RetrogeneDB ID: retro_cjac_2102

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:19702634..19702949(-)
• Located in intron of: ENSCJAG00000032315

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPC1
• Ensembl ID: ENSCJAG00000012552
• Aliases: BRP44L, MPC1
• Description: mitochondrial pyruvate carrier 1 [Source:HGNC Symbol;Acc:21606]

Sequence

>retro_cjac_2102
CTGGTTGTGCCAGTGGCCGACTATGTCCAAAGCAAGGATTTAAGGGACTACCTCATGAGTAGGCACTTCTGGGGCCCAGT
AGCCAACTGGGGTCTTCCCATTGCTGCCATCAATGACATGAAAAAGTCTCCAGAGATTATCAGTGGGTGGATGACATTTG
CCCTCTGTTGCTATTCTTTGACATTCCTGAGATTTGCCTACAAGGTCCAGCCTCGGAACTGGCTTCTGCTTGCATGCCAG
GAAACAAATGAAGTAGCCCAGCTCATCCAGGGAGGGCGGCTTATCAAACATGAGATGAGTAAAAAGGCATCTGCA

Alignment

ORF - retro_cjac_2102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 96.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVRKAADYVRSKDFRDYLMRKHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFAYKVQ
          LV...ADYV.SKD.RDYLM..HFWGPVANWGLPIAAINDMKKSPEIISG.MTFALCCYSLTF.RFAYKVQ
Retrocopy LVVPVADYVQSKDLRDYLMSRHFWGPVANWGLPIAAINDMKKSPEIISGWMTFALCCYSLTFLRFAYKVQ

Parental  PRNWLLFACHATNEVAQLIQGGRLIKYEMSKKASA
          PRNWLL.AC..TNEVAQLIQGGRLIK.EMSKKASA
Retrocopy PRNWLLLACQETNEVAQLIQGGRLIKHEMSKKASA

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	0.22 RPM	13.13 RPM
SRP051959_heart	0.18 RPM	28.98 RPM
SRP051959_kidney	0.35 RPM	37.36 RPM
SRP051959_liver	0.19 RPM	38.90 RPM
SRP051959_lung	0.36 RPM	7.61 RPM
SRP051959_lymph_node	0.78 RPM	7.42 RPM
SRP051959_skeletal_muscle	0.17 RPM	23.37 RPM
SRP051959_spleen	0.36 RPM	10.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2102 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027879	1 retrocopy	retro_btau_43,
Callithrix jacchus	ENSCJAG00000012552	2 retrocopies	retro_cjac_2102 , retro_cjac_4053,
Dasypus novemcinctus	ENSDNOG00000001205	1 retrocopy	retro_dnov_2139,
Homo sapiens	ENSG00000060762	1 retrocopy	retro_hsap_4675,
Myotis lucifugus	ENSMLUG00000000583	1 retrocopy	retro_mluc_28,
Mus musculus	ENSMUSG00000023861	3 retrocopies	retro_mmus_2037, retro_mmus_3420, retro_mmus_979,
Ornithorhynchus anatinus	ENSOANG00000004153	1 retrocopy	retro_oana_45,
Pongo abelii	ENSPPYG00000017166	1 retrocopy	retro_pabe_17,
Rattus norvegicus	ENSRNOG00000012415	3 retrocopies	retro_rnor_1111, retro_rnor_2632, retro_rnor_296,
Tursiops truncatus	ENSTTRG00000004456	1 retrocopy	retro_ttru_663,