RetrogeneDB ID: retro_pabe_2847

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:29358355..29359216(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000008259
• Aliases: None
• Description: Cytochrome c oxidase assembly protein COX11, mitochondrial [Source:UniProtKB/TrEMBL;Acc:H2NTL1]

Sequence

>retro_pabe_2847
ATGGGAGGGCTCTGGCATCCGGGATGGAGGCGCGTCGCTTTCTGTGGCTGGCGCTGGATCCACCCTGGGTCTCTAGCCAG
GGCTGCAGAGAGGGTAGAGCCGTTTCTTAGGCCAGAGTGGAGTGGGACAGGAGGTGCCGAGAGACGACTGTGGTGGCTTG
GGACATGGAAGCGCTGCAGCCTTCGAGCCCGGCATCCAGTATTGCAGCCGCCGCGGCGGCCTGAGAACTCGAACCCTCTC
ACGCGCGCGCAGCAGGAGGAGCGGCGGAGGCGGAACAAGACGACCTTCACTTACGTGGCCGCTGTCGCCGTGGGCATGCT
GGGGGCGTCCTACGCTGCCGTACCCCTTTATCGGCTCTATTGCCAGACTACTGGACTTGGAGGATCAGCAGTTGCAGGTC
ATGCCTCAGACCAGATTGAAAACATGGTGCCTGTTAAGGATCGAATCATTAAAATTAACTTTGATGCAGATGTGCATGCA
AATCTCCAGTGGAACTTTAGACCTCAGCAAACAGAAATATATGTGGTGCCAGGAGACACAGCACTGGCGTTTTACAGAGC
TAAGAATCCTACTGACAAACCAATAATTGGAATTTCAACATACAATGTTGTTCTGTTTGAAGCTGGACAGTATTTCAATA
AAATACAGTGCCTCTGTTTTGAAGAACAAAGGCTTAATCCCTAAGAGGAAGTGGATATGCTAGTGTTTTTCTACATTGAT
CCTGAATTTGCTAAAGACTCAAGAATGATTAATATTGATCTTATCAGTCTTTCTTACACTTTTTTTGAAGCAAAGGAAGG
GCACAAGTTGCCAGTTCCAGGATATAATTGAAGTCAGCAACTAAGTCTTCCTTCAAAGTTG

Alignment

ORF - retro_pabe_2847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGLWRPGWRRVAFCGWRWIHPGSPTRAAERVEPFLRPECSGTGGAGRGLRWLGTWKRCSLGARHPALQP
          MGGLW.PGWRRVAFCGWRWIHPGS..RAAERVEPFLRPE.SGTGGA.R.L.WLGTWKRCSL.ARHP.LQP
Retrocopy MGGLWHPGWRRVAFCGWRWIHPGSLARAAERVEPFLRPEWSGTGGAERRLWWLGTWKRCSLRARHPVLQP

Parental  PRRHKNSNPFTRAQKEEWRRRNKTTLTYVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHASDKIE
          PRR..NSNP.TRAQ.EE.RRRNKTT.TYVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHASD.IE
Retrocopy PRRPENSNPLTRAQQEERRRRNKTTFTYVAAVAVGMLGASYAAVPLYRLYCQTTGLGGSAVAGHASDQIE

Parental  NMVPVKDRIIKISFNADVHASLQWNFRPQQTEIYVVPGETALAFYRAKNPTDKPVIGISTYNIVPFEAGQ
          NMVPVKDRIIKI.F.ADVHA.LQWNFRPQQTEIYVVPG.TALAFYRAKNPTDKP.IGISTYN.V.FEAGQ
Retrocopy NMVPVKDRIIKINFDADVHANLQWNFRPQQTEIYVVPGDTALAFYRAKNPTDKPIIGISTYNVVLFEAGQ

Parental  YFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAEDPRMIKVDLITLSYTFFEAKEGHKLPVPGYNSSQQ
          YFNKIQC.CFEEQRLNP.EEVDM.VFFYIDPEFA.D.RMI..DLI.LSYTFFEAKEGHKLPVPGYN.SQQ
Retrocopy YFNKIQCLCFEEQRLNP*EEVDMLVFFYIDPEFAKDSRMINIDLISLSYTFFEAKEGHKLPVPGYN*SQQ

Parental  LSLPSKL
          LSLPSKL
Retrocopy LSLPSKL

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	5.81 RPM
SRP007412_cerebellum	0.12 RPM	8.63 RPM
SRP007412_heart	0.03 RPM	6.05 RPM
SRP007412_kidney	0.03 RPM	20.12 RPM
SRP007412_liver	0.00 RPM	12.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2847 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2847 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2847 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3442
Pan troglodytes	retro_ptro_2335

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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,