RetrogeneDB ID: retro_pabe_2680

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:120912730..120913303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL10
• Ensembl ID: ENSPPYG00000008881
• Aliases: None
• Description: mitochondrial ribosomal protein L10 [Source:HGNC Symbol;Acc:14055]

Sequence

>retro_pabe_2680
CAGGAGACAGGCCTCATCAGCCTTCTCCGCTGGGAGATAGCAGCGGTTTTCCAGGACAACCGAATGATAGCTGTCTGCCA
GAACGTGGCTCTGAGCGCAGAAGACAAGCTTCTTATGCGACACCAGCTGCGGAGACACAAGATCCTGATGAAGGTCTTCC
ACAACCAGGTCCTGAAGCTCTTCCTGGAGGATTCCAAGTACCAAAATCTGCTGCCCCTTTTTGTGGAGTACAACATGCTG
CTGGTCAGTGAAGAGCCCAAGGTCAAGGAGATGGTAAGGATCTTAAGGACTGTGCCATTCCTGCTGCTGCTAGGTGGCTA
CATCAATGACACAGATGCCATCCTCAGCAGGCAGGGCTTTATCAACTACTCCAGCCTTCCCAGCCTGCCCCTGGCACAGG
GGGAGCTTGTGGGAGGCCTCACTCCACTCATGGCCCAGACCCACTCCCTGCTCCAGCACCAGCCCCTGCAGTTGACCACC
CTATTGGACCAGTACATCAGACAGCAAGGCGAGAAGGATTCTGTCGTGTCAGCCAGTGGGAAGCCAGATCCTCCTGACCC
TGTTCCGGACTCG

Alignment

ORF - retro_pabe_2680 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.96 %
• Parental protein coverage: 84.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EETGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHKILMKVFPNQVLKPFLEDSKYQNL
          .ETGLI.LLR.EIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLR.HKILMKVF.NQVLK.FLEDSKYQNL
Retrocopy QETGLISLLRWEIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRRHKILMKVFHNQVLKLFLEDSKYQNL

Parental  LPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGCIDDT--ILSRQGFINYSKLPSLPLVQGELVGGL
          LPLFV..NMLLVSEEPKVKEMVRILRTVPFL.LLGG.I.DT..ILSRQGFINYS.LPSLPL.QGELVGGL
Retrocopy LPLFVEYNMLLVSEEPKVKEMVRILRTVPFLLLLGGYINDTDAILSRQGFINYSSLPSLPLAQGELVGGL

Parental  TRLTAQTHSLLQHQPLQLTTLLDQYIREQREKDSIMSANGKPD-PDPVPDS
          T.L.AQTHSLLQHQPLQLTTLLDQYIR.Q.EKDS..SA.GKPD.PDPVPDS
Retrocopy TPLMAQTHSLLQHQPLQLTTLLDQYIRQQGEKDSVVSASGKPDPPDPVPDS

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	32.07 RPM
SRP007412_cerebellum	0.00 RPM	26.27 RPM
SRP007412_heart	0.00 RPM	20.92 RPM
SRP007412_kidney	0.00 RPM	34.44 RPM
SRP007412_liver	0.00 RPM	19.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2680 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2680 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3234
Pan troglodytes	retro_ptro_2186

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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	ENSG00000159111	1 retrocopy	retro_hsap_3234,
Nomascus leucogenys	ENSNLEG00000001803	1 retrocopy	retro_nleu_952,
Otolemur garnettii	ENSOGAG00000006173	1 retrocopy	retro_ogar_989,
Pongo abelii	ENSPPYG00000008881	1 retrocopy	retro_pabe_2680 ,
Pan troglodytes	ENSPTRG00000009337	1 retrocopy	retro_ptro_2186,
Xenopus tropicalis	ENSXETG00000014749	1 retrocopy	retro_xtro_17,