RetrogeneDB ID: retro_cjac_166

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:79226661..79227627(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022861
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009494
• Aliases: None
• Description: None

Sequence

>retro_cjac_166
ATGTCTACTCGGGAGTCCTTTAACCCGGAAAGTTACGAATTGGACAAGAGCTTCCGGCTAACCAGATTCACTGAACTGAA
GGATACAGGCTGCAAAGTGCCCCAAGATGTCCTGCAGAAATTGCTGGAATCTTTACAGGAGAACCACTTCCAAGAAGATG
AACGGTTTCTGGGAAGCCTTCTGCCAAGGCTTGGCATTGGAATGGATACTTGTGTCATTCCTTTGAGGCATGCTGGGCTT
TCCTTGGTTCAAACCACAGATTACATTTACCCGATCGTAGACGACCCTTACATGATGGGCAGGATAGCATGTGCCAATGT
CCTCAGTGACCTTTACGCAATGGGGGTCACGGAATGTGACAATATGCTGATGCTCCTTGGAGTCAGTAATAAAATGACCG
ACAGGGAAAGGGATAAAGTGATGCCTCTGATTATCCAAGGTTTTAAAGATGCAGCTGAGGAAGCAGGAACATCTGTAACG
GGCGGCCAAACAGTACTAAACCCCTGGATTGTGCTGGGAGGAGTGGCTACCACTGTCTGCCAGCCCAATGAATTTATCAT
GCCAGACAATGCAGTGCCAGGGGACGTGCTGGTGTTGACGAAACCCCTGGGGACACAGGTGGCAGTGGCTGTGCACCAGT
GGCTGGATATTCCTGAGAAATGGAATAAGATTAAGCTAGTTGTCACCCAAGAAGATGTAGAGCTGGCCTACCAGGAGGCG
ATGATGAACATGGCGAGGCTCAACAGGACAGGCGGCCTCCTGATCTGTTTACCACGTGAGCAAGCAGCTCGGTTCTGTGC
AGAGATAAAGTCCCCCAAATATGGTGAAGGCCACCAAGCATGGATTATTGGGATTGTAGAGAAGGGCAACCGCACAGCCA
GAATCATGGGCAAACCCCGAATCATCGAGGTCGCACCGCAAGTGGCCACTCAAAATGTGAATCCCACACCGGGGGCCACC
TATTAA

Alignment

ORF - retro_cjac_166 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.08 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTRESFNPESYELDKSFRLTRFTELKGTGCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMDT
          MSTRESFNPESYELDKSFRLTRFTELK.TGCKVPQDVLQKLLESLQENHFQEDE.FLG...PRLGIGMDT
Retrocopy MSTRESFNPESYELDKSFRLTRFTELKDTGCKVPQDVLQKLLESLQENHFQEDERFLGSLLPRLGIGMDT

Parental  CVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKV
          CVIPLRH.GLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKV
Retrocopy CVIPLRHAGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDKV

Parental  MPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVA
          MPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVA
Retrocopy MPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVA

Parental  VHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLM
          VHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRT...L.
Retrocopy VHQWLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTGGLLI

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	0.00 RPM	7.65 RPM
SRP051959_heart	0.00 RPM	4.63 RPM
SRP051959_kidney	0.02 RPM	6.86 RPM
SRP051959_liver	0.04 RPM	9.10 RPM
SRP051959_lung	0.00 RPM	6.00 RPM
SRP051959_lymph_node	0.02 RPM	5.52 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.51 RPM
SRP051959_spleen	0.04 RPM	6.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_166 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_166 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013555	1 retrocopy	retro_amel_21,
Canis familiaris	ENSCAFG00000004743	2 retrocopies	retro_cfam_1787, retro_cfam_250,
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166 , retro_cjac_2219,
Dipodomys ordii	ENSDORG00000014119	1 retrocopy	retro_dord_792,
Equus caballus	ENSECAG00000014281	1 retrocopy	retro_ecab_77,
Felis catus	ENSFCAG00000003921	1 retrocopy	retro_fcat_96,
Homo sapiens	ENSG00000086475	3 retrocopies	retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Gorilla gorilla	ENSGGOG00000003806	2 retrocopies	retro_ggor_147, retro_ggor_2924,
Loxodonta africana	ENSLAFG00000004670	1 retrocopy	retro_lafr_125,
Macropus eugenii	ENSMEUG00000012188	1 retrocopy	retro_meug_245,
Myotis lucifugus	ENSMLUG00000001971	2 retrocopies	retro_mluc_2350, retro_mluc_728,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica	ENSMODG00000016864	1 retrocopy	retro_mdom_86,
Mustela putorius furo	ENSMPUG00000000948	1 retrocopy	retro_mputfur_20,
Mus musculus	ENSMUSG00000026662	1 retrocopy	retro_mmus_248,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii	ENSOGAG00000007807	1 retrocopy	retro_ogar_3026,
Ochotona princeps	ENSOPRG00000006587	3 retrocopies	retro_opri_271, retro_opri_655, retro_opri_670,
Procavia capensis	ENSPCAG00000015617	1 retrocopy	retro_pcap_341,
Pongo abelii	ENSPPYG00000002099	6 retrocopies	retro_pabe_1324, retro_pabe_1378, retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Pan troglodytes	ENSPTRG00000002303	3 retrocopies	retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Pteropus vampyrus	ENSPVAG00000002945	2 retrocopies	retro_pvam_115, retro_pvam_566,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,
Tursiops truncatus	ENSTTRG00000011114	1 retrocopy	retro_ttru_649,