RetrogeneDB ID: retro_ptro_239

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:181590003..181590622(+)
• Located in intron of: ENSPTRG00000001856

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A39
• Ensembl ID: ENSPTRG00000009272
• Aliases: None
• Description: None

Sequence

>retro_ptro_239
CTGAGCCCTTACCTCTACATAACCTTGGTAGCTGGTGTGCTGGCCCACCCTGGCACTATCACTGCAATCATCAGTGCCCT
GGAGCTTATGCAGACAAAGCTGCAGGTTCAGCATATGTTACACTATGTGCTGGTACCTGTGTTTGAGCTCCAGTGGCTTA
GAGTGGTTGGTGCTCACTGTGGCTGTTCCGGGGCCCCACTCTCCTTAGAGATGTGCCCTTCTCAGCCCTGTACTGGTTCA
ACTACGAGCTAGTGAAGAGCTGGCTGAATGGGCTCAGGCCAAAGGACCTCCATGGTCCCATGACAACCATAGGAGTCAGC
TTTGCAGCTGGCAGCATCACCATGATGCTGGCTACAGTGCCGACCCTAACCTTTGTCGTGATGAAGACTCAACACCAGGC
CACACTCGGAGTGATGGAAGCCGTGGAAGTGACATCCCTGGATGCGGACTCTACCTGGTTGCTCAGAGGTGGATCTGTGT
CAAGTCGGGCATCAGAGGGCTCTTTGCAGGCTTCCTCCCTTGGATCATCAAGTCTATCCCCTCCTATGCTATCACGATCA
CCACTTATGAGTTCAGCAAAAGTCTCTTAAAGAGACTCAATCAGGACCAGCATCTGGGC

Alignment

ORF - retro_ptro_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.72 %
• Parental protein coverage: 60.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTSDLYAPMVAGALARLGTVT-VISPLELMRTKLQAQHVSYREL-GACVRTAVAQGGWRSLWLGWGPTAL
          L...LY...VAG.LA..GT.T..IS.LELM.TKLQ.QH.....L.G.CV...VA..GW.SLWL..GPT.L
Retrocopy LSPYLYITLVAGVLAHPGTITAIISALELMQTKLQVQHMLHYVL<GTCV*APVA*SGWCSLWLFRGPTLL

Parental  RDVPFSALYWFNYELVKSWLNGLRPKD----QTSVGMSFVAGGISGTVAAVLTLPFDVVKTQRQVALGAM
          RDVPFSALYWFNYELVKSWLNGLRPKD.....T..G.SF.AG.I....A.V.TL.F.V.KTQ.Q..LG.M
Retrocopy RDVPFSALYWFNYELVKSWLNGLRPKDLHGPMTTIGVSFAAGSITMMLATVPTLTFVVMKTQHQATLGVM

Parental  EAVRVNPLHVDSTWLL-LQRIRAESGTKGLFAGFLPRIIKAAPSCAIMISTYEFGKSFFQRLNQDRLLG
          EAV.V..L..DSTWLL....I...SG..GLFAGFLP.IIK..PS.AI.I.TYEF.KS...RLNQD..LG
Retrocopy EAVEVTSLDADSTWLL<QRWICVKSGIRGLFAGFLPWIIKSIPSYAITITTYEFSKSLLKRLNQDQHLG

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	0.09 RPM	47.56 RPM
SRP007412_cerebellum	0.04 RPM	20.90 RPM
SRP007412_heart	0.00 RPM	11.75 RPM
SRP007412_kidney	0.08 RPM	213.32 RPM
SRP007412_liver	0.00 RPM	94.70 RPM
SRP007412_testis	0.00 RPM	59.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_239 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_239 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_290

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008556	1 retrocopy	retro_dnov_1866,
Echinops telfairi	ENSETEG00000002713	1 retrocopy	retro_etel_823,
Homo sapiens	ENSG00000013306	1 retrocopy	retro_hsap_290,
Myotis lucifugus	ENSMLUG00000001925	2 retrocopies	retro_mluc_2296, retro_mluc_646,
Monodelphis domestica	ENSMODG00000011561	1 retrocopy	retro_mdom_1102,
Pongo abelii	ENSPPYG00000008333	1 retrocopy	retro_pabe_383,
Pan troglodytes	ENSPTRG00000009272	1 retrocopy	retro_ptro_239 ,
Rattus norvegicus	ENSRNOG00000020994	2 retrocopies	retro_rnor_1892, retro_rnor_2884,
Ictidomys tridecemlineatus	ENSSTOG00000004189	1 retrocopy	retro_itri_447,