RetrogeneDB ID: retro_cjac_578

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:86210444..86210978(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019154
• Aliases: None
• Description: None

Sequence

>retro_cjac_578
AGGTATATTGAGATCTTCAGAAGTAGCAGGAGTGAAATCAAAGGATTTTATGATCCACCAAGAAGATTGCTGGGACAGTG
ACCGGGACCATATGATAGACCAACAGGAAGAAGAGGGGGTTATTATGGAGCTGGGCGTGGAAGTATGTATGACAGAATGC
GACGAGGAAGTGATGGATATGACGGTGGTTATGGAAGTTTTGATGACTATGGCGGCTATAATAATTATGGCTATGGGAAT
GATGGCTTTGATGACAGAATGAGAGATGGAAGAGGTATGGGAGGGCATGGCTATGGTGGAGCTGGTGATGCAAGTTCAGG
TTTTCATGGTGGTCATTTCGTACATATCAGAGGGTTGCCTTTTCGTGCAACTGAAAATGAAATTGCTAATTTCTTCTCAC
CATTAAATCCAATACGAGTTCATATTGATATTGGAGCTGATGGCAGAGCCACAGGAGAAGCAGATGTAGAGTTTGTGACA
CATGAAGATGCAGTAGCTGCCATGTCTAAAGATAAAAGTAACCATTTTAATAGA

Alignment

ORF - retro_cjac_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.82 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYIEIFRSSRSEIKGFYDPPRRLLGQRPGPYDRPIGGRGGYYGAGRGSMYDRMRRGGDGYDGGYGGFDDY
          RYIEIFRSSRSEIKGFYDPPRRLLGQ.PGPYDRP.G.RGGYYGAGRGSMYDRMRRG.DGYDGGYG.FDDY
Retrocopy RYIEIFRSSRSEIKGFYDPPRRLLGQ*PGPYDRPTGRRGGYYGAGRGSMYDRMRRGSDGYDGGYGSFDDY

Parental  GGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANFFSPLNPIRV
          GGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVH.RGLPFRATEN.IANFFSPLNPIRV
Retrocopy GGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHIRGLPFRATENEIANFFSPLNPIRV

Parental  HIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHR
          HIDIGADGRATGEADVEFVTHEDAVAAMSKDK.N...R
Retrocopy HIDIGADGRATGEADVEFVTHEDAVAAMSKDKSNHFNR

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	0.04 RPM	19.46 RPM
SRP051959_heart	0.02 RPM	28.63 RPM
SRP051959_kidney	0.00 RPM	24.69 RPM
SRP051959_liver	0.00 RPM	15.92 RPM
SRP051959_lung	0.00 RPM	34.32 RPM
SRP051959_lymph_node	0.00 RPM	38.93 RPM
SRP051959_skeletal_muscle	0.02 RPM	13.61 RPM
SRP051959_spleen	0.00 RPM	32.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_578 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_578 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000009931	1 retrocopy	retro_cjac_127,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578 ,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,