RetrogeneDB ID: retro_pabe_788

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:88228851..88229307(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB11
• Ensembl ID: ENSPPYG00000020284
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa [Source:HGNC Symbol;Acc:20372]

Sequence

>retro_pabe_788
ATGGCAGCTGGGCTGTTAAGTTTGAGCGCTCCCGGTCTTTTGGCGGCAGTGGCAACGCAAAGGCTCTTGGCCACCCATGT
CCGCTGGGAATCCAGCTTCTCCAGGACTGTGGTCGCCCTGTCTGCTGTGGTGGGAAAGGAGCCCCCGGAACTGACTGTAC
ATTGGCAGGAGGACCCAGATCCTGAGGACAAGAACTTCTATGAGAAGAACCCAGACTCCCATTGCTATGACAAGGACCCC
ATTTTGGACATCTGGAACATGTGAGTTGTCTTCTTCTTTGGCGTCTCCATTGTCCTGGTCCTTGGCAGCACCTTTGTGGC
CTATCTGCCTGATTACAGGATGCGAAAGTGGGCCCACTGCAGAGCTGAGATGCTTGTGAAATACCGAGAGGCCAAAGACC
TTCTCATCATGGAACCATGCTTCGACCCCAGCATGATCCAGCTGCCAGAGGATGAG

Alignment

ORF - retro_pabe_788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGLFGLSARRLLAAAATRGLPAARVRWESSFSRTVVAPSAVARKRLPEPTTQWQEDLDPEDENLYEKN
          MAAGL..LSA..LLAA.AT..L.A..VRWESSFSRTVVA.SAV..K..PE.T..WQED.DPED.N.YEKN
Retrocopy MAAGLLSLSAPGLLAAVATQRLLATHVRWESSFSRTVVALSAVVGKEPPELTVHWQEDPDPEDKNFYEKN

Parental  PDSHGYDKDPVLDVWNMRLVFFFGVSIILVLGSTFVAYLPDYRMKEWSRREAERLVKYREANGLPIMESN
          PDSH.YDKDP.LD.WNM..VFFFGVSI.LVLGSTFVAYLPDYRM..W....AE.LVKYREA..L.IME..
Retrocopy PDSHCYDKDPILDIWNM*VVFFFGVSIVLVLGSTFVAYLPDYRMRKWAHCRAEMLVKYREAKDLLIMEP-

Parental  CFDPSKIQLPEDE
          CFDPS.IQLPEDE
Retrocopy CFDPSMIQLPEDE

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	0.06 RPM	54.52 RPM
SRP007412_cerebellum	0.00 RPM	36.12 RPM
SRP007412_heart	0.00 RPM	40.88 RPM
SRP007412_kidney	0.00 RPM	54.89 RPM
SRP007412_liver	0.00 RPM	51.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_788 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_788 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_912
Pan troglodytes	retro_ptro_633
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,