RetrogeneDB ID: retro_pabe_680

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:20717927..20718212(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSPPYG00000019441
• Aliases: None
• Description: Protein transport protein Sec61 subunit beta [Source:UniProtKB/Swiss-Prot;Acc:Q5RB31]

Sequence

>retro_pabe_680
ATGCCTGGTCCGACCCCCAGTGTCACTAATGTGGGATCCTCAGGGCACTCTCCTAGCAAAGCCGTGGCCGCCTGGGCGGC
GAGATCCACTGTCCGGCAGAGGAAAAATGCCAGCTGTGGGACAAGGAGCGCAGGCCGCACGACCTCGGCAGGCACCGGGG
GGATGTGGTGATTCTATACAGAAGATTCACCTGGGCTCAAAGTTGGCCCTGTCCCAGTATTGGTTATGAGTCTTCTGTTC
ATCGCTTCTGTATTTATGTTGCACATTTGGGGCAAGTACACTCGT

Alignment

ORF - retro_pabe_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGP
          MPGPTPS.TNVGSSG.SPSKAVAA.AA.STVRQRKNASCGTRSAGRTTSAGTGGMW.FYTEDSPGLKVGP
Retrocopy MPGPTPSVTNVGSSGHSPSKAVAAWAARSTVRQRKNASCGTRSAGRTTSAGTGGMW*FYTEDSPGLKVGP

Parental  VPVLVMSLLFIASVFMLHIWGKYTR
          VPVLVMSLLFIASVFMLHIWGKYTR
Retrocopy VPVLVMSLLFIASVFMLHIWGKYTR

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	11.33 RPM
SRP007412_cerebellum	0.00 RPM	11.55 RPM
SRP007412_heart	0.00 RPM	5.90 RPM
SRP007412_kidney	0.03 RPM	26.22 RPM
SRP007412_liver	0.06 RPM	42.63 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_680 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_680 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_871
Pan troglodytes	retro_ptro_606
Gorilla gorilla	retro_ggor_708

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360, retro_btau_791,
Equus caballus	ENSECAG00000026930	1 retrocopy	retro_ecab_711,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777, retro_etel_1889, retro_etel_483, retro_etel_695,
Gorilla gorilla	ENSGGOG00000004205	1 retrocopy	retro_ggor_708,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Microcebus murinus	ENSMICG00000011121	4 retrocopies	retro_mmur_1037, retro_mmur_1631, retro_mmur_435, retro_mmur_543,
Myotis lucifugus	ENSMLUG00000001097	1 retrocopy	retro_mluc_2170,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679,
Nomascus leucogenys	ENSNLEG00000017055	1 retrocopy	retro_nleu_2844,
Otolemur garnettii	ENSOGAG00000004168	3 retrocopies	retro_ogar_1132, retro_ogar_2671, retro_ogar_823,
Pongo abelii	ENSPPYG00000019441	1 retrocopy	retro_pabe_680 ,