RetrogeneDB ID: retro_cjac_2483

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:144531525..144532019(-)
• Located in intron of: ENSCJAG00000019308

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016176
• Aliases: None
• Description: None

Sequence

>retro_cjac_2483
GCGCCTAACACCTACTTAGCTTGGGAGGGAATCAGCTGACTCGGCCAGAGATGTCCAGCTTCCAGATCAGCCTCAACCCG
CTCGGCTTCATCAAGATCCTCAAGTGGACTGCTTCTATCTTTACCTTTGCCACTTGTGGGGGTTTTAAGGGCCAAATAGA
AACTTAAGTGAGTTGTCTACCACAGTTACTGAGAATAAAACAATTACAGCTACTTTTGGTTATCCATTCAGGTTGAATTA
GGTATCCCTTGAGCCACCTCCAGGTATAAACGTGTGATGTAAATTGGAAAAGTCACCTCCTCATAGGCGATTACTCATTT
CCTGCAGAGTTCTATGCTTCCTTTGGAGTCTTTGTGCTCCTGTACTGCAAAGCTGCCCTTCTGCTTTATGTTGGCTAGAC
AAACCTATAGCTGGGTAGCTATAAACTTCCTGTGATTGACTGTGTTGTTGCCATTATTTTGTGACTGGTAAGCACTTCAA
CCTGGGCTAAAGCT

Alignment

ORF - retro_cjac_2483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.71 %
• Parental protein coverage: 66.92 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APNVYLVRQRISRLGQR-MSGFQINLNPLKEPLGFIKVLEWLASIFAFATCG-GFKGQTEIQVSCPPPPV
          APN.YL....IS.LGQR.MS.FQI.LN....PLGFIK.L.W.ASIF.FATCG.GF.G......S.....V
Retrocopy APNTYLAWEGIS*LGQR<MSSFQISLN----PLGFIKILKWTASIFTFATCG<GF*GPNR-NLSELSTTV

Parental  TENKTVTAVFGYPFRLNEASFQPPPG-VNVCDVNWKSFVLIGDYSSSAQFYVTFAVFVFLYCIAALLLYV
          TENKT.TA.FGYPFRLN..S...PP..V..CDVNWKS..LIGDYS..A.FY..F.VFV.LYC.AALLLYV
Retrocopy TENKTITATFGYPFRLN*VSLE-PPP>V*TCDVNWKSHLLIGDYSFPAEFYASFGVFVLLYCKAALLLYV

Parental  GYTSLYLDSRKLPMIDFVVTLVATFLWLVSTSAWAKA
          G.T.L.L.S.KLP.ID.VV......L.LVSTS.WAKA
Retrocopy G*TNL*LGSYKLPVIDCVVAII---L*LVSTSTWAKA

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	0.27 RPM	39.43 RPM
SRP051959_heart	0.18 RPM	37.94 RPM
SRP051959_kidney	0.20 RPM	59.59 RPM
SRP051959_liver	0.32 RPM	20.51 RPM
SRP051959_lung	0.21 RPM	54.45 RPM
SRP051959_lymph_node	0.37 RPM	30.43 RPM
SRP051959_skeletal_muscle	0.09 RPM	95.17 RPM
SRP051959_spleen	0.44 RPM	38.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2483 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2483 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016176	2 retrocopies	retro_cjac_1588, retro_cjac_2483 ,
Cavia porcellus	ENSCPOG00000009221	1 retrocopy	retro_cpor_239,
Equus caballus	ENSECAG00000009695	1 retrocopy	retro_ecab_340,
Homo sapiens	ENSG00000008282	1 retrocopy	retro_hsap_1817,
Gorilla gorilla	ENSGGOG00000006497	1 retrocopy	retro_ggor_1984,
Myotis lucifugus	ENSMLUG00000014980	3 retrocopies	retro_mluc_1884, retro_mluc_2083, retro_mluc_449,
Macaca mulatta	ENSMMUG00000019593	2 retrocopies	retro_mmul_1251, retro_mmul_1464,
Mus musculus	ENSMUSG00000020570	1 retrocopy	retro_mmus_3470,
Nomascus leucogenys	ENSNLEG00000008861	1 retrocopy	retro_nleu_2720,
Oryctolagus cuniculus	ENSOCUG00000015127	3 retrocopies	retro_ocun_1000, retro_ocun_1569, retro_ocun_331,
Otolemur garnettii	ENSOGAG00000008079	2 retrocopies	retro_ogar_1970, retro_ogar_2520,
Ochotona princeps	ENSOPRG00000006755	2 retrocopies	retro_opri_210, retro_opri_448,
Pongo abelii	ENSPPYG00000018292	1 retrocopy	retro_pabe_2370,
Pan troglodytes	ENSPTRG00000019570	2 retrocopies	retro_ptro_1173, retro_ptro_1939,
Rattus norvegicus	ENSRNOG00000009856	2 retrocopies	retro_rnor_2273, retro_rnor_2992,
Sorex araneus	ENSSARG00000013935	1 retrocopy	retro_sara_450,
Ictidomys tridecemlineatus	ENSSTOG00000020871	1 retrocopy	retro_itri_1243,
Tupaia belangeri	ENSTBEG00000009095	2 retrocopies	retro_tbel_2025, retro_tbel_2566,
Tarsius syrichta	ENSTSYG00000013296	2 retrocopies	retro_tsyr_1768, retro_tsyr_775,
Tursiops truncatus	ENSTTRG00000002848	1 retrocopy	retro_ttru_661,