RetrogeneDB ID: retro_cjac_1374

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:4627692..4628042(-)
• Located in intron of: ENSCJAG00000005148

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf85
• Ensembl ID: ENSCJAG00000001441
• Aliases: None
• Description: chromosome 9 open reading frame 85 [Source:HGNC Symbol;Acc:28784]

Sequence

>retro_cjac_1374
ATTCATGATGGATTATGTCAGCACTCTAAAGAAGTTCTTGAGTGGCGTGTAAAATATAGCAAATACAAACCACTATCAAA
GCCTTAAAAATGTGTTAAATGTTTACAACAGACGTTGGAGGATTCATATCACATTACGTGCAGACCACGTGCCTATGAAC
TTGAAATTTGTGCAAAATGTGGAAAGAAGACATTGCTATTCTGTTCAGTGAAGAACCAGGCCAATCAGAAAATGCTGAGA
ATAATCTAAGTTCCAGCCATAGAAGAAGCTGCAGGAGAAAAGAAGAAAGTGATGATGATTTAGATTTTGATATTGATTTA
GAAGACATAGGAGGAGACTGTCAAATTAAT

Alignment

ORF - retro_cjac_1374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 75.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LHDGVCQHCKEVLEWRVKYSKYKPLSKPKKCVKCLQKTVKDSYHIICRPCAYELEVCAKCGKKEDIVIPF
          .HDG.CQH.KEVLEWRVKYSKYKPLSKP.KCVKCLQ.T..DSYHI.CRP.AYELE.CAKCGKK.......
Retrocopy IHDGLCQHSKEVLEWRVKYSKYKPLSKP*KCVKCLQQTLEDSYHITCRPRAYELEICAKCGKKTLLFCSV

Parental  NNKS-EKTEHIENNPSSNHRRSCRRNEESDDDLDFDIDLEDTEGNHQMN
          .N..........N..SS..R.SCRR.EESDDDLDFDIDLED..G..Q.N
Retrocopy KNQA<QSENAENNLSSSHRR-SCRRKEESDDDLDFDIDLEDIGGDCQIN

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	1.11 RPM	6.32 RPM
SRP051959_heart	0.49 RPM	5.91 RPM
SRP051959_kidney	0.95 RPM	6.37 RPM
SRP051959_liver	0.52 RPM	4.29 RPM
SRP051959_lung	0.68 RPM	5.53 RPM
SRP051959_lymph_node	0.78 RPM	7.67 RPM
SRP051959_skeletal_muscle	0.63 RPM	3.82 RPM
SRP051959_spleen	0.82 RPM	7.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1374 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1374 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2397

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007254	1 retrocopy	retro_amel_730,
Bos taurus	ENSBTAG00000006831	1 retrocopy	retro_btau_39,
Canis familiaris	ENSCAFG00000001820	1 retrocopy	retro_cfam_2126,
Callithrix jacchus	ENSCJAG00000001441	2 retrocopies	retro_cjac_1283, retro_cjac_1374 ,
Cavia porcellus	ENSCPOG00000025848	2 retrocopies	retro_cpor_1538, retro_cpor_316,
Felis catus	ENSFCAG00000031942	1 retrocopy	retro_fcat_1955,
Homo sapiens	ENSG00000155621	2 retrocopies	retro_hsap_2104, retro_hsap_2895,
Myotis lucifugus	ENSMLUG00000024309	2 retrocopies	retro_mluc_2449, retro_mluc_2526,
Macaca mulatta	ENSMMUG00000018881	2 retrocopies	retro_mmul_670, retro_mmul_988,
Mustela putorius furo	ENSMPUG00000008971	1 retrocopy	retro_mputfur_1413,
Mus musculus	ENSMUSG00000035171	6 retrocopies	retro_mmus_1049, retro_mmus_2254, retro_mmus_2286, retro_mmus_2781, retro_mmus_2941, retro_mmus_3698,
Nomascus leucogenys	ENSNLEG00000001023	1 retrocopy	retro_nleu_1272,
Oryctolagus cuniculus	ENSOCUG00000024578	2 retrocopies	retro_ocun_703, retro_ocun_766,
Otolemur garnettii	ENSOGAG00000011302	1 retrocopy	retro_ogar_979,
Pongo abelii	ENSPPYG00000029745	2 retrocopies	retro_pabe_1996, retro_pabe_2397,
Pan troglodytes	ENSPTRG00000021018	2 retrocopies	retro_ptro_1543, retro_ptro_1958,
Rattus norvegicus	ENSRNOG00000027161	5 retrocopies	retro_rnor_1898, retro_rnor_2010, retro_rnor_2242, retro_rnor_2859, retro_rnor_2960,
Sorex araneus	ENSSARG00000004523	1 retrocopy	retro_sara_260,
Tupaia belangeri	ENSTBEG00000015556	6 retrocopies	retro_tbel_1998, retro_tbel_200, retro_tbel_2406, retro_tbel_2410, retro_tbel_3539, retro_tbel_940,