RetrogeneDB ID: retro_ptro_633

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:90127487..90127946(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB11
• Ensembl ID: ENSPTRG00000021836
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa (NDUFB11), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071810]

Sequence

>retro_ptro_633
ATGGCAGTTGGGCTGTTAAGTTTGAGCGCTCCCGGTCTTTTGGCGGCAGTGGCGACGCAAAGGCTCTTGGCCACCCACGT
CTGCTGGGAATCCAGCTTCTCCAGGACTGTGGTCGCCCTGTCTGCTGTGGTGGGAAAACAGCCCCCGGAACTGACCGTAC
ATTGGCAGGAGGACCCAGATCCTGAGGACAAAAACTTCTATGAGAAGAACCCAGACTCCCATTGCTATGACAAGGACCCC
ATTTTGGACATCTGGAACATGTGAGTTGTCTTCTTCTTTGGCGTCTCCATTGTCCTGGTCCTTGGCAGCACCTTTGTGGC
CTATCTGCCTGATTACAGGATGCGAGAGTGGGCCCACTGCAGAGCTGAGATGCTTGTGAAATACCGAGAGGCCAAAGACC
TTCCCATCATGGAATCCAACTGCTTCGACCCCAGCACGATCCAGTTGCCAGAGGATGAG

Alignment

ORF - retro_ptro_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGLFGLSARLLLAAAATRGLPAARVRWESSFSRTVVAPSAVAGKRPPEPTTQWQEDPEPEDENLYEKN
          MA.GL..LSA..LLAA.AT..L.A..V.WESSFSRTVVA.SAV.GK.PPE.T..WQEDP.PED.N.YEKN
Retrocopy MAVGLLSLSAPGLLAAVATQRLLATHVCWESSFSRTVVALSAVVGKQPPELTVHWQEDPDPEDKNFYEKN

Parental  PDSHGYDKDPVLDVWNMRLVFFFGVSIILVLGSTFVAYLPDYRMKEWSRREAERLVKYREANGLPIMESN
          PDSH.YDKDP.LD.WNM..VFFFGVSI.LVLGSTFVAYLPDYRM.EW....AE.LVKYREA..LPIMESN
Retrocopy PDSHCYDKDPILDIWNM*VVFFFGVSIVLVLGSTFVAYLPDYRMREWAHCRAEMLVKYREAKDLPIMESN

Parental  CFDPSKIQLPEDE
          CFDPS.IQLPEDE
Retrocopy CFDPSTIQLPEDE

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	0.02 RPM	53.14 RPM
SRP007412_cerebellum	0.00 RPM	27.68 RPM
SRP007412_heart	0.00 RPM	54.39 RPM
SRP007412_kidney	0.00 RPM	58.84 RPM
SRP007412_liver	0.00 RPM	40.62 RPM
SRP007412_testis	0.21 RPM	4.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_633 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_633 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_633 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_912
Pongo abelii	retro_pabe_788
Macaca mulatta	retro_mmul_1116

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147123	1 retrocopy	retro_hsap_912,
Macaca mulatta	ENSMMUG00000017422	2 retrocopies	retro_mmul_1116, retro_mmul_830,
Monodelphis domestica	ENSMODG00000018491	1 retrocopy	retro_mdom_1063,
Mus musculus	ENSMUSG00000031059	2 retrocopies	retro_mmus_245, retro_mmus_2602,
Pongo abelii	ENSPPYG00000020284	1 retrocopy	retro_pabe_788,
Pan troglodytes	ENSPTRG00000021836	1 retrocopy	retro_ptro_633 ,
Rattus norvegicus	ENSRNOG00000008329	1 retrocopy	retro_rnor_151,
Ictidomys tridecemlineatus	ENSSTOG00000026821	1 retrocopy	retro_itri_1084,