RetrogeneDB ID: retro_ptro_2358

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:71034249..71034711(+)
• Located in intron of: ENSPTRG00000018333

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSPTRG00000007889
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa (NDUFAB1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071820]

Sequence

>retro_ptro_2358
ATGGCAGCTTGTGTCTGCCACCTGCCCTTGGCCATCACACTGATGCGCCGGGTCCCATGCTGGCCACAGCCTGCTGCTCA
GCATCGCCTGTGCTCTGTGGGGACTCTGATGAGGCTGGGGCTTTGCAGCTGGCTCCACAGCGGGCTTTGGTGCTTGCGCA
TGTGCTGGGTAGAAGTTACACAGTCGTGCTGTCAGTATAGTGACTTGCCCCCTTTGACGTTAGAGGGAATCGAAGACTGT
CTTCTTTATATCTTGAAACCCTGTGACAGGATTGACCCAGAGAAGCTCTCAGTGAATTCTTACTTTATGAAAGACCTGTG
CTTGGACAGTTTGGACCAAGTAGAGAGTAAGCATGGTCATGGAAGATAAATTTGGGTTTGAAATTCCTGATACAGATGTG
GAAATTTAATATGTCCACAAGAAATTGTAGATTATATTGCAGATAAGAGAGATGTATATGAA

Alignment

ORF - retro_ptro_2358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.66 %
• Parental protein coverage: 96.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSAYVSRLPAAFAPLPRVR-MLAVAR-PLSTALCSAGTQTRLGTLQP--ALVLAQVPGR-VTQLCRQYSD
          ..A.V..LP.A.....RV..MLA.A....S..LC..........L.P..ALVLA.V.GR.VTQ.C.QYSD
Retrocopy MAACVCHLPLAITLMRRVP<MLATACCSASPVLCGDSDEAGALQLAPQRALVLAHVLGR>VTQSCCQYSD

Parental  MPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVE-IIMAMEDEFGFEIPDIDAE-KL
          .PPLTLEGI.D..LY.LK..D.IDPEKLSVNS.FMKDL.LDSLDQVE...M.MED.FGFEIPD.D.E..L
Retrocopy LPPLTLEGIEDCLLYILKPCDRIDPEKLSVNSYFMKDLCLDSLDQVE>VSMVMEDKFGFEIPDTDVE<NL

Parental  MCPQEIVDYIADKKDVYE
          .CPQEIVDYIADK.DVYE
Retrocopy ICPQEIVDYIADKRDVYE

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	0.04 RPM	44.36 RPM
SRP007412_cerebellum	0.04 RPM	18.39 RPM
SRP007412_heart	0.00 RPM	83.88 RPM
SRP007412_kidney	0.00 RPM	44.75 RPM
SRP007412_liver	0.03 RPM	23.31 RPM
SRP007412_testis	0.00 RPM	14.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2358 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2358 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3484
Gorilla gorilla	retro_ggor_2349
Pongo abelii	retro_pabe_2879

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens	ENSG00000004779	1 retrocopy	retro_hsap_3484,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus	ENSMICG00000007778	2 retrocopies	retro_mmur_1193, retro_mmur_120,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Pongo abelii	ENSPPYG00000007192	1 retrocopy	retro_pabe_2879,
Pan troglodytes	ENSPTRG00000007889	1 retrocopy	retro_ptro_2358 ,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Ictidomys tridecemlineatus	ENSSTOG00000024657	2 retrocopies	retro_itri_281, retro_itri_916,