RetrogeneDB ID: retro_cjac_146

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:92045515..92045869(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022996
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014253
• Aliases: None
• Description: None

Sequence

>retro_cjac_146
ATGAAGTGGATGTTCAAGGAGGACCACTCTTTGGAACACAGATGCGTGGAGTCCGCGAAGATCCGAGCGAAATATCCTGA
CCGGGTTCCGGTGATTGTGGAAAAGGTCTCAGGCTCTCAGATTGTTGACATTGACAAACGGAAGTACTTGGTTCCATCTG
ATATCACTGTGGCTCAGTTCATGTGGATCATCAGGAAAAGGATCCAGCTTCCTTCTGAAAAGGCGATCTTCCTGTTTGTG
GATAAGACAGTCCCACAGTCCAGCCTAACTATGGGACAGCTTTACCAGAAGGAAAAAGATGAAGATGGATTCTTGTATGT
GGCCTACAGCGGAGAGAACACTTTTGGCTTCTGA

Alignment

ORF - retro_cjac_146 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQL
          MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQL
Retrocopy MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQL

Parental  PSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFGF
          PSEKAIFLFVDKTVPQSSLTMGQLY.KEKDEDGFLYVAYSGENTFGF
Retrocopy PSEKAIFLFVDKTVPQSSLTMGQLYQKEKDEDGFLYVAYSGENTFGF

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	0.02 RPM	8.10 RPM
SRP051959_heart	0.02 RPM	13.12 RPM
SRP051959_kidney	0.02 RPM	13.49 RPM
SRP051959_liver	0.00 RPM	9.47 RPM
SRP051959_lung	0.00 RPM	13.36 RPM
SRP051959_lymph_node	0.02 RPM	12.74 RPM
SRP051959_skeletal_muscle	0.09 RPM	21.16 RPM
SRP051959_spleen	0.00 RPM	11.89 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_146 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_146 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Canis familiaris	ENSCAFG00000031455	1 retrocopy	retro_cfam_639,
Callithrix jacchus	ENSCJAG00000004473	3 retrocopies	retro_cjac_1114, retro_cjac_1519, retro_cjac_779,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146 ,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Erinaceus europaeus	ENSEEUG00000011134	1 retrocopy	retro_eeur_337,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Gorilla gorilla	ENSGGOG00000012299	2 retrocopies	retro_ggor_2761, retro_ggor_342,
Loxodonta africana	ENSLAFG00000017065	2 retrocopies	retro_lafr_234, retro_lafr_543,
Microcebus murinus	ENSMICG00000011981	1 retrocopy	retro_mmur_1473,
Myotis lucifugus	ENSMLUG00000015112	1 retrocopy	retro_mluc_1207,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540,
Mustela putorius furo	ENSMPUG00000009894	1 retrocopy	retro_mputfur_993,
Mus musculus	ENSMUSG00000031950	5 retrocopies	retro_mmus_2637, retro_mmus_2655, retro_mmus_3240, retro_mmus_456, retro_mmus_506,
Nomascus leucogenys	ENSNLEG00000013048	2 retrocopies	retro_nleu_1560, retro_nleu_580,
Pongo abelii	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,