RetrogeneDB ID: retro_ptro_3189

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:24534584..24536060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM48A
• Ensembl ID: ENSPTRG00000005791
• Aliases: None
• Description: None

Sequence

>retro_ptro_3189
ATGGATCGAGATTTAGAACAGGCTCTGGATCGCGCAGAGAATATCACTGAAATTGCCCAACAGAGACGTCCTAGAAGGAG
ATACTCACCTAGGGCGGGAAAAACTCTGCAGGAAAAACTTTATGACATTTATGTTGAAGAATGTGGAAAAGAGCCTGAGG
ATCCTCAGGAATTGAGAAGCAATGTAAACTTGTTAGAAAAGCTTGTTAGGAGAGAGTCCTTGCCATGTTTACTGGTCAAT
CTATACCCAGGCAATCAGGGGTATTCTGTGATGCTCCAGAGAGAAGATGGGTCCTTTGCAGAGACCATTCGGCTGCCTTA
TGAAGAAAGGGCATTGCTGGACTACTTGGATGCAGAAGAATTACCCCCTGCTTTGGGTGATGTCCTGGATAAAGCTTCGG
TTAACATTTTTCATAGTGGGTGTGTCATAGTAGAAGTTCGTGACTACAGGCAGTCCAGTAATATGCAACCTCCTGGTTAC
CAAAGCAGGCATATTCTTCTACGTCCAACCATGCAGACTTTAGCTCCTGAGGTGAAGACGATGACAAGAGATGGCGAGAA
ATGGAGCCAGGAAGACAAATTTCTGCTTGAGAGTCAACTGATCTTAGAGACAGCTGAACCACTGTGTCTTGATCCTTCTG
TAGCAGTTGCCTGCACTGCAAACAGGCTGCTGTACAACAAGCAAAAGATGAATACCGACCCGATGGAACAGTGCCTCCAG
AGGTATTCGTGGTCCTCTGTAAAGCCACAGCAGGAGCAGTCTGACTGTCCACCTCCTCCTGAGCTGAGAGTGTCGACTTC
TGGCCAAAAAGAAGAAAGAAAAGTAGGTCAGCCTTGTGAGCTGAACATTGCTAAAGCAGGAAGTTGTGTAGACACGTGGA
AACGCACACCCTGTGATTTGGCCGTGCCTTCAGAAATGGATGTGGAGACACTTGCTAAAGGGTATCAGTCCGTCACAGCT
GCTGACCCACAGCTCCCAGTCTGGCCAGCCCAGGAGGTAGAAGACCCTTTCAGACATGCATGGGAAGCTGGCTGTCAGGC
CTGGGACACCAAGCCAAACATCATGCAGTCGTTTAATGATCCGCTTCTCTGTGGTAAAATACGGCCACGTAAAAAAGCCA
GGCAGAAGAGCCAGAAGTCTCCCTGGCAGCCCTTCCCAGATGACCATTCAGCTTGTCTCAGGCCTGGGTCAGAGACTGAT
GCTGGGAGGGCAGTGAGTCAGGCCCAGGAATCAGTGCAGAGCAAAGTCAAAGGTCCAGGCAAGATGTCACACAGCTCCAG
TGGCCCAGCCAGTGTCAGTCAGCTCTCTTCATGGAAAACACCAGAACAGCCTGATCCTGTGTGGGTCCAGTCTTCAGTAT
CGGGTAAGGGAGAGAAACATCCACCTCCCCACCCCCAACTTCCCTCAAGCTCAGGAAAGATTTCCTCAGGTAACAATTTT
CCCCCACAACAGGCAGGCAGCCCTCTTAAGCGTCCA

Alignment

ORF - retro_ptro_3189 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 63.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQALELALDRAEYVIESARQRPPKRKYLSSGRKSVFQKLYDLYIEECEKEPE-VKKLRRNVNLLEKLVM
          M...LE.ALDRAE...E.A.QR.P.R.Y.....K....KLYD.Y.EEC.KEPE....LR.NVNLLEKLV.
Retrocopy MDRDLEQALDRAENITEIAQQRRPRRRYSPRAGKTLQEKLYDIYVEECGKEPEDPQELRSNVNLLEKLVR

Parental  QETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCG
          .E.L.CL.VNLYPGN.GYS.ML....GS..ETIRLPYEE..LL.YLDAEELPP.L.D.L.K..VNIFH.G
Retrocopy RESLPCLLVNLYPGNQGYSVMLQREDGSFAETIRLPYEERALLDYLDAEELPPALGDVLDKASVNIFHSG

Parental  CVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCL
          CVI.E.RDYRQSSNM..PGYQSRHILLRPTMQTL...V...T.D..KW.QEDK.LLESQLIL.TAEPLCL
Retrocopy CVIVEVRDYRQSSNMQPPGYQSRHILLRPTMQTLAPEVKTMTRDGEKWSQEDKFLLESQLILETAEPLCL

Parental  DPSIAVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPPPPQLRLLDFLQKRKERKAGQHY
          DPS.AV.CTANRLLYNKQKMNT.PM..C..RYS.SS...QQ..S.CPPPP.LR.....QK..ERK.GQ..
Retrocopy DPSVAVACTANRLLYNKQKMNTDPMEQCLQRYSWSSVKPQQEQSDCPPPPELRVSTSGQK-EERKVGQPC

Parental  DLKISKAGNCVDMWKRSPCNLAIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDVKDDYVFECEAGTQYQK
          .L.I.KAG.CVD.WKR.PC.LA.PSE.DVE..AK...S....D.Q..VWPA..V.D......EAG.Q...
Retrocopy ELNIAKAGSCVDTWKRTPCDLAVPSEMDVETLAKGYQSVTAADPQLPVWPAQEVEDPFRHAWEAGCQAWD

Parental  TKLTILQSLGDPLYYGKIQPCKADEESDSQMSPSHSSTDDHSNWFIIGSKTDAERVVNQYQELVQNEAKC
          TK..I.QS..DPL..GKI.P.K......SQ.SP.....DDHS.....GS.TDA.R.V.Q.QE.VQ...K.
Retrocopy TKPNIMQSFNDPLLCGKIRPRKKARQK-SQKSPWQPFPDDHSACLRPGSETDAGRAVSQAQESVQSKVKG

Parental  PVKMSHSSSGSASLSQVSPGKETDQTETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNYFTPQQTSSF
          P.KMSHSSSG.AS.SQ.S..K...Q...V.VQSSV.GKG.KH.PP...LPSSSG..SSGN.F.PQQ..S.
Retrocopy PGKMSHSSSGPASVSQLSSWKTPEQPDPVWVQSSVSGKGEKHPPPHPQLPSSSGKISSGNNFPPQQAGSP

Parental  LKSP
          LK.P
Retrocopy LKRP

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	13.76 RPM
SRP007412_cerebellum	0.04 RPM	25.88 RPM
SRP007412_heart	0.03 RPM	12.30 RPM
SRP007412_kidney	0.05 RPM	21.50 RPM
SRP007412_liver	0.00 RPM	7.50 RPM
SRP007412_testis	1.05 RPM	210.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3189 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3189 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4794
Pongo abelii	retro_pabe_3729
Macaca mulatta	retro_mmul_2555
Equus caballus	retro_ecab_1101

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052, retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479, retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189 ,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193,