RetrogeneDB ID: retro_ptro_804

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:20139891..20140507(+)
• Located in intron of: ENSPTRG00000005685

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E1
• Ensembl ID: ENSPTRG00000010648
• Aliases: None
• Description: Solute carrier family 35, member E1 [Source:UniProtKB/TrEMBL;Acc:K7B5M5]

Sequence

>retro_ptro_804
GCCGCCACGCTGTGCTTCTTGCTTCAGAACATTTTCTCCAAAAAGATCTTGAGAGATTTGCGGATCCACCATCTCCCGCT
GCTCAACATCTTGGGCTGCCACGCTGTTTTTTTATGATCCCCACCTGGGTTCTGGTGGACCTCTCAGCTTTCCTGGTCAG
CAGCGACTTGACTACGTCTCACAGTGGCCCTGGATGCTCCTGCTTCTGGCTGTCAGCGGCTTCTGTAACTTTGCCTAGAA
TGTCATTGCCTTCAGCATCCTCAACCTCGTCAGCTCTCTGAGCTATTCAGTTGTCAATGCCACCAAGAGAATCATGGTCA
TCACAGTGTCCCTGATCATGCTGCCCAACCCAGTCACCAGCACCAATGTCCTGGGCATAATGACTGCCATCCTCGGGGTC
TTCCTCTACAACAAGACCAAGTAAGATGCAAACCAGCAAGTCAGGAAGCACCTCCTCCTGGCACCACAGTGGACCTGAGC
AGCAAGGAACATCACCAGAGCCCACTGGAGAAGCCCCACCAATGGCCTCCTCTTCCCCCAGCACGGGGACTATCATGGCT
GCAACAATATCTTAACAGACCACTTCCAGTACAGCTGGCAGAGCTACCCACACTCT

Alignment

ORF - retro_ptro_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 56.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AATLCFSLQNIFSKKVLRDSRIHHLRLLNILGCHAVF-FMIPTWVLVDLSAFLVSSDLT-YVYQWPWTLL
          AATLCF.LQNIFSKK.LRD.RIHHL.LLNILGCHAVF.FMIPTWVLVDLSAFLVSSDLT.YV.QWPW.LL
Retrocopy AATLCFLLQNIFSKKILRDLRIHHLPLLNILGCHAVF<FMIPTWVLVDLSAFLVSSDLT<YVSQWPWMLL

Parental  LLAVSGFCNFAQNVIAFSILNLVSPLSYSVANATKRIMVITVSLIMLRNPVTSTNVLGMMTAILGVFLYN
          LLAVSGFCNFA.NVIAFSILNLVS.LSYSV.NATKRIMVITVSLIML.NPVTSTNVLG.MTAILGVFLYN
Retrocopy LLAVSGFCNFA*NVIAFSILNLVSSLSYSVVNATKRIMVITVSLIMLPNPVTSTNVLGIMTAILGVFLYN

Parental  KTKYDANQQARKHLL-PVTTADLSSKERHRSPLEKPH-NGLLFPQHGDYQYGRNNILTDHFQYSRQSYPN
          KTK.DANQQ.RKHLL.P.TT.DLSSKE.H.SPLEKPH.NGLLFPQHGDY..G.NNILTDHFQYS.QSYP.
Retrocopy KTK*DANQQVRKHLL<PGTTVDLSSKEHHQSPLEKPH>NGLLFPQHGDY-HGCNNILTDHFQYSWQSYPH

Parental  S
          S
Retrocopy S

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	0.13 RPM	7.94 RPM
SRP007412_cerebellum	0.50 RPM	12.37 RPM
SRP007412_heart	0.03 RPM	4.52 RPM
SRP007412_kidney	0.21 RPM	9.36 RPM
SRP007412_liver	0.26 RPM	5.56 RPM
SRP007412_testis	0.00 RPM	1.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_804 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_804 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000127526	1 retrocopy	retro_hsap_1170,
Nomascus leucogenys	ENSNLEG00000005563	1 retrocopy	retro_nleu_2854,
Pongo abelii	ENSPPYG00000009692	1 retrocopy	retro_pabe_981,
Pan troglodytes	ENSPTRG00000010648	1 retrocopy	retro_ptro_804 ,