RetrogeneDB ID: retro_ptro_2930

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03152575.1:700..1111(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FRG1
• Ensembl ID: ENSPTRG00000016671
• Aliases: None
• Description: None

Sequence

>retro_ptro_2930
AGAATCGCCCTGAAATCTGGCTATGGAAAATATCTTGGTATAAATTCAGATGAACTTGTTGTTGGGCATTCAGATGCAAT
TGGACCAAGAGAACAATGGGAACCAGCCTTTCAAAATGGGAAAATGGCTTTGTTGGCCTCAAATAGCTGCTTTATTAGAT
GCAATGAAGCAGGGGACATAGAAGCAAAAAGTAAAACAGCAGGAGAAGAAGAAATGATCAAGATTAGATCCTGTGCTGAA
AAAGAAACCACGAAAAAAGATGACATTCCAGAAGAAGACAAAGGAAATGTAAAACAATGTGAAATCAATTATGTAAAGAA
ATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGTAAAGAAGAGAGTAAAATTCTTAAAAAGGCTCAGAAAGATGGAT
TTTTGCATGAG

Alignment

ORF - retro_ptro_2930 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.89 %
• Parental protein coverage: 53.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RIALKSGYGKYLGINSDGLVVGRSDAIGPREQWEPVFQNGKMALLASNSCFIRCNEAGDIEAKSKTAGEE
          RIALKSGYGKYLGINSD.LVVG.SDAIGPREQWEP.FQNGKMALLASNSCFIRCNEAGDIEAKSKTAGEE
Retrocopy RIALKSGYGKYLGINSDELVVGHSDAIGPREQWEPAFQNGKMALLASNSCFIRCNEAGDIEAKSKTAGEE

Parental  EMIKIRSCAERETKKKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKISKEDSKILKKARKDGFLHE
          EMIKIRSCAE.ET.KKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKISKE.SKILKKA.KDGFLHE
Retrocopy EMIKIRSCAEKETTKKDDIPEEDKGNVKQCEINYVKKFQSFQDHKLKISKEESKILKKAQKDGFLHE

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	0.38 RPM	10.33 RPM
SRP007412_cerebellum	0.04 RPM	16.42 RPM
SRP007412_heart	0.00 RPM	11.57 RPM
SRP007412_kidney	0.00 RPM	14.91 RPM
SRP007412_liver	0.00 RPM	14.47 RPM
SRP007412_testis	0.00 RPM	20.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2930 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2930 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022277	7 retrocopies	retro_cpor_1349, retro_cpor_1350, retro_cpor_1359, retro_cpor_1361, retro_cpor_1362, retro_cpor_1363, retro_cpor_864,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464,
Otolemur garnettii	ENSOGAG00000005749	2 retrocopies	retro_ogar_1523, retro_ogar_2535,
Pan troglodytes	ENSPTRG00000016671	1 retrocopy	retro_ptro_2930 ,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,