RetrogeneDB ID: retro_ptro_3042

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392075.1:2045427..2045782(-)
• Located in intron of: ENSPTRG00000005811

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGS17
• Ensembl ID: ENSPTRG00000029367
• Aliases: None
• Description: None

Sequence

>retro_ptro_3042
ATGTGAAAAAGGCAGCAGTCCCAAAATGAAGGAACACCTGCTGTGTCTCAAGCGCCTGGAAACCAGAGGCCCAACAACAT
CTGTTGCTTTTGTTGGTGCTGTTGTTGCAGCTGCTCCTGCCTCACTGTTAGGAATGAAGAAAGGGGAAAATGCAGGAAGA
ACCACACACACTACAAAAATGGAGAGTATCCAGGTCCTAGAGGAATGCTAAAACCCCACTGCAGAGGAAGTCTTGCCCTG
GTCTCAAAATTTTGACAAGATGATGAAGGCCCCAGCAGGAAGAAACCTTTTCAGAGAGTTCCTCTGAACAGAATACAACA
AAGAGAACCTACTTTTCTGGATTGCCTGTGAAGAC

Alignment

ORF - retro_ptro_3042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.83 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRKRQQSQNEGTPAVSQAPGNQRPNNTCCFCWCCCC-SCSCLTVRNEERGENAGRPTHTTKMESIQVLEE
          M.KRQQSQNEGTPAVSQAPGNQRPNN.CCFCWC.CC.............GENAGR.THTTKMESIQVLEE
Retrocopy M*KRQQSQNEGTPAVSQAPGNQRPNNICCFCWC-CC>AAAPASLLGMKKGENAGRTTHTTKMESIQVLEE

Parental  CQNPTAEEVLSWSQNFDKMMKAPAGRNLFREFLRTEYSEENLLFWLACED
          C.NPTAEEVL.WSQNFDKMMKAPAGRNLFREFL.TEY..ENLLFW.ACED
Retrocopy C*NPTAEEVLPWSQNFDKMMKAPAGRNLFREFL*TEYNKENLLFWIACED

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	0.02 RPM	0.55 RPM
SRP007412_cerebellum	0.00 RPM	1.29 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.03 RPM	0.10 RPM
SRP007412_liver	0.03 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3042 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3042 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3042 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1254
Gorilla gorilla	retro_ggor_987
Macaca mulatta	retro_mmul_1309

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000091844	1 retrocopy	retro_hsap_1254,
Gorilla gorilla	ENSGGOG00000026033	1 retrocopy	retro_ggor_987,
Macaca mulatta	ENSMMUG00000019078	1 retrocopy	retro_mmul_1309,
Nomascus leucogenys	ENSNLEG00000015461	1 retrocopy	retro_nleu_2092,
Oryctolagus cuniculus	ENSOCUG00000021054	1 retrocopy	retro_ocun_1922,
Pan troglodytes	ENSPTRG00000029367	1 retrocopy	retro_ptro_3042 ,