RetrogeneDB ID: retro_ptro_849

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:18412239..18413875(-)
• 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_849
ACTCCAGGCCACTTTCTGACTGACAGGATTCAGGATGCCCTGTGTGCCCTAGAGGGTTCCCAGGCTCTGGAACCCAAAGG
TGGTGAGGGATCTGAAGGAGCAGAGGCTGAGGAGGGTCCAGGGACAGAAACAGAGACAGTCCTGCCTGTCTCCACACTGA
ACTTCTGCCCAGAGATCCAGATTGACATAGCAGACAAGGAGCTAGAACAAGGAGAAGTTACCACCTCTGTTACAGCTTTG
CTGGAGGGGCCGGAAAAGACCTGCTCCTCACGGCCCTCATGCTTAGAGAAGGATCTCACCAATGATGTGACCTACCTTGA
TCCTAGTCTGCCACCAGTTCTGCTTTCCTCCTCTCCACCTGGTCCTCTCAGCTCAGCCACCTTCAGCTTTGAGCCCCTAA
GCAGTCCAGATGGCCCAGTTGTCATCCAGAACCTTCATATCACTGGCACCATTACAGCCTGAGAGCACAGTGGCACCAGA
TTGCACCCATGCACACGCTGTACTGTGAAGTATGAGACATCCCTTGATGGTGAAAACAGCAGCCTGCAGCAGCTGGCCTA
CCACACTGTGAATCACCGCTATTGGGAGTTCTTGAATCTGCAGGCCATCAGGAGAAGAAACCAGATCTATGAAAGTTCAT
TAAGAATGTGAAGGGTCCTAAAAATCTCTTTCCAGATCTTCCATTTGGAAACATGGACAGTGACAGAGTAGAAGCCTGTA
AGAGCCTCCTATAATAATTCCTGAAGCAACTGTGTGCCATTCCAGAGATTGCTAACAACAGTGAGGAGGTGCAGGAGTTT
CTTGCTGTGAACACAGATGCTCGCATTTCCTTTGTCAAGAAACCATTTATGGTCTCTAGAATAGAGAAGATGGTGGTGAG
TGCCATTGTGGACACCTTGAAGACAGCATTTCCTTGCTCTGAATCCCAGGGCCCCACAGAGGAGCTGAGTGAGGCCGAGA
CTGAAAGCAGGTCCCATACAGAAGGTAAGAAGGCTAGCAAGTCCAGGCTGAGGTTCTTACCCAGTAAAATTTCTCCAGCA
CTAAGTGTGACTGAAGCACAAGACAAGATTCTTTATTGTCTCCAGGAAGGCAATGTGGAGTCCAAGACCCTATCCATGTC
TGGGATGGAATCTTTTATTGAAAAACAGACAAAGTTACTGGAGATGGAGGCAACAGAAGCCCCAGAAAAAGATCCTGAAC
AACTTCCCAAAGGACACGTGGACAGCTGCTTGTCAGATGCAGCTGTGCCAGCCCACGATCCAGCAACGACGGTTCAGGAA
CAGAGACAGAGTTAGCTGACACAGCCCTGAATCTGCTTCTCTTGCTACTAACAGAACAGTGGAAATGGCTGTGTACTGAA
AACATGTAGATGTTTCTTTGTCTTATCTTTGGTACCCTAGTTCAAAGGTGGCTAGAGGTGCAGGTAGCTAATTTAACAAG
TCCACAGTGCTGGGTGCAGTACCTCTGGCTTCTTCAGGAGTCTACCTGGCCTGGTGGAGTTTTGCCTAAGTTTCCACAGC
CTGTAAGGACCCAGGAGCAGAAACTGGCTGCTGAGAAACAGGCTTTGCAGAGCCTAATGGGAGTCCTCCCAGATCTCATA
GTAGAAATTCTTGGGGTGAACAAATGCCAGCTGAGT

Alignment

ORF - retro_ptro_849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.7 %
• Parental protein coverage: 55.04 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TPGRFLSDRIQDALCALEGSQALEPTDGEASEGAEAEEGPGTETETGLPVSTLNSCPEIHIDTADKEIEQ
          TPG.FL.DRIQDALCALEGSQALEP..GE.SEGAEAEEGPGTETET.LPVSTLN.CPEI.ID.ADKE.EQ
Retrocopy TPGHFLTDRIQDALCALEGSQALEPKGGEGSEGAEAEEGPGTETETVLPVSTLNFCPEIQIDIADKELEQ

Parental  GDVTTSVTALLKGPEKTCPSRPSCLEKDLTNDVSSLDPTLPPVLLSSSPPGPLSSATFSFEPLSSPDGPV
          G.VTTSVTALL.GPEKTC.SRPSCLEKDLTNDV..LDP.LPPVLLSSSPPGPLSSATFSFEPLSSPDGPV
Retrocopy GEVTTSVTALLEGPEKTCSSRPSCLEKDLTNDVTYLDPSLPPVLLSSSPPGPLSSATFSFEPLSSPDGPV

Parental  IIQNLRITGTITAREHSGTGFHPYTLYTVKYETALDGENSSGLQQLAYHTVNRRYREFLNLQT-RLEEKP
          .IQNL.ITGTITA.EHSGT..HP.T..TVKYET.LDGENSS.LQQLAYHTVN.RY.EFLNLQ....E.KP
Retrocopy VIQNLHITGTITA*EHSGTRLHPCTRCTVKYETSLDGENSS-LQQLAYHTVNHRYWEFLNLQA<HQEKKP

Parental  DLRKFIKNVKGPKKLFPDLPFGNMDSDRVEAHKSLLESFLKQLCAIPEIA-NSEEVQEFLALNTDARIAF
          DL.KFIKNVKGPK.LFPDLPFGNMDSDRVEA.KSLL..FLKQLCAIPEIA.NSEEVQEFLA.NTDARI.F
Retrocopy DL*KFIKNVKGPKNLFPDLPFGNMDSDRVEACKSLL**FLKQLCAIPEIANNSEEVQEFLAVNTDARISF

Parental  VKKPFMVSRIDKMVVSAIVDTLKTAFPRSEPQSPTEELSEAETESKSQTEGKKASKSRLRFSSSKISPAL
          VKKPFMVSRI.KMVVSAIVDTLKTAFP.SE.Q.PTEELSEAETES.S.TEGKKASKSRLRF..SKISPAL
Retrocopy VKKPFMVSRIEKMVVSAIVDTLKTAFPCSESQGPTEELSEAETESRSHTEGKKASKSRLRFLPSKISPAL

Parental  SVTEAQDKILYCLQEGNVESETLSMSAMESFIEKQTKLLEMQPSKAPEKDPEQPPKGRVDSCVSDAAVPA
          SVTEAQDKILYCLQEGNVES.TLSMS.MESFIEKQTKLLEM....APEKDPEQ.PKG.VDSC.SDAAVPA
Retrocopy SVTEAQDKILYCLQEGNVESKTLSMSGMESFIEKQTKLLEMEATEAPEKDPEQLPKGHVDSCLSDAAVPA

Parental  QDP-SNSDPGTETELADTALDLLLLLLTEQWKWLCTENMQKFLRLIFGTLVQRWLEVQVANLTSPQRWVQ
          .DP.SN...GTETELADTAL.LLLLLLTEQWKWLCTENM..FL.LIFGTLVQRWLEVQVANLTSPQ.WVQ
Retrocopy HDP<SNDGSGTETELADTALNLLLLLLTEQWKWLCTENM*MFLCLIFGTLVQRWLEVQVANLTSPQCWVQ

Parental  YLRLLQESIWPGGVLPKFPRPVRTQEQKLAAEKQALQSLMGVLPDLVVEILGVNKCRLS
          YL.LLQES.WPGGVLPKFP.PVRTQEQKLAAEKQALQSLMGVLPDL.VEILGVNKC.LS
Retrocopy YLWLLQESTWPGGVLPKFPQPVRTQEQKLAAEKQALQSLMGVLPDLIVEILGVNKCQLS

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	0.42 RPM	226.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_849 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_849 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1235

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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 ,