RetrogeneDB ID: retro_ptro_800

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:133118634..133118952(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLAC8
• Ensembl ID: ENSPTRG00000016226
• Aliases: None
• Description: None

Sequence

>retro_ptro_800
GTGCTGATGGTCGTTGTGGGAGTCGGTCTCGGTCCGGCACCCCAGAACTCCAACTGGCAGACAGGCATGTGTGACTGCTT
CAGCGACTGTGGAGTCTGTCTCTGTGGCACGTATTGTCTCCCGTGCCTTGGGTGTCAAGTTGCAGCTGATATGAATGAAT
GCTGTGTGGAGCAAGCGTCGCAATGAGGACTCTACAGGACCTGATATGGTATCCCTGGATCTATTTGTGATGATTATATG
GCAACCCTTTGCGGTCCTCCTTGTACTCTTTGCCAAATCAAGAGAGATATCAACAGAAGGAGAGTCATGCGTACTTTC

Alignment

ORF - retro_ptro_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 93.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVVTQPGVGPGPAPQNSNWQTGMCDCFSDCGVCLCGTFCFPCLGCQVAADMNECCLCGTSVAMRTLYRTR
          V.....GVG.GPAPQNSNWQTGMCDCFSDCGVCLCGT.C.PCLGCQVAADMNEC..C........LYRT.
Retrocopy VLMVVVGVGLGPAPQNSNWQTGMCDCFSDCGVCLCGTYCLPCLGCQVAADMNEC--CVEQASQ*GLYRT*

Parental  YGIPGSICDDYMATLCCPHCTLCQIKRDINRRRAMRTF
          YGIPGSICDDYMATLC.P.CTLCQIKRDINRRR.MRTF
Retrocopy YGIPGSICDDYMATLCGPPCTLCQIKRDINRRRVMRTF

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	0.64 RPM	1.09 RPM
SRP007412_cerebellum	0.82 RPM	2.58 RPM
SRP007412_heart	0.06 RPM	1.43 RPM
SRP007412_kidney	0.39 RPM	2.80 RPM
SRP007412_liver	0.13 RPM	12.18 RPM
SRP007412_testis	1.26 RPM	0.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_800 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_800 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1165

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145287	1 retrocopy	retro_hsap_1165,
Gorilla gorilla	ENSGGOG00000007464	1 retrocopy	retro_ggor_910,
Monodelphis domestica	ENSMODG00000019309	1 retrocopy	retro_mdom_950,
Mus musculus	ENSMUSG00000029322	1 retrocopy	retro_mmus_1051,
Otolemur garnettii	ENSOGAG00000017232	1 retrocopy	retro_ogar_714,
Pan troglodytes	ENSPTRG00000016226	1 retrocopy	retro_ptro_800 ,
Rattus norvegicus	ENSRNOG00000002217	2 retrocopies	retro_rnor_1489, retro_rnor_1878,