RetrogeneDB ID: retro_cjac_1739

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:21171524..21172110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020971
• Aliases: None
• Description: None

Sequence

>retro_cjac_1739
CAAGATACTGGTTTTGCTCAAGTACCACTTGCTGGAGCTGCCAGGGGTCCAGGGATTGGCAGGGCTGCTGGCAGAGGAAT
CCCATCTGGGGTTCCCATGCCCCAGGTTCCTGCAGGACTTGCTGGGCCAGTCCATGGGGTTGGTGGGCCATCTCAACAGG
TGATGACCCCGCAAGGAAGGGGCACTGTTGCAGCTGCTGCCACAGCCAGTATTGCTGGGGCCCTGACTCAGTGCCCACCT
GGCTGTGGGGTCCTCCCTCTGCATGGGCTGAGAAGCACCCACTCCAGGCATGATGGGCCCACCTCCTGGTATGAGGCCTC
CTATGGGTCCCCCAGTGGGGATCCCTCCTGGAAGACAGACTCCAATGGGCATGCCCACTCCAGGAATGCAGCCTCCTCCC
CCTGGGATGTGAGGCCTTCTTTGACCCTTGGCCACAGCATATGGAAGTAGCTCCGCAGAGGTGCAGGCTCGATTCCTCAG
GGCTACGTTACCACAGATCTGTTATGCTGCTGTTTGCGGTGTCTCACCAGGTTGTCTGGTTTCCCTTACAGGGCCCCCTC
CCCTGGGAATGCACCCACCAAGGCCC

Alignment

ORF - retro_cjac_1739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.56 %
• Parental protein coverage: 69.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAA
          .DTG.A.VPLAGAA.GPGIGRAAGRGIP.GVPMPQ.PAGLAGPV.GVGGPSQQVMTPQGRGTVAAAA...
Retrocopy QDTGFAQVPLAGAARGPGIGRAAGRGIPSGVPMPQVPAGLAGPVHGVGGPSQQVMTPQGRGTVAAAA---

Parental  TASIAGAPTQYPPGRG-GPPPP-MGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPP
          TASIAGA.TQ.PPG.G.GPP...MG..AP.PGMMGPPPGMRPPMGPP.GIPPGR.TPMGMP.PGM.PPPP
Retrocopy TASIAGALTQCPPGCG<GPPSA<MG*EAPTPGMMGPPPGMRPPMGPPVGIPPGRQTPMGMPTPGMQPPPP

Parental  -GCEAFFDPWPQSMEVAPQRCGLDSSGPRYHRPVCLLCCCSRSLTGLSGFLTGP-PPPGMRPPRP
          .GCEAFFDPWPQ.MEVAPQRC.LDSSG.RYHR.V.LL...S.........L.GP.PP.GM.PPRP
Retrocopy >GCEAFFDPWPQHMEVAPQRCRLDSSGLRYHRSVMLLFAVSHQVVWFP--LQGP<PPLGMHPPRP

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	18.19 RPM
SRP051959_heart	0.00 RPM	10.84 RPM
SRP051959_kidney	0.02 RPM	14.49 RPM
SRP051959_liver	0.02 RPM	14.49 RPM
SRP051959_lung	0.00 RPM	14.27 RPM
SRP051959_lymph_node	0.00 RPM	20.73 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.98 RPM
SRP051959_spleen	0.00 RPM	15.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1739 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1739 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739 ,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Mus musculus	ENSMUSG00000027404	3 retrocopies	retro_mmus_2938, retro_mmus_3450, retro_mmus_554,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Ochotona princeps	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Rattus norvegicus	ENSRNOG00000006961	2 retrocopies	retro_rnor_2825, retro_rnor_474,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,