RetrogeneDB ID: retro_ptro_1243

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:1840134..1842614(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX19
• Ensembl ID: ENSPTRG00000004487
• Aliases: None
• Description: None

Sequence

>retro_ptro_1243
GTGATTATTTGAGATTTTATATTATCCTGGTACTGTTCTGAGAGCCAGGAGCCAGCCTTTGAAGAGGAAATGGAGGCAGC
CATGAAAGAGTTGGTCCAGGAGCTTCAGAGGAGGATGAGCATGATGGACCATCATGCTCTTGCTCAGAGTGTTCTGACTC
TCTGTCGTTTTTCACCTGCAGAGCTACATTCAGGCAAAGGAGGCCACTACAGGGAAGAATGGTCCAGTTGAGCCTTCCCA
CCTCTGGGAGGCTTACTGCCGGGCTACTGCCCCACATCCTGCTGTGCACAGCCCCAATGCTGAAGTCACCTATACATGTG
GTATTGTGAATTTGTTGCTTCAAGGGCTGGTGCCCAAGTCCCACTTGGAGACTCATACTGGATGCCATGTAGTGGTTGAA
CTCATCATATGCAGTGTAGTCTTACCACTGATCAGCAGGCTGTCAGATGCTGACTGGATCCACCTTGTCCTCATGGGTAT
CTTTTCCAAGGCTAGAGATCCAACACCCTGCCCAGCCAGTGGCCCTGAACAGCCCTCAGTGCCCACGTCTCTGCCACTTA
TTGCTGAGGTACAGCAGCTTCCAGAAGGGAGGGCTCCTTCTCCAGTAGCAGCCCCAGGGTTCCTAAGTAAACAGTGAGCC
AGAGATTCCTGCAGGCCCCTCCTCAGAGGTTGAAGGTGGCCATGAAGCTGTAGAGGGAGATTTGGGTGCAATGTCTGAAA
AAAGAAAAGTAGGAAACAACTCATCTCATTTCCTATAGCCAAATACTTGAGGCCCCCTGTTCTTATGTGGAGACTCAGAG
CTGGAGTCTCCGCTGTCTGAAGTAGGCTAAGAAACCATCATGCTCATGACTCTAGGCCACTTTCTGTCTGACAGGATTCA
GGATGCCCTGTGTGCCCTAGAGGGTTCCCAGGCTCTGGAACCCAAAGGTGGTGAGGGATCTGAAGGAGTAGAGGCTGAGG
GTCCAGGGACAGAAACAGAGACAGTCCTGCCTGTCTCCACACTGAACTTCTGCCCAGAGATACAGATTGACATAGCAGAC
AAGGAGATAGAACAAGGAGAAGTTACCACCTCTGTTACAGCTTTGCTGGAGGGGCTGGAAAAGACCTGCTCCTCACGGCC
CTCATGCTTAGAGAAGGATCTCACCAATGATGTGACCTACCTTGATCCTAGTCTGCCACCAGTTCTGCTTTCCTCCTCTT
CACCTGGTCCTCTCAGCTCAGCCACCTTCAGCTTTGAGCCCCTAAGCAGTCCAGATGGCCCAGTTGTCATCCAGAACCTT
CATATCACTGGCACCATTACAGCCCGAGAGCACAGTGGCACCGGATTGCACCCATGCACACGCTATACTGTGAAGTGTGC
GACATCCCTTGACGGTGAAAACAGCAGCCTGCAGCAGCTGGCCTACCACACTGTGAATCACCGCTATTGGGAGTTCTTGA
ATCTGCAGGCCATCAGGAGAAGAAACCAGATCTATGAAAGTTCATAAAAAATGTGAAGGGTTCTAAAAAGCTCTTTCCAG
ATCTTCCATTTGGAAAACATAGACAGTGACAGAGTAGAAGCCCGAAAGAGCCTCCTATAATAATTCCTTAAGCGATTGTG
TGCCATTCCGGAGATCGCTAACAGTGAGGAGGTGCAGGAGTTTCTTGCTGTGAACACAGATGCTCACGTTTCCTTTGTCA
AGAAACCATTTATGGTCTCTAGAATAGAGAAGATGGTGGTGAGTGCCATTGTGGACAACTTGAAGACAGCATTTCCTTGC
TCTGAATCCCAGGGCCCCACAGAGGAGCTGAGTGAGGCCGAGACTGAAAGCAGGTCCCAAACAGAAGGCAAGAAGGCTAG
CAAGTCCAGGCTGAGGTTCTCATCCAGTAAAATTTCTCCAGCACTAAGTGTGACTGAAGCACAAGACAAGATTCTTTATT
GTCTCCAGGAAGGCAATGTGGAGTCCAAGACCCTATCCATGTCTGGGATGGAATCTTTTATTGAAAAACAGACAAAGTTA
CTGGAGATGCAGCCAACAGAAGCCCCAGAAAAAGATCCTGAACAACTTCCCAAAGGACATGTGGACAGTTGCTTGTCAGA
TGCAGCTGTGCCAGCCCAAGATCCCAGCAACAGCGATTCAGGAACAGAGACAGAGTTAGCTGACACAGCCCTGAATCTGC
TTCTCTTGCTACTAACAGAACAGTGGAAATGGCTGTGTACTGAAAACATGCAGAAGTTTCTTCGTCTTATCTTTGGTACC
CTAGTTCAAAGGTGGCTAGAGGGGCAGGTAGCTAATTTAACAAGTCCACAGTGCTGGGTGCAGTACCTCTGGCTTCTTCA
GGAGTCCATCTGGCCTGGTGGAGTTTTGCCTAAGTTTCCACGGCCTGTAAGGACCCAGTAGCAGAAACTGGCTGCTGAGA
AACAGGCTTTGCAGAGCCTAATGGGAGTCTTCCCAGATCTCATAGTAGAAATTCTTGGGGTGAACAAATGCCAGCTGAGT

Alignment

ORF - retro_ptro_1243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.3 %
• Parental protein coverage: 83.37 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MIIRDFVLSWYRSVSQEPAFEEEMEAAMKGLVQELRRRMSVMDSHALAQSVLTLCGC-HLQSYIQAKEAT
          .II.DF.LSWY.S.SQEPAFEEEMEAAMK.LVQEL.RRMS.MD.HALAQSVLTLC...HLQSYIQAKEAT
Retrocopy VII*DFILSWYCSESQEPAFEEEMEAAMKELVQELQRRMSMMDHHALAQSVLTLCRF>HLQSYIQAKEAT

Parental  AGKNGPVEPSHLWEAYCRATAPHPAVHSPSAEVTYTRGVVNLLLQGLVPKPHLETRTGRHVVVELITCNV
          .GKNGPVEPSHLWEAYCRATAPHPAVHSP.AEVTYT.G.VNLLLQGLVPK.HLET.TG.HVVVELI.C.V
Retrocopy TGKNGPVEPSHLWEAYCRATAPHPAVHSPNAEVTYTCGIVNLLLQGLVPKSHLETHTGCHVVVELIICSV

Parental  ILPLISRLSDPDWIHLVLVGIFSKARDPAPCPASAPEQPSLPTSLPLIAEVEQLPEGRA-SPVAAPVFLS
          .LPLISRLSD.DWIHLVL.GIFSKARDP.PCPAS.PEQPS.PTSLPLIAEV.QLPEGRA.SPVAAP.FLS
Retrocopy VLPLISRLSDADWIHLVLMGIFSKARDPTPCPASGPEQPSVPTSLPLIAEVQQLPEGRAPSPVAAPGFLS

Parental  -YSEPEGSAGPSPEVEEGHEAVEGDLGGMCEERKVGNNSSHFLQPNLRGPLFLCEDSELESPLSELGRET
          ..SEPE..AGPS.EVE.GHEAVEGDLG.M.E.RKVGNNSSHFL.PN..GPLFLC.DSELESPLSE.G.ET
Retrocopy >NSEPEIPAGPSSEVEGGHEAVEGDLGAMSEKRKVGNNSSHFL*PNT*GPLFLCGDSELESPLSEVG*ET

Parental  IMLMTPGRFLSDRIQDALCALEGSQALEPTDGEASEGAEAEEGPGTETETGLPVSTLNSCPEIHIDTADK
          IMLMT.G.FLSDRIQDALCALEGSQALEP..GE.SEG.EA.EGPGTETET.LPVSTLN.CPEI.ID.ADK
Retrocopy IMLMTLGHFLSDRIQDALCALEGSQALEPKGGEGSEGVEA-EGPGTETETVLPVSTLNFCPEIQIDIADK

Parental  EIEQGDVTTSVTALLKGPEKTCPSRPSCLEKDLTNDVSSLDPTLPPVLLSSSPPGPLSSATFSFEPLSSP
          EIEQG.VTTSVTALL.G.EKTC.SRPSCLEKDLTNDV..LDP.LPPVLLSSS.PGPLSSATFSFEPLSSP
Retrocopy EIEQGEVTTSVTALLEGLEKTCSSRPSCLEKDLTNDVTYLDPSLPPVLLSSSSPGPLSSATFSFEPLSSP

Parental  DGPVIIQNLRITGTITAREHSGTGFHPYTLYTVKYETALDGENSSGLQQLAYHTVNRRYREFLNLQT-RL
          DGPV.IQNL.ITGTITAREHSGTG.HP.T.YTVK..T.LDGENSS.LQQLAYHTVN.RY.EFLNLQ....
Retrocopy DGPVVIQNLHITGTITAREHSGTGLHPCTRYTVKCATSLDGENSS-LQQLAYHTVNHRYWEFLNLQA<HQ

Parental  EEKPDLRKFIKNVKGPKKLFPDLPFG-NMDSDRVEAHKSLLESFLKQLCAIPEIANSEEVQEFLALNTDA
          E.KPDL.KFIKNVKG.KKLFPDLPFG.N.DSDRVEA.KSLL..FLK.LCAIPEIANSEEVQEFLA.NTDA
Retrocopy EKKPDL*KFIKNVKGSKKLFPDLPFG>NIDSDRVEARKSLL**FLKRLCAIPEIANSEEVQEFLAVNTDA

Parental  RIAFVKKPFMVSRIDKMVVSAIVDTLKTAFPRSEPQSPTEELSEAETESKSQTEGKKASKSRLRFSSSKI
          ...FVKKPFMVSRI.KMVVSAIVD.LKTAFP.SE.Q.PTEELSEAETES.SQTEGKKASKSRLRFSSSKI
Retrocopy HVSFVKKPFMVSRIEKMVVSAIVDNLKTAFPCSESQGPTEELSEAETESRSQTEGKKASKSRLRFSSSKI

Parental  SPALSVTEAQDKILYCLQEGNVESETLSMSAMESFIEKQTKLLEMQPSKAPEKDPEQPPKGRVDSCVSDA
          SPALSVTEAQDKILYCLQEGNVES.TLSMS.MESFIEKQTKLLEMQP..APEKDPEQ.PKG.VDSC.SDA
Retrocopy SPALSVTEAQDKILYCLQEGNVESKTLSMSGMESFIEKQTKLLEMQPTEAPEKDPEQLPKGHVDSCLSDA

Parental  AVPAQDPSNSDPGTETELADTALDLLLLLLTEQWKWLCTENMQKFLRLIFGTLVQRWLEVQVANLTSPQR
          AVPAQDPSNSD.GTETELADTAL.LLLLLLTEQWKWLCTENMQKFLRLIFGTLVQRWLE.QVANLTSPQ.
Retrocopy AVPAQDPSNSDSGTETELADTALNLLLLLLTEQWKWLCTENMQKFLRLIFGTLVQRWLEGQVANLTSPQC

Parental  WVQYLRLLQESIWPGGVLPKFPRPVRTQEQKLAAEKQALQSLMGVLPDLVVEILGVNKCRLS
          WVQYL.LLQESIWPGGVLPKFPRPVRTQ.QKLAAEKQALQSLMGV.PDL.VEILGVNKC.LS
Retrocopy WVQYLWLLQESIWPGGVLPKFPRPVRTQ*QKLAAEKQALQSLMGVFPDLIVEILGVNKCQLS

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	67.37 RPM
SRP007412_cerebellum	0.00 RPM	70.12 RPM
SRP007412_heart	0.03 RPM	69.92 RPM
SRP007412_kidney	0.00 RPM	91.82 RPM
SRP007412_liver	0.00 RPM	38.72 RPM
SRP007412_testis	0.21 RPM	226.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1243 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1243 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1919

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000120451	2 retrocopies	retro_hsap_1235, retro_hsap_1919,
Pongo abelii	ENSPPYG00000004069	1 retrocopy	retro_pabe_3531,
Pan troglodytes	ENSPTRG00000004487	3 retrocopies	retro_ptro_1243 , retro_ptro_3076, retro_ptro_849,