RetrogeneDB ID: retro_ptro_1200

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:2073007..2073855(-)
• Located in intron of: ENSPTRG00000008544

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCUR1
• Ensembl ID: ENSPTRG00000017740
• Aliases: None
• Description: mitochondrial calcium uniporter regulator 1 [Source:HGNC Symbol;Acc:21097]

Sequence

>retro_ptro_1200
GTGCCCTCCCTGCACTTGACCGCCGCCGCTCCGTGCCGGCAGCCTAGGGACTGGGAGCGCTCATGCCTTGGGTATGCCGC
CCCACTGGCTGGACAAAGCGGCACGTGGATGTGCCTGTGGGGCCTTGCCCCGGGCATCGCTGCTGCTGCCAGCGCCCTTC
ACCCATGCTTCAGCATGGTGCCCATACTCACTTCCTGCAGGAGTCTGCTGGATACCTGCAGCTGGAGCACAGGAGAGATT
TCAGCTCTTCTGGGAGTAGGAAGCTCTCCTTTGACACTCGTTCCTTAGTGTGCTTTCTGGAAGACCATGGGTTTGCTACT
CAGCAAGCAGAAATCATTGTGTCTGCATTGGTCAAGGTACTGGAGGCCAACGTGGACATCGTCTACAAAGATATGGCCAC
CAAGATGCAGCAGGAGATCGCTCTTCAGCAAATAATGTCTCAGACTGTGAATGTGAAAAACGATATGATTACTTTGGAGA
AGAGTGAATTTTCAGCCCTCAGAGCAGAACGTGAGAAAATAAAACTCAAACTACATCAGTTAAAACAAGTAATGGATGAA
GTGATTAAAATCCGAACAGATACTAAATTAGACTTCAACCTAGAAAAGAGCAGAGTAAAAGAATTGTATTCGTTGAATGA
AAGGAAGCTGCTGGAATTGAGAACAGAAATAGTGACATTGCATGCCCAGCAAGATCGGGCCGTCACCCAGAGAGATAGGA
AGATAGAAACTGAGGATGCTGGCCCCAAAACCATGCTTGAGTCATACAAGCTTGATAATATTAAATATTTAGCAGGGTCT
ATATTTACGTGCCTAACAGTAGCTCTGGGATTTTATCACCTATGGATC

Alignment

ORF - retro_ptro_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.22 %
• Parental protein coverage: 79.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPSPRLAAAAPRRQLGDWERSRLGYAAPPAGRSGAWRCSPGVAAAAGALPQYHGPAPALVSCRRE-LSLS
          VPS..L.AAAP.RQ..DWERS.LGYAAP.AG.SG.W.C..G.A....A......P....V......L..S
Retrocopy VPSLHLTAAAPCRQPRDWERSCLGYAAPLAGQSGTWMCLWGLAPGIAAAASALHPCFSMVPILTS<LQES

Parental  AGSLQLERKRRDFTSSGSRKLYFDTHALVCLLEDNGLATQQAEIIVSALVKILEANMDIVYKDMVTKMQQ
          AG.LQLE..RRDF.SSGSRKL.FDT..LVC.LED.G.ATQQAEIIVSALVK.LEAN.DIVYKDM.TKMQQ
Retrocopy AGYLQLEH-RRDFSSSGSRKLSFDTRSLVCFLEDHGFATQQAEIIVSALVKVLEANVDIVYKDMATKMQQ

Parental  EITFQQVMSQIANVKKDMIILEKSEFSALRAENEKIKLELHQLKQQVMDEVIKVRTDTKLDFNLEKSRVK
          EI..QQ.MSQ..NVK.DMI.LEKSEFSALRAE.EKIKL.LHQLKQ.VMDEVIK.RTDTKLDFNLEKSRVK
Retrocopy EIALQQIMSQTVNVKNDMITLEKSEFSALRAEREKIKLKLHQLKQ-VMDEVIKIRTDTKLDFNLEKSRVK

Parental  ELYSLNEKKLLELRTEIVALHAQQDRALTQTDRKIETEVAGLKTMLESHKLDNIKYLAGSIFTCLTVALG
          ELYSLNE.KLLELRTEIV.LHAQQDRA.TQ.DRKIETE.AG.KTMLES.KLDNIKYLAGSIFTCLTVALG
Retrocopy ELYSLNERKLLELRTEIVTLHAQQDRAVTQRDRKIETEDAGPKTMLESYKLDNIKYLAGSIFTCLTVALG

Parental  FYRLWI
          FY.LWI
Retrocopy FYHLWI

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	0.07 RPM	5.24 RPM
SRP007412_cerebellum	0.07 RPM	4.77 RPM
SRP007412_heart	0.03 RPM	10.00 RPM
SRP007412_kidney	0.05 RPM	15.22 RPM
SRP007412_liver	0.03 RPM	7.37 RPM
SRP007412_testis	0.00 RPM	10.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1200 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1200 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1795
Gorilla gorilla	retro_ggor_1320
Callithrix jacchus	retro_cjac_2522

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628, retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018, retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273, retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819, retro_ogar_3178,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200 ,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,