RetrogeneDB ID: retro_cjac_503

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:14872856..14873144(-)
• Located in intron of: ENSCJAG00000020979

Retrocopy information

• Ensembl ID: ENSCJAG00000021748
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSCJAG00000011279
• Aliases: None
• Description: Sec61 beta subunit [Source:HGNC Symbol;Acc:16993]

Sequence

>retro_cjac_503
ATGCCTGGTCCGACCCCCAGTGGCACTAACGTGGGATCCTCAGGGAGCTCTCCCAGCAAAGCGGTGGCTGCCCGGGCGGC
AGGATCCACTGTTTGGCAGAGGAAAAATGCCAGCTGTGGAACAAGGAGCGCAGGCCGCACGACCTCGGTAGGCACTGGGG
GGATGTGGCGATTCTACACAGAAGATTCACCTGGGCTCAAAGTTGGCCCTGTTCCAGTATTGGTTATGAGTCTTCTGTTC
ATCGTTTCAGTATTTATGTTGCACATTTGGGGCAAGTACACTCGTTCG

Alignment

ORF - retro_cjac_503 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGP
          MPGPTPSGTNVGSSG.SPSKAVAARAAGSTV.QRKNASCGTRSAGRTTS.GTGGMWRFYTEDSPGLKVGP
Retrocopy MPGPTPSGTNVGSSGSSPSKAVAARAAGSTVWQRKNASCGTRSAGRTTSVGTGGMWRFYTEDSPGLKVGP

Parental  VPVLVMSLLFIASVFMLHIWGKYTRS
          VPVLVMSLLFI.SVFMLHIWGKYTRS
Retrocopy VPVLVMSLLFIVSVFMLHIWGKYTRS

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
SRP051959_colon	0.18 RPM	9.03 RPM
SRP051959_heart	0.12 RPM	2.96 RPM
SRP051959_kidney	0.24 RPM	7.81 RPM
SRP051959_liver	0.35 RPM	24.32 RPM
SRP051959_lung	0.15 RPM	5.11 RPM
SRP051959_lymph_node	0.18 RPM	6.46 RPM
SRP051959_skeletal_muscle	0.04 RPM	2.29 RPM
SRP051959_spleen	0.11 RPM	9.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_503 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_503 has 0 orthologous retrocopies within eutheria group .

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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,