RetrogeneDB ID: retro_ptro_1888

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:48997435..48998024(-)
• Located in intron of: ENSPTRG00000014881

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18A
• Ensembl ID: ENSPTRG00000018209
• Aliases: None
• Description: None

Sequence

>retro_ptro_1888
ATGGCGGCCTTTGAGGCTCTGGTGTCTGGCTGTGGGCAGCTTCCCTGTGGGCTCCTAGCAGGCCCAGCAGTGACCAGCTG
GTCTCAGCTTCCAGCTCGTGGGTTCAGGGAAGTGGTGGAAATCCAAGAAGGAAAGACAACTATAATTGAAGGCCGTATCA
CAGTGACTCCCAAGGAGAGTCCAAATCCTCCTAACCCCTCTGGCCAGTGCCCCATCTGCCATTGGAACCTGAACCACAAG
TAAAACTATGATGATGTTTTGCTGCTTAGCCAGTTCATCCAGCCCCATGGAGGCATGCTGCCCCGAAAGATCACAGGCCT
ATGACAGGAAGAGAACTGCAAGATTGAGGAGTGTGTGAAGATGGCCTACCGAGCAGGTCTGTTACCAAATCACAGGCCTC
AGCTTCCTGAAGGAGTTGTTCCAAAGGGCAAACCCCAATTCAACCAGTACCTGACCCACTGGGGTCCCCGCACCCTCATG
CCCATCTACAAAAAAAGGCCTCCCCTGGAACAGGGCGTTCATGGCCTTGGGGTCAACCCTCCTGAGGGACAATGTCTGCT
ACTCAAGAACACCTTGGAAGCTGTATCAC

Alignment

ORF - retro_ptro_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALKALVSGCGRLLRGLLAGPAATSWSRLPARGFREVVEIQEGKTTIIEGRITATPKESPNPPNPSGQC
          MAA..ALVSGCG.L..GLLAGPA.TSWS.LPARGFREVVEIQEGKTTIIEGRIT.TPKESPNPPNPSGQC
Retrocopy MAAFEALVSGCGQLPCGLLAGPAVTSWSQLPARGFREVVEIQEGKTTIIEGRITVTPKESPNPPNPSGQC

Parental  PICRWNLKHKYNYDDVLLLSQFIRPHGGMLPRKITGLCQEEHRKIEECVKMAHRAGLLPNHRPRLPEGVV
          PIC.WNL.HK.NYDDVLLLSQFI.PHGGMLPRKITGL.QEE..KIEECVKMA.RAGLLPNHRP.LPEGVV
Retrocopy PICHWNLNHK*NYDDVLLLSQFIQPHGGMLPRKITGL*QEENCKIEECVKMAYRAGLLPNHRPQLPEGVV

Parental  PKSKPQLNRYLTRWAPGSVKPIYKKGP-RWNRVRMPVGSPLLRDNVCYSRTPWKLYH
          PK.KPQ.N.YLT.W.P....PIYKK.P..WNR..M..GS.LLRDNVCYSRTPWKLYH
Retrocopy PKGKPQFNQYLTHWGPRTLMPIYKKRP>PWNRAFMALGSTLLRDNVCYSRTPWKLYH

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	0.07 RPM	29.37 RPM
SRP007412_cerebellum	0.25 RPM	15.45 RPM
SRP007412_heart	0.03 RPM	13.87 RPM
SRP007412_kidney	0.10 RPM	25.86 RPM
SRP007412_liver	0.13 RPM	23.57 RPM
SRP007412_testis	0.00 RPM	10.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1888 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1888 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2787
Pongo abelii	retro_pabe_2230
Callithrix jacchus	retro_cjac_1386

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017382	1 retrocopy	retro_cjac_1386,
Homo sapiens	ENSG00000096080	1 retrocopy	retro_hsap_2787,
Macropus eugenii	ENSMEUG00000013986	1 retrocopy	retro_meug_1966,
Pongo abelii	ENSPPYG00000017282	1 retrocopy	retro_pabe_2230,
Pan troglodytes	ENSPTRG00000018209	1 retrocopy	retro_ptro_1888 ,
Tarsius syrichta	ENSTSYG00000001390	1 retrocopy	retro_tsyr_862,