RetrogeneDB ID: retro_ptro_327

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:103981680..103982245(-)
• Located in intron of: ENSPTRG00000001017

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD2
• Ensembl ID: ENSPTRG00000018757
• Aliases: None
• Description: Pan troglodytes superoxide dismutase 2, mitochondrial (SOD2), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001009022]

Sequence

>retro_ptro_327
CACAGCCTCCTAGGCTTATCTTATGATTATGGTGCCCTGGGGCCTAATATTAATGTACACATCATACAGCTAAACCACAG
AAAATACCAGGTCATTGGGTGAATAACTTGACTGCCTTCAAGGAGAAATAAAAAGAGGTTCTGGTAAAAGGTGATGTTAG
AATCCAGATAACTCTTCAGCCTGCACTTAAGTTCAGTGGTAGAGACCATATTACTCTTACCATTTTATGGACAAACCTCA
GCCTCAGTGGTAGTGGAGGATTGAAAGGGGAGTTTCTGGGAGCCATCAAATATTACTTTTGTTCCTTTGATTCACTTAAG
GAGAAGCTGACAGATGTATCTGTTAGTATTCAAAGTTCCAGTTGTGGTTGGCTTGGTTTCATTAAGTAAAAGAACTCTTA
TAGATCATTGCTTGTCCTAATCAGGATCCATTGCAAAGATCATCAGGACTTATTCTACTTTTGGGGATTGGTGTATGGAA
GTTCTCTTAACTGTCTTCAGCATAAAAAATGTCAGACTTGATTATCCAAAAGCTTTTTTGGAGTGTAATCAACTGAGAGA
ATGTA

Alignment

ORF - retro_ptro_327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.55 %
• Parental protein coverage: 84.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HSLPDLPYDYGALEPHINAQIMQLHHSKHHAA-YVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGG
          HSL..L.YDYGAL.P.IN..I.QL.H.K......VNNL....EK..E.L.KGDV..QI.LQPALKF.G..
Retrocopy HSLLGLSYDYGALGPNINVHIIQLNHRKYQVI<WVNNLTAFKEK*KEVLVKGDVRIQITLQPALKFSGRD

Parental  HINHSIFWTNLSPNGGGEPKGEMLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGH-LQIAA
          HI...I.WTNLS..G.G..KGE.L.AIK..F.SFD..KEKLT..SV..Q.S..GWLGF.K.....L.I.A
Retrocopy HITLTILWTNLSLSGSGGLKGEFLGAIKYYFCSFDSLKEKLTDVSVSIQSSSCGWLGFIK*KNS<L*IIA

Parental  CPNQDPLQGTTGLIPLLGIDVWEHA-YYLQYK-NVRPDYLKA-IWNVINWENV
          CPNQDPLQ...GLI.LLGI.VW......LQ.K.NVR.DY.KA..W.VIN.ENV
Retrocopy CPNQDPLQRSSGLILLLGIGVWKFS>NCLQHK>NVRLDYPKA>FWSVIN*ENV

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	50.57 RPM
SRP007412_cerebellum	0.00 RPM	75.68 RPM
SRP007412_heart	0.00 RPM	223.76 RPM
SRP007412_kidney	0.00 RPM	410.69 RPM
SRP007412_liver	0.00 RPM	3765.38 RPM
SRP007412_testis	0.00 RPM	87.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_327 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_327 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_430
Gorilla gorilla	retro_ggor_419

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015466	1 retrocopy	retro_amel_786,
Canis familiaris	ENSCAFG00000000671	1 retrocopy	retro_cfam_1795,
Choloepus hoffmanni	ENSCHOG00000003215	4 retrocopies	retro_chof_1952, retro_chof_1966, retro_chof_2620, retro_chof_937,
Callithrix jacchus	ENSCJAG00000011664	1 retrocopy	retro_cjac_3032,
Dasypus novemcinctus	ENSDNOG00000007907	1 retrocopy	retro_dnov_1653,
Equus caballus	ENSECAG00000011797	2 retrocopies	retro_ecab_70, retro_ecab_840,
Echinops telfairi	ENSETEG00000016400	1 retrocopy	retro_etel_731,
Felis catus	ENSFCAG00000002843	1 retrocopy	retro_fcat_1200,
Homo sapiens	ENSG00000112096	1 retrocopy	retro_hsap_430,
Gorilla gorilla	ENSGGOG00000008212	1 retrocopy	retro_ggor_419,
Myotis lucifugus	ENSMLUG00000012242	1 retrocopy	retro_mluc_528,
Monodelphis domestica	ENSMODG00000007521	1 retrocopy	retro_mdom_373,
Mustela putorius furo	ENSMPUG00000005045	1 retrocopy	retro_mputfur_1382,
Nomascus leucogenys	ENSNLEG00000011061	1 retrocopy	retro_nleu_1023,
Otolemur garnettii	ENSOGAG00000017100	1 retrocopy	retro_ogar_1123,
Pongo abelii	ENSPPYG00000017143	1 retrocopy	retro_pabe_292,
Pan troglodytes	ENSPTRG00000018757	1 retrocopy	retro_ptro_327 ,
Pteropus vampyrus	ENSPVAG00000005302	1 retrocopy	retro_pvam_288,
Rattus norvegicus	ENSRNOG00000019048	1 retrocopy	retro_rnor_2221,
Sarcophilus harrisii	ENSSHAG00000014795	1 retrocopy	retro_shar_210,
Ictidomys tridecemlineatus	ENSSTOG00000008738	1 retrocopy	retro_itri_1432,
Tupaia belangeri	ENSTBEG00000002100	1 retrocopy	retro_tbel_665,
Tarsius syrichta	ENSTSYG00000000457	1 retrocopy	retro_tsyr_183,
Tursiops truncatus	ENSTTRG00000014364	1 retrocopy	retro_ttru_265,