RetrogeneDB ID: retro_pabe_871

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:90632192..90633108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL2
• Ensembl ID: ENSPPYG00000016630
• Aliases: None
• Description: mitochondrial ribosomal protein L2 [Source:HGNC Symbol;Acc:14056]

Sequence

>retro_pabe_871
ATGGCCCTGTGGGCACTGACCTGTGCTCTGCACTGTCTGTGCCTGGCACCCCCGACCGTTGCCACTTCCATCCCGAGTCT
GTTCCCTGCCTCCCAGGTGATGAACAATGCCCTCTTCCAATGGCCCTCTGCCTTGATGTTGCTCCCCTGCTACCAAATCC
TTACTTCTATGGCCCTTAGTGCCAACTTTGTGTCTTGAAAGAGTCATATCAAGTACACCATTAAACCAGTGAAGATGAGA
AAGTCTGGAGGTGAGGACCACACAGGCCAGATCTGGGTGCACGGTATTGGCAGGGGCCACAAGCAACATTATTGCATGAT
TGACTTTTGTGTTTCTGGCCTGAGGAGGAGACCAAGTCAGGACCCTTTGAGGAGAAGGTTATCCAAGTCCACCGTGATCC
CTGTAGGTCAGCAGACATAGCTCTGGTTGCTGGGGGTAGCCAGAAACACTGGATCATCACCACAGAAAACATGCAGGCTG
GAGATACAATCCTGAACTCTAACCACATAGGCCAAATGGCAGTTGCTGCTCAGGAAGGGGATGCACATCCACTTGGGGCT
CTGCCTGTGGGAACCCTCATCAACAACATGGAAAGTGAGCCAGGCCGGGGTGCCCAGCATATCCGAGCTGCAGGGACGTG
TAGTGTGTTACTGTGGAAGGTGAATGGCACAACCATTATCCAGCTGCCCTCTAAGAGGCAGATGCAGGTGCTGGAAACAT
GCATAGCAACAGTAGGCTGAGTATCCAACACTGATCATAACAAACAGGTCACTGGCAGGGCAGGTCACAACCGTTGGCTG
GGCAAGAGGCCTTCCAGTGGGCTAGGCACCACAAGGGGTGCTGAGCTGGCTGAAAGATTTGGCCACTACCCTTCATGAAG
AGTTATGTGAAGCTGCCTTCTGATGCTGCCCAAAGC

Alignment

ORF - retro_pabe_871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALWALTRALRSLSLAPPTVAAPAPSLFPAAQMMNNGLLQQPSALMLLPCRPILTSVALNANFVSWKSRT
          MALWALT.AL..L.LAPPTVA...PSLFPA.Q.MNN.L.Q.PSALMLLPC..ILTS.AL.ANFVS.KS..
Retrocopy MALWALTCALHCLCLAPPTVATSIPSLFPASQVMNNALFQWPSALMLLPCYQILTSMALSANFVS*KSHI

Parental  KYTIAPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDF-LRFRPEE-TKSGPFEEKVIQVRYDPCRSAD
          KYTI.PVKMRKSGG.DHTG.I.VHGIG.GHKQ.Y.MIDF.L.F.PEE.TKSGPFEEKVIQV..DPCRSAD
Retrocopy KYTIKPVKMRKSGGEDHTGQIWVHGIGRGHKQHYCMIDF<LCFWPEEETKSGPFEEKVIQVHRDPCRSAD

Parental  IALVAGGSRKRWIIATENMQAGDTILNSNHIGRMAVAAREGDAHPLGALPVGTLINNVESEPGRGAQYIR
          IALVAGGS.K.WII.TENMQAGDTILNSNHIG.MAVAA.EGDAHPLGALPVGTLINN.ESEPGRGAQ.IR
Retrocopy IALVAGGSQKHWIITTENMQAGDTILNSNHIGQMAVAAQEGDAHPLGALPVGTLINNMESEPGRGAQHIR

Parental  AAGTCGVLLRKVNGTAIIQLPSKRQMQVLETCVATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSG-RWHR
          AAGTC.VLL.KVNGT.IIQLPSKRQMQVLETC.ATVG.VSN.DHNK.V.G.AG.NRWLGKRP.SG...H.
Retrocopy AAGTCSVLLWKVNGTTIIQLPSKRQMQVLETCIATVG*VSNTDHNKQVTGRAGHNRWLGKRPSSG<ARHH

Parental  KGGWAGRKIQPLPPMKSYVKLPSAAAQS
          KG..AG.KI.PLP.MKSYVKLPS.AAQS
Retrocopy KGC*AG*KIWPLPFMKSYVKLPSDAAQS

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	18.41 RPM
SRP007412_cerebellum	0.00 RPM	6.20 RPM
SRP007412_heart	0.03 RPM	12.10 RPM
SRP007412_kidney	0.00 RPM	29.53 RPM
SRP007412_liver	0.03 RPM	21.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_871 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_871 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1039
Pan troglodytes	retro_ptro_709
Gorilla gorilla	retro_ggor_820
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,