RetrogeneDB ID: retro_cjac_378

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:35390776..35391220(-)
• Located in intron of: ENSCJAG00000015266

Retrocopy information

• Ensembl ID: ENSCJAG00000023088
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018851
• Aliases: None
• Description: None

Sequence

>retro_cjac_378
GCATCGTCGGTGCTGGCGCTGAGGATCTGGACAGCCATTACATCCTTGCTGAGCCCCCCTCCGGCTACAGCTCTTGCTGT
CAGATATGCTTCCAAGAAGACGGGTGGTAGCTCCAAAAACCTCAGTGGAAAGTCATCAGGCAGACGCCTAGGCATTAAGA
AAATGGAAGGACACCATGTTCATGCTGGGAACATCCTTGGAACACAGCTCCATTTCCACTGGCACCCAGGTGCCCATGTG
GGTTTTGGGAAGAATAAATGTCTGTATGCCCTGGAAGAGGGGATAGTCCACTACGCTAAGGATGTCTACGTGCCTCATCC
CAGAAACACGGAGGCTGTGGATCTCATCACCAGGCTGCCCAAGGGTGCTGTGCTCTACAAGACTTTTGTCGACGTGGTTC
CTACCAAGCCTGAGGGCACCTTCAAACTGGTAGCTATGCTTGAA

Alignment

ORF - retro_cjac_378 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASAAVALRIRTAVTSLLSPSPATALAVRYASKKTGGSSKNLGGKSSGRRLGIKKMEGHYVHAGNILGTQR
          AS...ALRI.TA.TSLLSP.PATALAVRYASKKTGGSSKNL.GKSSGRRLGIKKMEGH.VHAGNILGTQ.
Retrocopy ASSVLALRIWTAITSLLSPPPATALAVRYASKKTGGSSKNLSGKSSGRRLGIKKMEGHHVHAGNILGTQL

Parental  HFRWHPGAHVGLGKNKCLYALEEGIVHYTKDVYVPHPRNMEAVDLITRLPKGAVLYKTFVHVVPTKPEGT
          HF.WHPGAHVG.GKNKCLYALEEGIVHY.KDVYVPHPRN.EAVDLITRLPKGAVLYKTFV.VVPTKPEGT
Retrocopy HFHWHPGAHVGFGKNKCLYALEEGIVHYAKDVYVPHPRNTEAVDLITRLPKGAVLYKTFVDVVPTKPEGT

Parental  FKLVAML
          FKLVAML
Retrocopy FKLVAML

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	4.53 RPM
SRP051959_heart	0.00 RPM	4.67 RPM
SRP051959_kidney	0.00 RPM	5.32 RPM
SRP051959_liver	0.02 RPM	6.00 RPM
SRP051959_lung	0.02 RPM	3.14 RPM
SRP051959_lymph_node	0.09 RPM	3.47 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.79 RPM
SRP051959_spleen	0.02 RPM	3.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_378 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_378 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017031	1 retrocopy	retro_cfam_1454,
Choloepus hoffmanni	ENSCHOG00000005103	1 retrocopy	retro_chof_943,
Callithrix jacchus	ENSCJAG00000018851	2 retrocopies	retro_cjac_28, retro_cjac_378 ,
Dasypus novemcinctus	ENSDNOG00000023845	2 retrocopies	retro_dnov_1233, retro_dnov_1731,
Erinaceus europaeus	ENSEEUG00000010549	3 retrocopies	retro_eeur_126, retro_eeur_22, retro_eeur_9,
Echinops telfairi	ENSETEG00000014252	2 retrocopies	retro_etel_13, retro_etel_893,
Microcebus murinus	ENSMICG00000009698	1 retrocopy	retro_mmur_624,
Macaca mulatta	ENSMMUG00000017231	1 retrocopy	retro_mmul_64,
Mus musculus	ENSMUSG00000024414	2 retrocopies	retro_mmus_1696, retro_mmus_2918,
Oryctolagus cuniculus	ENSOCUG00000004601	2 retrocopies	retro_ocun_1026, retro_ocun_1936,
Otolemur garnettii	ENSOGAG00000005385	1 retrocopy	retro_ogar_53,