RetrogeneDB ID: retro_ptro_94

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:56316363..56317299(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000021953
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSPTRG00000004358
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_ptro_94
ATGGACTTAAAACTAAAAGACTGTGAATTTTGGTACAGTCTCCATGGCCAGGTCCCAGGGATGCTGGACTGGGACATGAG
GAATGAGTTATTTCTGCCTTGTACCACAGACCAGTGCTCTTTAGCTGAGCAAATCCTTGCCAAATACAGAGTCGGAGTAA
TGAAGCCCCCAGAAATGCCTCAGAAGAGGATATCCAGTCCTGATGGAGATGGTCCTCCCTGTGAACCCAATCTGTGGATG
TGGGTGAACCCCAATATCGTGTGCCCCCTTGGCAGCCAGGAGGCCCCAAAGCCCAGTGGAAAAGAGGATCTGACAAACAT
TTCTCCTTTCCCTCAGCCCCCACAAAAAGACGAAGGGTCTAACTGCTCAGAGGACAAAGTGGTAGAGTCTCTGCCATCTT
CCTCCAGTGAGCAGTTTCCTTTACAGAAGCAGGGTATCCATTCCCCCAGTGACTTTGAGCTCACAGAAGAGGAGGCTGAG
GAACAAGACGACAACTCCCTCCAGTCCCCTGAAATGAAATGTTTCCAGAGCCAGAAACTATGGCAAATCGACAGCCAACA
GAAGTCCTGGCAAAGGCCCCCTCTCAATTGTAGCCACCTTATTGCCCTAGCCTTAAGAAACAACCCCCACTGTGGCCTCA
GTGTGCAGGAGATCTACAATTTCACCCGACAGCATTTCCCCTTTTTCTGGACAGCTCCGGATGGCTGGAAGAGCACCATT
CATTACAACCTCTGCTTCCTGGACAGCTTTGAGAAGGTGCCAGACAGCCTTAAGGATGAAGATAATGCAAGACCTCGCTC
TTGCCTTTGGAAGCTCACTAAGGAGGGGCACCGCCGCTTTTGGGAGGAGACTCGTGCCTTAGCCTTTGCTCAAAGGGAGA
GAATCCAAGAGTGCATGAGTCAGCCAGAGTTGTTGACCTCTCTCTTTGATCTTTGA

Alignment

ORF - retro_ptro_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNELFLAFTTSHLSLAEQKLARYKLRIVKPPKLPLEKKPNPDKDGPDYEPNLWMWVNPNIVYPPGKLEV
          M.NELFL..TT...SLAEQ.LA.Y.....KPP..P......PD.DGP..EPNLWMWVNPNIV.P.G..E.
Retrocopy MRNELFLPCTTDQCSLAEQILAKYRVGVMKPPEMPQKRISSPDGDGPPCEPNLWMWVNPNIVCPLGSQEA

Parental  SGRRKREDLTSTLPSSQPPQKEEDASCSEAAGVESLSQSSSKRSPPRKRFAFSPSTWELTEEEEAEDQED
          ......EDLT...P..QPPQK.E...CSE...VESL..SSS...P..K....SPS..ELTEEE.AE.Q.D
Retrocopy PKPSGKEDLTNISPFPQPPQKDEGSNCSEDKVVESLPSSSSEQFPLQKQGIHSPSDFELTEEE-AEEQDD

Parental  SSSVALPSPHKRAPLQSRRLRQASSQAGRLWSRPPLNYFHLIALALRNSSPCGLNVQQIYSFTRKHFPFF
          .S...L.SP......QS..L.Q..SQ....W.RPPLN..HLIALALRN...CGL.VQ.IY.FTR.HFPFF
Retrocopy NS---LQSPEMKC-FQSQKLWQIDSQQ-KSWQRPPLNCSHLIALALRNNPHCGLSVQEIYNFTRQHFPFF

Parental  RTAPEGWKNTVRHNLCFRDSFEKVPVSMQGGASTRPRSCLWKLTEEGHRRFAEEARALASTRLESIQQCM
          .TAP.GWK.T...NLCF.DSFEKVP.S.......RPRSCLWKLT.EGHRRF.EE.RALA....E.IQ.CM
Retrocopy WTAPDGWKSTIHYNLCFLDSFEKVPDSLKDEDNARPRSCLWKLTKEGHRRFWEETRALAFAQRERIQECM

Parental  SQPDVMPFLFDL
          SQP.....LFDL
Retrocopy SQPELLTSLFDL

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.53 RPM	1.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_94 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_94 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_94 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_72
Pongo abelii	retro_pabe_69
Callithrix jacchus	retro_cjac_4066
Bos taurus	retro_btau_189

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94 ,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158,