RetrogeneDB ID: retro_ptro_2335

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:28704638..28705470(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX11
• Ensembl ID: ENSPTRG00000009422
• Aliases: None
• Description: COX11 cytochrome c oxidase assembly homolog [Source:UniProtKB/TrEMBL;Acc:K7DPG0]

Sequence

>retro_ptro_2335
ATGGGAGGGCTCTGGCATCCGGGATGGAGGCGCGTCGCTTTCTGTGGCTGGCGCTGGATCCACCCTGGGTCTCCAGCCAC
GGCTGCAGAGAGGGTAGAGCGGTTTCTTAGGCCAGAGTGGAGTGGGACAGGAGGTGCCCAGAGACGACTGTGGTGGCTTG
AGACATGGAAGCGCTGCAGCCTTTGAGCCCGGTATCCAGCATTGCAGCCGCCGCGGCGGCCTAAGAGCTCAAACCCTTTC
AGGCGCGCGCAAGAGGAGGAGCGGCGGCGGCGGCGGAACAAGACGACCCTCACTTAACGTGGCCGCTGTCGCCGTGGGCA
TGCTGGGGGCGTCCTACGCTGCCGTTCCCCTTTATCGGCTCTATTGCCAGACTACTGGACTTGGAGGATCAGCAGTTTCA
GGTCATGCCTCAGACCAGATTGAAAACATGGTGCCTGTTAAGGATCGAATCATTAAAATTAACTTTGATGCAGATGTGCA
TGCAAGTCTTCAGTGGAACTTTAGACCTCAGCAAACAGAAATATATGTGGTGCCAGGAGACACTGCACTGGGGTTTTACA
GAGCTAAGAATCCTGCTGACAAACCACTAATTGGAATTTCTACATACAATGTTGTTCCATTTGAAGCTGGACAGTATTTC
AATAAAATACAGTGCTTCTGTTTTGAAGAACAAAGGCTTAATCCCCAAGAGGAAGTAGATATGCCAGTGTTTTTCTACAT
TGATCCTGAATTTGCTAAAGACCCAAGAATGATTAATGTTGATCTTATCACTCTTTCTTACACTTTTTTTGAAGCAAAGG
AAGGGCACAATTTGCCAGTTCCAGGATATAAC

Alignment

ORF - retro_ptro_2335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGLWRPAWRGVAFCGWRWIHPGSPTRAAERVEPFLRPEWSGTGGAERGLRWLGTWKRCSLPFRHPALQP
          MGGLW.P.WR.VAFCGWRWIHPGSP..AAERVE.FLRPEWSGTGGA.R.L.WL.TWKRCSL..R.PALQP
Retrocopy MGGLWHPGWRRVAFCGWRWIHPGSPATAAERVERFLRPEWSGTGGAQRRLWWLETWKRCSL*ARYPALQP

Parental  PRRPKSSNPFTRAQEE-KRRRQNKTTLT-YVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHASDK
          PRRPKSSNPF.RAQEE..RRR.NKTTLT..VAAVAVGMLGASYAAVPLYRLYCQTTGLGGSAV.GHASD.
Retrocopy PRRPKSSNPFRRAQEEERRRRRNKTTLT>NVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSAVSGHASDQ

Parental  IENMVPVKDRIIKISFNADVHASLQWNFRPQQTEIYVVPGETALAFYRAKNPTDKPVIGISTYNIVPFEA
          IENMVPVKDRIIKI.F.ADVHASLQWNFRPQQTEIYVVPG.TAL.FYRAKNP.DKP.IGISTYN.VPFEA
Retrocopy IENMVPVKDRIIKINFDADVHASLQWNFRPQQTEIYVVPGDTALGFYRAKNPADKPLIGISTYNVVPFEA

Parental  GQYFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAEDPRMIKVDLITLSYTFFEAKEGHKLPVPGYN
          GQYFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFA.DPRMI.VDLITLSYTFFEAKEGH.LPVPGYN
Retrocopy GQYFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAKDPRMINVDLITLSYTFFEAKEGHNLPVPGYN

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	0.07 RPM	19.05 RPM
SRP007412_cerebellum	0.11 RPM	10.36 RPM
SRP007412_heart	0.03 RPM	16.67 RPM
SRP007412_kidney	0.00 RPM	24.82 RPM
SRP007412_liver	0.00 RPM	9.79 RPM
SRP007412_testis	0.00 RPM	12.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2335 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2335 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3442
Pongo abelii	retro_pabe_2847

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335 ,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,