RetrogeneDB ID: retro_pabe_2230

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:98315368..98315956(+)
• Located in intron of: ENSPPYG00000013909

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18A
• Ensembl ID: ENSPPYG00000017282
• Aliases: None
• Description: mitochondrial ribosomal protein S18A [Source:HGNC Symbol;Acc:14515]

Sequence

>retro_pabe_2230
ATGGCGGCCTTTGAGGCTCTGGTGTCTGGCTGTGGGCAGCTTCCCTGTGGGCTCCTAGCAGGCCCAGCAGTGACCAGCTG
ATCTCAGCTTCCAGCTCGCAGGTTCAGGGACGTGGTGGAGATCCAAGAAGGAAAGACAACTATAATTGAAGGCTGTATCA
CAGCGACTCCCAAGAAGAGTCCAAATCCTCCTAACCCCTCTGGCCAGTGCCCCATCTGCCATTGGAACCTGAACCACAAG
TAAAACTATGATGATCTTTTGCTGCTTAGCCAGTTCATCCAGCCTCATGGAGGCATGCTGCCCCGAAAGATCACAGGCCT
ATGACGGGAAGAGCACTGCAAGATCGAGGAGTGTGTGAAGATGGCCTACAGAGCAGGTCTGTTACCAAATCACAGGCCTC
AGCTTCCTGAAGGAGTTGTTCCAAAGGGCAAACCCCAACTCAACTAGTACCTGACCCACTGGGGTCCCCACACCCTCATG
CCCATCTACAAAAAAGGCCTCCCCTGGAACAGGGCGTTCATGGCCTTGGGGTCACCCCTCCTGAGGGACAATGTCTGCTA
CTCAAGAACACCTTGGAAGCTGTATCAC

Alignment

ORF - retro_pabe_2230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALKALVSGCGRFFRGLLAGPAATSWSRLPARGFREVVEIQEGKTTIIEGRITATPKESPNPPNPSGQC
          MAA..ALVSGCG....GLLAGPA.TS.S.LPAR.FR.VVEIQEGKTTIIEG.ITATPK.SPNPPNPSGQC
Retrocopy MAAFEALVSGCGQLPCGLLAGPAVTS*SQLPARRFRDVVEIQEGKTTIIEGCITATPKKSPNPPNPSGQC

Parental  PICRWNLKHKYNYDDVLLLSQFIRPHGGMLPRKITGLCQEEHRKIEECVKMAHRAGLLPNHRPRLPEGVV
          PIC.WNL.HK.NYDD.LLLSQFI.PHGGMLPRKITGL..EEH.KIEECVKMA.RAGLLPNHRP.LPEGVV
Retrocopy PICHWNLNHK*NYDDLLLLSQFIQPHGGMLPRKITGL*REEHCKIEECVKMAYRAGLLPNHRPQLPEGVV

Parental  PKSKPQLNRYLTRWAPGSVKPIYKKGPRWNRVRMPVGSPLLRDNVCYSGTPWKLYH
          PK.KPQLN.YLT.W.P....PIYKKG..WNR..M..GSPLLRDNVCYS.TPWKLYH
Retrocopy PKGKPQLN*YLTHWGPHTLMPIYKKGLPWNRAFMALGSPLLRDNVCYSRTPWKLYH

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	8.68 RPM
SRP007412_cerebellum	0.00 RPM	4.01 RPM
SRP007412_heart	0.00 RPM	4.70 RPM
SRP007412_kidney	0.00 RPM	9.65 RPM
SRP007412_liver	0.00 RPM	5.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2230 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2230 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2787
Pan troglodytes	retro_ptro_1888
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,