RetrogeneDB ID: retro_cjac_254

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:122433504..122433813(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022496
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004008
• Aliases: None
• Description: None

Sequence

>retro_cjac_254
ATGGCAGGACAGGCGTTTAGAAAGTTTCTCCCACTCTTTGACCGAGTATTGGTTGAAAGGAGTGCTGCTGAAACTGTAAC
CAAAGGAGGCATTATGCTTCCAGAAAAATCTCAAGGAAAGGTATTGCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCTA
AAGGAAAGGGTGGAGAGATTCAACCAGTTAGCGTGAAGGTTGGAGATAAAGTTCTTCTCCCAGAATATGGAGGCACCAAA
GTAGTTCTAGATGACAAGGATTATTTCCTATTTAGAGATGGTGACATTCTTGGAAAGTATGTAGACTGA

Alignment

ORF - retro_cjac_254 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK
          MAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK
Retrocopy MAGQAFRKFLPLFDRVLVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDK

Parental  VLLPEYGGTKVVLDDKDYFLFRDGDILGKYVD
          VLLPEYGGTKVVLDDKDYFLFRDGDILGKYVD
Retrocopy VLLPEYGGTKVVLDDKDYFLFRDGDILGKYVD

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	12.76 RPM
SRP051959_heart	0.00 RPM	12.89 RPM
SRP051959_kidney	0.00 RPM	26.25 RPM
SRP051959_liver	0.00 RPM	40.57 RPM
SRP051959_lung	0.00 RPM	10.74 RPM
SRP051959_lymph_node	0.00 RPM	17.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.37 RPM
SRP051959_spleen	0.00 RPM	14.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_254 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007417	17 retrocopies	retro_chof_1048, retro_chof_1160, retro_chof_143, retro_chof_1476, retro_chof_1561, retro_chof_1755, retro_chof_1880, retro_chof_2052, retro_chof_2053, retro_chof_226, retro_chof_303, retro_chof_414, retro_chof_420, retro_chof_86, retro_chof_907, retro_chof_91, retro_chof_940,
Callithrix jacchus	ENSCJAG00000004008	1 retrocopy	retro_cjac_254 ,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Erinaceus europaeus	ENSEEUG00000005040	6 retrocopies	retro_eeur_132, retro_eeur_278, retro_eeur_474, retro_eeur_611, retro_eeur_657, retro_eeur_698,
Homo sapiens	ENSG00000115541	18 retrocopies	retro_hsap_1066, retro_hsap_1152, retro_hsap_1351, retro_hsap_1524, retro_hsap_1646, retro_hsap_1703, retro_hsap_2248, retro_hsap_2402, retro_hsap_2480, retro_hsap_2812, retro_hsap_2813, retro_hsap_3455, retro_hsap_3540, retro_hsap_366, retro_hsap_3664, retro_hsap_4194, retro_hsap_495, retro_hsap_963,
Gorilla gorilla	ENSGGOG00000027944	17 retrocopies	retro_ggor_1051, retro_ggor_117, retro_ggor_1243, retro_ggor_1545, retro_ggor_157, retro_ggor_1676, retro_ggor_1821, retro_ggor_1956, retro_ggor_1957, retro_ggor_1958, retro_ggor_2331, retro_ggor_2391, retro_ggor_2476, retro_ggor_2492, retro_ggor_775, retro_ggor_841, retro_ggor_897,
Mus musculus	ENSMUSG00000073676	11 retrocopies	retro_mmus_1005, retro_mmus_1719, retro_mmus_1750, retro_mmus_1934, retro_mmus_2483, retro_mmus_2485, retro_mmus_301, retro_mmus_3077, retro_mmus_386, retro_mmus_872, retro_mmus_877,
Procavia capensis	ENSPCAG00000009541	1 retrocopy	retro_pcap_330,
Sus scrofa	ENSSSCG00000016078	7 retrocopies	retro_sscr_103, retro_sscr_1059, retro_sscr_106, retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,