RetrogeneDB ID: retro_ptro_770

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:68722960..68723269(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRELID2
• Ensembl ID: ENSPTRG00000017368
• Aliases: None
• Description: PRELI domain containing 2 [Source:UniProtKB/TrEMBL;Acc:K7D322]

Sequence

>retro_ptro_770
GTAACTAACATCCAATTAAAAGAGGAGTCATGGCTCAATCCTCAAGAAAGAAACATGATTATATGGAGTCATTGCCTTAT
GTGGACACAGTATGCATTTAGGAAGGAAAAGTCAGTCTTCTGGGAAAGTGTGGAAAATCCAAATTGGACAGAGCTCATTG
AAAAAGGCAAGATTTCAGTCACTGGAGCTGTATTTCTCAACTGCATTTTGGAAACTTTTGCCAGCACATTCTTAAGACAG
GGAGCTCAGAAGGGAATTTGAATCGTGGAGATGCTGCTAAAGGAACAGTATGGTGCCCCCTTAGCTGAA

Alignment

ORF - retro_ptro_770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.64 %
• Parental protein coverage: 54.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPNIQLEEESWLNPRERNMAIRSHCLTWTQYASMKEESVFRESMENPNWTEFIQRGRISITGVGFLNCVL
          V.NIQL.EESWLNP.ERNM.I.SHCL.WTQYA..KE.SVF.ES.ENPNWTE.I..G.IS.TG..FLNC.L
Retrocopy VTNIQLKEESWLNPQERNMIIWSHCLMWTQYAFRKEKSVFWESVENPNWTELIEKGKISVTGAVFLNCIL

Parental  ETFASTFLRQGAQKGIRIMEMLLKEQCGAPLAE
          ETFASTFLRQGAQKGI.I.EMLLKEQ.GAPLAE
Retrocopy ETFASTFLRQGAQKGI*IVEMLLKEQYGAPLAE

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	0.52 RPM
SRP007412_cerebellum	0.00 RPM	0.18 RPM
SRP007412_heart	0.00 RPM	0.52 RPM
SRP007412_kidney	0.00 RPM	1.18 RPM
SRP007412_liver	0.00 RPM	1.08 RPM
SRP007412_testis	0.00 RPM	1.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_770 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_770 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1134
Macaca mulatta	retro_mmul_877

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001222	1 retrocopy	retro_cpor_821,
Echinops telfairi	ENSETEG00000005000	2 retrocopies	retro_etel_1464, retro_etel_1676,
Homo sapiens	ENSG00000186314	1 retrocopy	retro_hsap_1134,
Macaca mulatta	ENSMMUG00000013588	1 retrocopy	retro_mmul_877,
Mus musculus	ENSMUSG00000056671	1 retrocopy	retro_mmus_1260,
Nomascus leucogenys	ENSNLEG00000009800	1 retrocopy	retro_nleu_928,
Otolemur garnettii	ENSOGAG00000010025	2 retrocopies	retro_ogar_2400, retro_ogar_2477,
Pan troglodytes	ENSPTRG00000017368	1 retrocopy	retro_ptro_770 ,
Tursiops truncatus	ENSTTRG00000016708	1 retrocopy	retro_ttru_1875,