RetrogeneDB ID: retro_ptro_1652

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:153519376..153520332(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM8A1
• Ensembl ID: ENSPTRG00000017751
• Aliases: None
• Description: None

Sequence

>retro_ptro_1652
GAAGTGTCGGAAGCTGCGGCGCCGTGGGAGAGGCCGGCGCGGCTGAGCGCCCTTGGGTGCTCCTGGCGAGTGCACGAGTG
ACTGTGGCAGTCCTGCTGCGGCTACCTCACCTGGCGCAGTGGCCCCGCTACACTCCCCGACTGCTGTAGCCCCCAACCGT
CCCGGCAGAGCTTCTCTTTGGAGGCACTGCCGTCCCCCAGGCCGCGGCGCCGCCATCCCCGCGGCTGGGCTATTACAACC
CCTTCTACTTCCTGAGCCCCAGGGCCGCGGGGGCCTGACCCGGGGGCAGCTGCTGGCATCAGCACCCCTGCTACAGTCAC
GTGCCTGGGACCCTGGGTTCCTCATGTGCAGGCGTCAATCCGGGCCACTCCAGTGACAAAGGTAGGATCTGCAGCCCCTT
CCCGAAGCCCGAGTGAGACCGGGCAACCGGCAGGCAAAGAATATGTTATTCCATCCTTGGGCCACGGGTGGCAAGGATGG
TGGATTTCTTTATTATCTTCTTTGTAAAAGCAACCATTGTCTTAAGCATTATGCACCTCAGTGGGATAAAGGATATCTCT
AAGTTTGCTATGCATTATATAATGGAAGAAATAGATGAGGACACATCAATGGAAGACTTGCTGAAAATGATGGTTGTGGC
TCTTATATACAGATTATTAGTTTGTTTTTATGAGATAATTTTCATTTGGGGAGCAGGTGGAGCTACCCCAGGGAAGCTCT
TGATGGGGCTTCGAGTTGTGACACGTGATACATTAGTGCTTATTGCACTAAGTCGTGTTTTAGTGATTCCTTTTTCAAAT
GTTAGCATTACAACGTCCACTATACGAGCTTTGATCAAGAATTTTTTGATTGCTTCTTTTTTCCCTGCTTTTATCACACT
GCTGTTTTTTCAACATAATCGAACAGCCTATGACATTGTAGCAGGAACCATTGTGGTAAAAAGAAATGGGGTCAGA

Alignment

ORF - retro_ptro_1652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 78.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EAPEAAAPRERPARLSAREYSRQVHEWLWQSYCGYLTWHSGLAAFPAYCSPQPSPQSFPS-GGAAVPQAA
          E..EAAAP.ERPARLSA...S..VHE.LWQS.CGYLTW.SG.A..P..CSPQPS.QSF...GG.AVPQAA
Retrocopy EVSEAAAPWERPARLSALGCSWRVHE*LWQSCCGYLTWRSGPATLPDCCSPQPSRQSFSL<GGTAVPQAA

Parental  APPPPQLGYYNPFYFLSPGAAG-PDPRTAAGISTPAPVAGLGPRAPHVQASVRATPVTRVGSAA-PSRSP
          APP.P.LGYYNPFYFLSP.AAG.PDP..AAGISTPA.V..LGP..PHVQAS.RATPVT.VGSAA.P...P
Retrocopy APPSPRLGYYNPFYFLSPRAAG>PDPGAAAGISTPATVTCLGPWVPHVQASIRATPVTKVGSAA<PFPKP

Parental  SETGRQAGREYVIPSLAHRFMAEMVDFFILFFIKATIVLSIMHLSGIKDISKFAMHYIIEEIDEDTSMED
          .E..R..GR.....S......A.MVDFFI.FF.KATIVLSIMHLSGIKDISKFAMHYI.EEIDEDTSMED
Retrocopy -E*DRATGRQRICYSILGPRVARMVDFFIIFFVKATIVLSIMHLSGIKDISKFAMHYIMEEIDEDTSMED

Parental  LQKMMVVALIYRLLVCFYEIICIWGAGGATPGKFLLGLRVVTCDTSVLIAPSRVLVIPSSNVSITTSTIR
          L.KMMVVALIYRLLVCFYEII.IWGAGGATPGK.L.GLRVVT.DT.VLIA.SRVLVIP.SNVSITTSTIR
Retrocopy LLKMMVVALIYRLLVCFYEIIFIWGAGGATPGKLLMGLRVVTRDTLVLIALSRVLVIPFSNVSITTSTIR

Parental  ALIKNFSIASFFPAFITLLFFQHNRTAYDIVAGTIVVKRNGVR
          ALIKNF.IASFFPAFITLLFFQHNRTAYDIVAGTIVVKRNGVR
Retrocopy ALIKNFLIASFFPAFITLLFFQHNRTAYDIVAGTIVVKRNGVR

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	37.86 RPM
SRP007412_cerebellum	0.00 RPM	39.72 RPM
SRP007412_heart	0.00 RPM	21.77 RPM
SRP007412_kidney	0.00 RPM	37.19 RPM
SRP007412_liver	0.00 RPM	49.79 RPM
SRP007412_testis	0.00 RPM	82.62 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1652 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1652 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2166
Macaca mulatta	retro_mmul_904

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137414	2 retrocopies	retro_hsap_2166, retro_hsap_4922,
Macaca mulatta	ENSMMUG00000001992	1 retrocopy	retro_mmul_904,
Monodelphis domestica	ENSMODG00000024641	1 retrocopy	retro_mdom_1866,
Nomascus leucogenys	ENSNLEG00000001130	2 retrocopies	retro_nleu_2828, retro_nleu_460,
Pan troglodytes	ENSPTRG00000017751	2 retrocopies	retro_ptro_1652 , retro_ptro_3296,