RetrogeneDB ID: retro_ptro_606

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:48069930..48070215(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041813
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSPTRG00000021184
• Aliases: None
• Description: Sec61 beta subunit [Source:HGNC Symbol;Acc:16993]

Sequence

>retro_ptro_606
ATGCCTGGTCCGACCCCCAGTGGCACTAATGTGGGATCCTCAGGACACTCTCCCAGCAAAGCCGTGGCCGCCCGGGCGGC
AAGATCCACTGTCCGGCAGAGGAAAAATGCCAGCTGTGGGACAAGGAGCGCAGGCCGCACGACCTCGGCAGGCACATGGC
GGATGTGGCGATTCTACACAGAAGATTCACCTGGGCTCAAAGTTGGTCCTGTTCCAGTATTGGTTATGAGCCTTCTGTTC
ATCTCTTCTGTATTTATGTTGCACATTTGGGGCAAGTACACTCGT

Alignment

ORF - retro_ptro_606 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGP
          MPGPTPSGTNVGSSG.SPSKAVAARAA.STVRQRKNASCGTRSAGRTTSAGT..MWRFYTEDSPGLKVGP
Retrocopy MPGPTPSGTNVGSSGHSPSKAVAARAARSTVRQRKNASCGTRSAGRTTSAGTWRMWRFYTEDSPGLKVGP

Parental  VPVLVMSLLFIASVFMLHIWGKYTR
          VPVLVMSLLFI.SVFMLHIWGKYTR
Retrocopy VPVLVMSLLFISSVFMLHIWGKYTR

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	14.34 RPM
SRP007412_cerebellum	0.00 RPM	10.18 RPM
SRP007412_heart	0.00 RPM	6.06 RPM
SRP007412_kidney	0.00 RPM	37.34 RPM
SRP007412_liver	0.03 RPM	61.11 RPM
SRP007412_testis	0.00 RPM	10.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_606 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_606 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_871
Gorilla gorilla	retro_ggor_708
Pongo abelii	retro_pabe_680

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360, retro_btau_791,
Callithrix jacchus	ENSCJAG00000011279	1 retrocopy	retro_cjac_503,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777, retro_etel_1889, retro_etel_483, retro_etel_695,
Homo sapiens	ENSG00000106803	1 retrocopy	retro_hsap_871,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679,
Pan troglodytes	ENSPTRG00000021184	1 retrocopy	retro_ptro_606 ,
Rattus norvegicus	ENSRNOG00000006345	1 retrocopy	retro_rnor_1589,