RetrogeneDB ID: retro_ptro_2248

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:37322241..37322529(-)
• Located in intron of: ENSPTRG00000017015

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATP6V1G1
• Ensembl ID: ENSPTRG00000021290
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1; V-type proton ATPase subunit G 1 [Source:UniProtKB/TrEMBL;Acc:H2QXR5]

Sequence

>retro_ptro_2248
ATGGCCAGTCAGTCTCAGGGGATCCAGTAGCTGCTGCAGGTTGCTGAAAAGGGTGTCTGAGATCTGCAGTGAAAGAACCG
GAGGGAGAAGCAGGCCAAAGCAGCAGTTCAAGGTGAAATTGAACAATATTGCCTGCAGAGGGAGGAAGAGTTCAAGGCCA
AGGAGGCTGCTGCCCTGCGATCCCAAGGCAGCTGCAGCACTAAAGTAGAGGAGACCCAGGAGAAGAGAACCATCTGGAAG
CAGTTTAGGCAGAAGAGGGGTGAAGTCTTGGCCTTTTTCTGCAACATC

Alignment

ORF - retro_ptro_2248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.15 %
• Parental protein coverage: 89.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAAALGSRGSCS
          MASQSQGIQ.LL......AEK.......KNRR.KQAK...Q.EIEQY.LQRE.EFKAKEAAAL.S.GSCS
Retrocopy MASQSQGIQ*LL----QVAEKGV*DLQ*KNRREKQAKAAVQGEIEQYCLQREEEFKAKEAAALRSQGSCS

Parental  TEVEKETQEKMTILQTYFRQNRDEVLDNLLAFVCDI
          T.VE.ETQEK.TI....FRQ.R.EVL....AF.C.I
Retrocopy TKVE-ETQEKRTIWK-QFRQKRGEVL----AFFCNI

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	29.10 RPM
SRP007412_cerebellum	0.00 RPM	37.68 RPM
SRP007412_heart	0.00 RPM	23.99 RPM
SRP007412_kidney	0.00 RPM	68.75 RPM
SRP007412_liver	0.00 RPM	40.23 RPM
SRP007412_testis	0.11 RPM	52.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2248 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2248 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3198
Gorilla gorilla	retro_ggor_1331
Macaca mulatta	retro_mmul_2018

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020461	3 retrocopies	retro_cjac_1788, retro_cjac_2513, retro_cjac_76,
Dasypus novemcinctus	ENSDNOG00000008083	15 retrocopies	retro_dnov_1173, retro_dnov_1447, retro_dnov_1475, retro_dnov_1504, retro_dnov_1588, retro_dnov_1645, retro_dnov_193, retro_dnov_1998, retro_dnov_2179, retro_dnov_218, retro_dnov_2416, retro_dnov_245, retro_dnov_336, retro_dnov_479, retro_dnov_790,
Dipodomys ordii	ENSDORG00000014850	5 retrocopies	retro_dord_434, retro_dord_466, retro_dord_614, retro_dord_640, retro_dord_749,
Echinops telfairi	ENSETEG00000008080	3 retrocopies	retro_etel_350, retro_etel_594, retro_etel_996,
Homo sapiens	ENSG00000136888	3 retrocopies	retro_hsap_3198, retro_hsap_4049, retro_hsap_763,
Gorilla gorilla	ENSGGOG00000004011	4 retrocopies	retro_ggor_1331, retro_ggor_2215, retro_ggor_2717, retro_ggor_632,
Loxodonta africana	ENSLAFG00000013437	2 retrocopies	retro_lafr_1002, retro_lafr_39,
Myotis lucifugus	ENSMLUG00000008657	2 retrocopies	retro_mluc_373, retro_mluc_839,
Macaca mulatta	ENSMMUG00000004899	4 retrocopies	retro_mmul_1783, retro_mmul_2018, retro_mmul_2046, retro_mmul_331,
Monodelphis domestica	ENSMODG00000019574	1 retrocopy	retro_mdom_1675,
Mus musculus	ENSMUSG00000039105	5 retrocopies	retro_mmus_2028, retro_mmus_2784, retro_mmus_2787, retro_mmus_3316, retro_mmus_819,
Nomascus leucogenys	ENSNLEG00000016833	2 retrocopies	retro_nleu_1151, retro_nleu_3045,
Pan troglodytes	ENSPTRG00000021290	2 retrocopies	retro_ptro_2248 , retro_ptro_2744,
Ictidomys tridecemlineatus	ENSSTOG00000015857	5 retrocopies	retro_itri_1102, retro_itri_1235, retro_itri_1281, retro_itri_1340, retro_itri_1669,
Tupaia belangeri	ENSTBEG00000010985	2 retrocopies	retro_tbel_2147, retro_tbel_786,
Tarsius syrichta	ENSTSYG00000011474	3 retrocopies	retro_tsyr_1865, retro_tsyr_2141, retro_tsyr_614,