RetrogeneDB ID: retro_ptro_2704

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:86658505..86659030(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf29
• Ensembl ID: ENSPTRG00000005277
• Aliases: None
• Description: chromosome 12 open reading frame 29 [Source:HGNC Symbol;Acc:25322]

Sequence

>retro_ptro_2704
GATCAGCCATAGCTTTGGGCCCAACTAGATAGAAAGCTCAACAAACAAGTTGAAAAAAGATTTTAAAATCTTTTACATTC
AAATGAAAACCCAAAATAATTTTTTTGGAACGTTGAGGAGGACTTCAAACCGGCTCTAGAGTGCTGGATACCAGCAAAGG
AAATAGAACAAATAAATGGGAACCCAGTGCCTAATGAAAATAGATACATTCCTGATTGGGTACCAGTATAGAAAAACAAC
AAACAGTATTGCTAGCATTCCTCTGTAGTTAATTATGAATTTGAAATTGCCCTGGTACTAAAACATCATGCTGATGATTC
TGGACTTTTGGAAATTACTGCAGTGCCACTATCAGATCTCTTAGAACAAACACTGGAGCTCACAGGAAAAAATATCAATG
GAAACCCATATGCGTTAGGGAGCAAGAAACATCCATTACATCTTCTTATACCACATGGAGCATTTCAAATAAGAAATCTA
CCTTCGTTGAAGCACAATGATATCATGTCCTGGTTTGAAGGTTGC

Alignment

ORF - retro_ptro_2704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.29 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DQPYLWARLDRKPNKQAEKRFKNFLHSKENPKEFFWNVEEDFKPAPECWIPAKETEQINGNPVPDENGHI
          DQP.LWA.LDRK.NKQ.EKRF.N.LHS.ENPK.FFWNVEEDFKPA.ECWIPAKE.EQINGNPVP.EN..I
Retrocopy DQP*LWAQLDRKLNKQVEKRF*NLLHSNENPK*FFWNVEEDFKPALECWIPAKEIEQINGNPVPNENRYI

Parental  PGWVPVEKNNKQYCWHSSVVNYEFEIALVLKHHPDDSGLLEISAVPLSDLLEQTLELIGTNINGNPYGLG
          P.WVPV.KNNKQYC.HSSVVNYEFEIALVLKHH.DDSGLLEI.AVPLSDLLEQTLEL.G.NINGNPY.LG
Retrocopy PDWVPV*KNNKQYC*HSSVVNYEFEIALVLKHHADDSGLLEITAVPLSDLLEQTLELTGKNINGNPYALG

Parental  SKKHPLHLLIPHGAFQIRNLPSLKHNDLVSWFEDC
          SKKHPLHLLIPHGAFQIRNLPSLKHND..SWFE.C
Retrocopy SKKHPLHLLIPHGAFQIRNLPSLKHNDIMSWFEGC

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	0.04 RPM	9.08 RPM
SRP007412_cerebellum	0.00 RPM	7.74 RPM
SRP007412_heart	0.00 RPM	2.04 RPM
SRP007412_kidney	0.00 RPM	3.64 RPM
SRP007412_liver	0.00 RPM	2.06 RPM
SRP007412_testis	0.00 RPM	7.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2704 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2704 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3984
Gorilla gorilla	retro_ggor_2674

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011011	1 retrocopy	retro_chof_1262,
Homo sapiens	ENSG00000133641	1 retrocopy	retro_hsap_3984,
Gorilla gorilla	ENSGGOG00000005986	1 retrocopy	retro_ggor_2674,
Loxodonta africana	ENSLAFG00000013286	1 retrocopy	retro_lafr_706,
Macaca mulatta	ENSMMUG00000015860	1 retrocopy	retro_mmul_715,
Nomascus leucogenys	ENSNLEG00000005396	1 retrocopy	retro_nleu_1905,
Pan troglodytes	ENSPTRG00000005277	1 retrocopy	retro_ptro_2704 ,
Rattus norvegicus	ENSRNOG00000006973	1 retrocopy	retro_rnor_1625,
Tupaia belangeri	ENSTBEG00000005256	1 retrocopy	retro_tbel_94,
Tarsius syrichta	ENSTSYG00000014665	1 retrocopy	retro_tsyr_1572,