RetrogeneDB ID: retro_ptro_709

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:89895170..89895680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL2
• Ensembl ID: ENSPTRG00000018186
• Aliases: None
• Description: mitochondrial ribosomal protein L2 [Source:HGNC Symbol;Acc:14056]

Sequence

>retro_ptro_709
TCAGCAGACATAGCTCTGGTTGCTGGGGGTAGCCAGAAACACTGGATCATCACCACAGAAAACTTGCAGGCTGGAGATAC
AATCCTGAACTCTAACCACATAGGCCAAATGGCAGTTGCTGCTCAGGAAGGGGATGCACATCCACTTGGGGCTCTGCCTG
TGGGAACCCTCATCAACAACATGGAAATTGAGCCAGGCCGGGGTGCCCAGTATATCCAAGCTGCAGGGACGTGTAGTGTG
CTACTGTGGAAGGTGAATGGCACAACCGTTATCCAGCTGCCCTCTAAGAGGCAGATGCAGGTGCTGGAAACATGCATAGC
AACAGTAGGCTGAGTATCCAACACTGATCATAACAAACAGGTCACTGGCAGGGCAGGTCACAACCGTTGGCTGGGCAAGA
GGCCTTCCAGTGGGCTACAGCACTGCAAGGGGTGCTGGGCTGGCCGAAAGATTTGGCCACTACCCTTCATGAAGAGTTAT
GTGAAGCTGCCTTCTGATGCTGCCCAAAGC

Alignment

ORF - retro_ptro_709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.94 %
• Parental protein coverage: 66.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TADIALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGDAHPLGALPVGTLINNVESEPGRGAQ
          .ADIALVAGGS.K.WII.TEN.QAGDTILNSNHIG.MAVAA.EGDAHPLGALPVGTLINN.E.EPGRGAQ
Retrocopy SADIALVAGGSQKHWIITTENLQAGDTILNSNHIGQMAVAAQEGDAHPLGALPVGTLINNMEIEPGRGAQ

Parental  YIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETCVATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRW
          YI.AAGTC.VLL.KVNGT..IQLPSKRQMQVLETC.ATVG.VSN.DHNK.V.G.AG.NRWLGKRP.SG..
Retrocopy YIQAAGTCSVLLWKVNGTTVIQLPSKRQMQVLETCIATVG*VSNTDHNKQVTGRAGHNRWLGKRPSSGLQ

Parental  HRKGGWAGRKIRPLPPMKSYVKLPSAAAQS
          H.KG.WAGRKI.PLP.MKSYVKLPS.AAQS
Retrocopy HCKGCWAGRKIWPLPFMKSYVKLPSDAAQS

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	0.61 RPM	23.88 RPM
SRP007412_cerebellum	1.68 RPM	23.66 RPM
SRP007412_heart	2.74 RPM	17.81 RPM
SRP007412_kidney	2.04 RPM	34.34 RPM
SRP007412_liver	4.19 RPM	55.35 RPM
SRP007412_testis	2.00 RPM	21.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_709 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_709 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1039
Gorilla gorilla	retro_ggor_820
Pongo abelii	retro_pabe_871
Macaca mulatta	retro_mmul_827

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005134	1 retrocopy	retro_acar_136,
Callithrix jacchus	ENSCJAG00000005116	1 retrocopy	retro_cjac_3318,
Homo sapiens	ENSG00000112651	1 retrocopy	retro_hsap_1039,
Gorilla gorilla	ENSGGOG00000010552	1 retrocopy	retro_ggor_820,
Macaca mulatta	ENSMMUG00000002450	1 retrocopy	retro_mmul_827,
Nomascus leucogenys	ENSNLEG00000004370	1 retrocopy	retro_nleu_912,
Otolemur garnettii	ENSOGAG00000034421	2 retrocopies	retro_ogar_1582, retro_ogar_1842,
Pongo abelii	ENSPPYG00000016630	1 retrocopy	retro_pabe_871,
Pan troglodytes	ENSPTRG00000018186	1 retrocopy	retro_ptro_709 ,
Rattus norvegicus	ENSRNOG00000018057	1 retrocopy	retro_rnor_555,