RetrogeneDB ID: retro_ptro_3076

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL393540.1:86268..88014(-)
• 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_3076
ACAACTCATCTCATTTCCTTAAATACTTGAGGCCCCCTGTTCTTATGTGAAGACTCAGAGCTGGAGTCTCCGCTGTCTGA
AGTAGGCTAAGAAACCATCATGCTCATGACTCCAGGCCACTTTCTGACTGACAGGATTCAGGATGCCCTGTGTGCCCTAG
AGGGTTCCCAGGCTCTGGAACCCAAAGGTGGTGAGGGATCTGAAGGAGCAGAGGCTGAGGAGGGTCCAGGGACAGAAACA
GAGACAGTCCTGCCTGTCTCCACACTGAACTTCTGCCCAGAGATCCAGATTGACATAGCAGACAAGGAGCTAGAACAAGG
AGAAGTTACCACCTCTGTTACAGCTTTGCTGGAGGGGCTGGAAAAGACCTGCTCCTCACGGCCCTCATGCTTAGAGAAGG
ATCTCACCAATGATATGACCTACCTTGATCCTAGTCTGCCACCAGTTCTGCTTTCCTCCTCTTCACCTGGTCCTCTCAGC
TCAGCCACCTTCAGCTTTAAGCCCCTAAGCAGTCCAGATGGCCCAGTTGTCATCCAGAACCTTCATATCACTGGCACCAT
TACAGCCCAAGAGCACAGTGGCACCAGATTGCACCCATGCACACGCTATACTGTGAAGTGTGAGACATCCCTTGACGGTG
AAAACAGCAGCCTGCAGCAGCTGGCCTACCACACTGTGAATCACCGCTATTGGGAGTTCTTGAATCTGCAGGCCATCAGG
AGAAGAAACCAGATCTATGAAAGTTCATTAAAAATGTGAAGGGTTCTAAAAAGCTCTTTCCAGATCTTCCATTTGGAAAA
CATAGACAGTGACAGAGTAGAAGCCCGAAAGAGCCTCCTATAATAATTCCTGAAGCAACTGTGTGCCATTCCAGAGATTG
CTAACAACAGTGAGGAGGTGCAGGAGTTTCTTGCTGTGAACACAGATGCTCACGTTTCCTTTGTCAAGAAACCATTTATG
GTCTCTAGAATAGAGAAGATGGTGGTGAGTGCCATTGTGGACAACTTGAAGACAGCATTTCCTTGCTCCGAATCCCAGAG
CCCCACAGAGGAGCTGAGTGAGGCCGAGACTGAAAGCAGGTCCCATACAGAAGGTAAGAAGGCTAGGAAGTCCAGGCTGA
GGTTCTCATCCAGTAAAATTTCTCCAGCACTAAGTGTGACTGAAGCACAAGACAAGATTCTTTATTGTCTCCAGGAAGGC
AATGTGGAGTCCAAGACCCTATCCATGTCTGGGATGGAATCTTTTATTGAAAAACAGACAAAGTTACTGGAGATGGAGGC
AACAGAAGCCCCAGAAAAAGATCCTGAACAACTTCCCAAAGGACATGTGGACAGTTGCTTGTCAGATGCAGCTGTGCCAG
CCCAAGATCCCAGCAACAGCGATTCAGGAACAGAGACAGAGTTAGCTGACACAGCCCTGAATCTGCTTCTCTTGCTACTA
ACAGAACAGTGGAAATGGCTGTGTACTGAAAACATGCAGAAGTTTCTTCGTCTTATCTTTGCTACCCTAGTTCAAAGGTG
GCTAGAGGTGCAGGTAGCTAATTTAACAAGTCCACAGTGCTGGGTGCAGTACCTCTGGCTTCTTCAGGAGTCTATCTGGC
CTGGTGGAGTTTTGCCTAAGTTTCCACGGCCTGTAAGGACCCAGGAGCAGAAACTGGCTGCTGAGAAACAGGCTTTGCAG
AGCCTAATGGGAGTCTTCCCAGATCTCATAGTAGAAATTCTTGGGGTGAACAAATGCCAGCTGAGT

Alignment

ORF - retro_ptro_3076 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.81 %
• Parental protein coverage: 58.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSHFLQPNLRGPLFLCEDSELESPLSELGRETIMLMTPGRFLSDRIQDALCALEGSQALEPTDGEASEGA
          ..H....N..GPLFLCEDSELESPLSE.G.ETIMLMTPG.FL.DRIQDALCALEGSQALEP..GE.SEGA
Retrocopy TTHLISLNT*GPLFLCEDSELESPLSEVG*ETIMLMTPGHFLTDRIQDALCALEGSQALEPKGGEGSEGA

Parental  EAEEGPGTETETGLPVSTLNSCPEIHIDTADKEIEQGDVTTSVTALLKGPEKTCPSRPSCLEKDLTNDVS
          EAEEGPGTETET.LPVSTLN.CPEI.ID.ADKE.EQG.VTTSVTALL.G.EKTC.SRPSCLEKDLTND..
Retrocopy EAEEGPGTETETVLPVSTLNFCPEIQIDIADKELEQGEVTTSVTALLEGLEKTCSSRPSCLEKDLTNDMT

Parental  SLDPTLPPVLLSSSPPGPLSSATFSFEPLSSPDGPVIIQNLRITGTITAREHSGTGFHPYTLYTVKYETA
          .LDP.LPPVLLSSS.PGPLSSATFSF.PLSSPDGPV.IQNL.ITGTITA.EHSGT..HP.T.YTVK.ET.
Retrocopy YLDPSLPPVLLSSSSPGPLSSATFSFKPLSSPDGPVVIQNLHITGTITAQEHSGTRLHPCTRYTVKCETS

Parental  LDGENSSGLQQLAYHTVNRRYREFLNLQT-RLEEKPDLRKFIKNVKGPKKLFPDLPFG-NMDSDRVEAHK
          LDGENSS.LQQLAYHTVN.RY.EFLNLQ....E.KPDL.KFIKNVKG.KKLFPDLPFG.N.DSDRVEA.K
Retrocopy LDGENSS-LQQLAYHTVNHRYWEFLNLQA<HQEKKPDL*KFIKNVKGSKKLFPDLPFG>NIDSDRVEARK

Parental  SLLESFLKQLCAIPEIAN-SEEVQEFLALNTDARIAFVKKPFMVSRIDKMVVSAIVDTLKTAFPRSEPQS
          SLL..FLKQLCAIPEIAN.SEEVQEFLA.NTDA...FVKKPFMVSRI.KMVVSAIVD.LKTAFP.SE.QS
Retrocopy SLL**FLKQLCAIPEIANNSEEVQEFLAVNTDAHVSFVKKPFMVSRIEKMVVSAIVDNLKTAFPCSESQS

Parental  PTEELSEAETESKSQTEGKKASKSRLRFSSSKISPALSVTEAQDKILYCLQEGNVESETLSMSAMESFIE
          PTEELSEAETES.S.TEGKKA.KSRLRFSSSKISPALSVTEAQDKILYCLQEGNVES.TLSMS.MESFIE
Retrocopy PTEELSEAETESRSHTEGKKARKSRLRFSSSKISPALSVTEAQDKILYCLQEGNVESKTLSMSGMESFIE

Parental  KQTKLLEMQPSKAPEKDPEQPPKGRVDSCVSDAAVPAQDPSNSDPGTETELADTALDLLLLLLTEQWKWL
          KQTKLLEM....APEKDPEQ.PKG.VDSC.SDAAVPAQDPSNSD.GTETELADTAL.LLLLLLTEQWKWL
Retrocopy KQTKLLEMEATEAPEKDPEQLPKGHVDSCLSDAAVPAQDPSNSDSGTETELADTALNLLLLLLTEQWKWL

Parental  CTENMQKFLRLIFGTLVQRWLEVQVANLTSPQRWVQYLRLLQESIWPGGVLPKFPRPVRTQEQKLAAEKQ
          CTENMQKFLRLIF.TLVQRWLEVQVANLTSPQ.WVQYL.LLQESIWPGGVLPKFPRPVRTQEQKLAAEKQ
Retrocopy CTENMQKFLRLIFATLVQRWLEVQVANLTSPQCWVQYLWLLQESIWPGGVLPKFPRPVRTQEQKLAAEKQ

Parental  ALQSLMGVLPDLVVEILGVNKCRLS
          ALQSLMGV.PDL.VEILGVNKC.LS
Retrocopy ALQSLMGVFPDLIVEILGVNKCQLS

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	0.00 RPM	69.92 RPM
SRP007412_kidney	0.00 RPM	91.82 RPM
SRP007412_liver	0.00 RPM	38.72 RPM
SRP007412_testis	0.00 RPM	226.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3076 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3076 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3076 has 0 orthologous retrocopies within eutheria group .

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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,