCGATGTGAAAAAGCAGATTAAGCACATGATGGCTTTCATTGAGCAGGAAGCCAATGAGAAAGC
AGAGGAAATCGATGCCAAGGCTGAGGAAGAGTTTAACATTGAGAAAGGACGCCTCGTGCAAACCCAACGACTGAAGATTA
TGGAGTATTATGAGAAAAAGGAGAAGCAGATAGAGCAGCAGAAGAAAATCCTGATGTCCACCATGAGGAATCAGGCGAGG
CTGAAAGTCCTGAGAGCCCGAAATGACCTCATCTCAGATTTGCTCAGTGAGGCGAAGCTGAGACTCAGCAGGATTGTGGA
GGACCCAGAGGTCTACCAGGGGCTGCTGGATAAACTGGTGCTCCAGGGTCTGCTCCGACTGCTGGAACCTGTGATGATTG
TACGCTGCCGGCCACAAGACCTCCTCCTGGTGGAGGCTGCTGTACAAAAAGCCATCCCCGAGTACATGACAATTTCCCAG
AAACATGTGGAGGTCCAGATTGATAAAGAGGCATACCTGGCTGTGAATGCAGCTGGAGGTGTGGAGGTCTACAGTGGCAA
TCAGAGAATAAAGGTTTCAAATACCTTGGAAAGCCGACTGGATCTCTCAGCCAAGCAAAAGATGCCAGAAATACGAATGG
CCTTGTTTGGTGCTAACACCAACAGAAAGTTCTTTATATAA

Alignment

ORF - retro_hsap_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.23 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKI
          MALSD.DV.KQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKI
Retrocopy MALSDVDVKKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKI

Parental  QMSNLMNQARLKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQD
          .MS...NQARLKVLRAR.DLI.DLL.EAK.RLS..V.D...YQ.LLD.LVLQGL..LLEP.MIVRCR.QD
Retrocopy LMSTMRNQARLKVLRARNDLISDLLSEAKLRLSRIVEDPEVYQGLLDKLVLQGLLRLLEPVMIVRCRPQD

Parental  FPLVKAAVQKAIPMYKIATKNDVDVQIDQESYLPEDIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPE
          ..LV.AAVQKAIP.Y.......V.VQID.E.YL....AGGVE.Y.G...IKVSNTLESRLDL.A.Q.MPE
Retrocopy LLLVEAAVQKAIPEYMTISQKHVEVQIDKEAYLAVNAAGGVEVYSGNQRIKVSNTLESRLDLSAKQKMPE

Parental  VRGALFGANANRKF
          .R.ALFGAN.NRKF
Retrocopy IRMALFGANTNRKF

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	0.52 RPM	85.75 RPM
bodymap2_adrenal	2.07 RPM	95.63 RPM
bodymap2_brain	1.43 RPM	275.30 RPM
bodymap2_breast	1.30 RPM	76.62 RPM
bodymap2_colon	0.39 RPM	110.33 RPM
bodymap2_heart	0.55 RPM	130.46 RPM
bodymap2_kidney	0.74 RPM	191.87 RPM
bodymap2_liver	0.76 RPM	52.15 RPM
bodymap2_lung	0.23 RPM	95.48 RPM
bodymap2_lymph_node	1.26 RPM	78.59 RPM
bodymap2_ovary	1.35 RPM	77.09 RPM
bodymap2_prostate	1.35 RPM	139.39 RPM
bodymap2_skeletal_muscle	1.05 RPM	94.19 RPM
bodymap2_testis	18.95 RPM	95.98 RPM
bodymap2_thyroid	1.73 RPM	107.70 RPM
bodymap2_white_blood_cells	2.91 RPM	127.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_21 was not detected

EST

2 EST(s) were mapped to retro_hsap_21 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF887170	46739440	46739656	99.6	215	1	214
BF887184	46739499	46739656	95.6	153	4	148

TSS

No TSS is located nearby retro_hsap_21 retrocopy 5' end.

Lab

retro_hsap_21 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_21 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_105
Pongo abelii	retro_pabe_189
Macaca mulatta	retro_mmul_139
Mus musculus	retro_mmus_122
Rattus norvegicus	retro_rnor_383
Oryctolagus cuniculus	retro_ocun_88
Canis familiaris	retro_cfam_73
Equus caballus	retro_ecab_84

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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,
Procavia capensis	ENSPCAG00000016094	1 retrocopy	retro_pcap_455,
Pongo abelii	ENSPPYG00000011560	1 retrocopy	retro_pabe_189,
Rattus norvegicus	ENSRNOG00000011905	1 retrocopy	retro_rnor_383,
Sarcophilus harrisii	ENSSHAG00000008300	2 retrocopies	retro_shar_501, retro_shar_780,
Sus scrofa	ENSSSCG00000000767	3 retrocopies	retro_sscr_788, retro_sscr_789, retro_sscr_83,
Ictidomys tridecemlineatus	ENSSTOG00000022031	3 retrocopies	retro_itri_579, retro_itri_630, retro_itri_64,
Tarsius syrichta	ENSTSYG00000010679	5 retrocopies	retro_tsyr_1093, retro_tsyr_1812, retro_tsyr_23, retro_tsyr_532, retro_tsyr_797,
Tursiops truncatus	ENSTTRG00000015931	1 retrocopy	retro_ttru_1,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	2.85 RPM
CEU_NA11843	2.64 RPM
CEU_NA11930	2.15 RPM
CEU_NA12004	3.15 RPM
CEU_NA12400	2.74 RPM
CEU_NA12751	1.77 RPM
CEU_NA12760	2.38 RPM
CEU_NA12827	3.25 RPM
CEU_NA12872	3.65 RPM
CEU_NA12873	3.29 RPM
FIN_HG00183	3.10 RPM
FIN_HG00277	3.07 RPM
FIN_HG00315	3.04 RPM
FIN_HG00321	1.87 RPM
FIN_HG00328	2.49 RPM
FIN_HG00338	2.55 RPM
FIN_HG00349	1.79 RPM
FIN_HG00375	3.72 RPM
FIN_HG00377	2.82 RPM
FIN_HG00378	2.34 RPM
GBR_HG00099	2.76 RPM
GBR_HG00111	2.04 RPM
GBR_HG00114	2.31 RPM
GBR_HG00119	3.09 RPM
GBR_HG00131	1.67 RPM
GBR_HG00133	3.09 RPM
GBR_HG00134	1.88 RPM
GBR_HG00137	2.67 RPM
GBR_HG00142	3.00 RPM
GBR_HG00143	2.27 RPM
TSI_NA20512	2.91 RPM
TSI_NA20513	2.25 RPM
TSI_NA20518	1.83 RPM
TSI_NA20532	2.92 RPM
TSI_NA20538	2.72 RPM
TSI_NA20756	4.10 RPM
TSI_NA20765	2.32 RPM
TSI_NA20771	2.30 RPM
TSI_NA20786	1.91 RPM
TSI_NA20798	2.78 RPM
YRI_NA18870	2.27 RPM
YRI_NA18907	3.19 RPM
YRI_NA18916	2.67 RPM
YRI_NA19093	2.89 RPM
YRI_NA19099	4.13 RPM
YRI_NA19114	2.44 RPM
YRI_NA19118	2.01 RPM
YRI_NA19213	2.25 RPM
YRI_NA19214	2.56 RPM
YRI_NA19223	1.99 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).