RetrogeneDB ID: retro_ptro_2186

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:120239359..120239932(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL10
• Ensembl ID: ENSPTRG00000009337
• Aliases: None
• Description: mitochondrial ribosomal protein L10 [Source:HGNC Symbol;Acc:14055]

Sequence

>retro_ptro_2186
CAGGAGACGGGCCTCATCAGACTCCTCTGCCGGGAGATAGCAGCAGTTTTCCAGGACAACCGAATGATAGCTATCTGCCA
GAGCGTGGCTCTGAGCGTAGAAGATAAGCTTCTTATGCGACACCAGCGGCGGAAACACAAGATCCTGATGAAGGTCTTCC
ACAACCAGGTCCTGAAGCCCTTCCTGGAGGACTCCAATTACCAAAATCTGCTGCCCCTTTTTGTGGGGCACAACATGCTG
CTGGTCAGTGAAGAGCCCAAGGTCAAGGAGATGGTAAGGATCTTAAGGACTGTGCCATTCCTGCTGCTGCTAGGTGGCTG
CATCAATGACGTAGATGCCATCCTCAGCAGGCAGGGCTTTATCAACTACTCCAGCCTTCCTAGCCTGCCCCTGGCACAGG
GGGAGCTTGTGGGAGGCCTCACCCCACTCATGGCCCAGACCCACTCCCTGCTCCAGCACCAGCCCCTTAAGTTGACCACC
CTATTGGACCAGTACATCAGACAGCAAAGCGAGAAGGATTCTGTCGTGCCGGCCAATGGGAAGCCAGATCCTCCTGACCC
TGTTCCGGACTCG

Alignment

ORF - retro_ptro_2186 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 69.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEIGLIRLLRREIAAVFQDNRMIAVCQNVALSAEDKLLMRHQLRKHKILMKVFPNQVLKPFLEDSKYQNL
          .E.GLIRLL.REIAAVFQDNRMIA.CQ.VALS.EDKLLMRHQ.RKHKILMKVF.NQVLKPFLEDS.YQNL
Retrocopy QETGLIRLLCREIAAVFQDNRMIAICQSVALSVEDKLLMRHQRRKHKILMKVFHNQVLKPFLEDSNYQNL

Parental  LPLFVGHNMLLVSEEPKVKEMVRILRTVPFLPLLGGCID--DTILSRQGFINYSKLPSLPLVQGELVGGL
          LPLFVGHNMLLVSEEPKVKEMVRILRTVPFL.LLGGCI...D.ILSRQGFINYS.LPSLPL.QGELVGGL
Retrocopy LPLFVGHNMLLVSEEPKVKEMVRILRTVPFLLLLGGCINDVDAILSRQGFINYSSLPSLPLAQGELVGGL

Parental  TCLTAQTHSLLQHQPLQLTTLLDQYIREQREKDSVMSANGKPD-PDPVPDS
          T.L.AQTHSLLQHQPL.LTTLLDQYIR.Q.EKDSV..ANGKPD.PDPVPDS
Retrocopy TPLMAQTHSLLQHQPLKLTTLLDQYIRQQSEKDSVVPANGKPDPPDPVPDS

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	0.11 RPM	23.58 RPM
SRP007412_cerebellum	0.00 RPM	27.78 RPM
SRP007412_heart	0.00 RPM	32.03 RPM
SRP007412_kidney	0.00 RPM	44.67 RPM
SRP007412_liver	0.07 RPM	24.35 RPM
SRP007412_testis	1.26 RPM	24.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2186 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2186 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2186 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3234
Pongo abelii	retro_pabe_2680

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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,