RetrogeneDB ID: retro_cjac_4053

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:39483263..39483557(+)
• Located in intron of: ENSCJAG00000003800

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_4053
GCACTGTGGCAGAAGACCAGAAATTACTTCCTGAGCAAGGAGTTCCGGGAATACGTGACCAGCACTCACTTTTGGGGTCC
CGTGGCCAACTGGGGCCTGCCACTGGCTGCCTTTAAGGACATGAAGGAGTCGCCGGAGCTCATCAGTGGCCGCATGACTA
CTGCGCTCATCTTCTACTCGGCGATCTTCATACGCTTCGCCTACCGCGTACAGCCTCGAAACCTGCTGCTGATGGCGTGC
CACGGCACCAACGTGGTGGCTCAGAGTGTGCAGGCCAGTCGCTACCTACACTAC

Alignment

ORF - retro_cjac_4053 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 89.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALVRKAADYVRSKDFRDYLMRKHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFAYKV
          AL..K...Y..SK.FR.Y....HFWGPVANWGLP.AA..DMK.SPE.ISGRMT.AL..YS..F.RFAY.V
Retrocopy ALWQKTRNYFLSKEFREYVTSTHFWGPVANWGLPLAAFKDMKESPELISGRMTTALIFYSAIFIRFAYRV

Parental  QPRNWLLFACHATNEVAQLIQGGRLIKY
          QPRN.LL.ACH.TN.VAQ..Q..R...Y
Retrocopy QPRNLLLMACHGTNVVAQSVQASRYLHY

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	0.11 RPM	13.13 RPM
SRP051959_heart	0.16 RPM	28.98 RPM
SRP051959_kidney	0.07 RPM	37.36 RPM
SRP051959_liver	0.02 RPM	38.90 RPM
SRP051959_lung	0.20 RPM	7.61 RPM
SRP051959_lymph_node	0.07 RPM	7.42 RPM
SRP051959_skeletal_muscle	0.33 RPM	23.37 RPM
SRP051959_spleen	0.13 RPM	10.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4053 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4053 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4053 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_296

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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,