RetrogeneDB ID: retro_cjac_2660

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:122352585..122352909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3K
• Ensembl ID: ENSCJAG00000011568
• Aliases: None
• Description: DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL;Acc:B0VX71]

Sequence

>retro_cjac_2660
CTGCTGCTGTTCTACCCTGGCTGTGGGAATGGGCTGATCATAGAGGAGGGACAGCACTGCTGCCGCTTCGCCTGCGGCAC
ATGCCCCTGTGTGCACAACGTCACCCACAAGGTAACAAATCGGAAGTACTCAAAGCTGAAAGAGGGGGCTAATAGGCTTG
GGGGAGCAGCTGCCCGGGAGGATGCTGACTCTACCGCAGGGCCCTGTCCCAGAGGAGAACTTCTTCATGCTTACTGCATG
TAGCCTCAAACCCGCTCTGCAGACGAGCCAAAGACCACCTTCTACCAGCGCTGCAGGGCTCAGTGTGGGCACCACAGAAG
GGAG

Alignment

ORF - retro_cjac_2660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLFCPGCGNGLIVEEGQRCHRFACNTCPYVHNITRKVTNRKYPKLKEVDDVLGGAAAWENVDSTAEPCP
          .LLF.PGCGNGLI.EEGQ.C.RFAC.TCP.VHN.T.KVTNRKY.KLKE....LGGAAA.E..DSTA.PCP
Retrocopy LLLFYPGCGNGLIIEEGQHCCRFACGTCPCVHNVTHKVTNRKYSKLKEGANRLGGAAAREDADSTAGPCP

Parental  KCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD
          ..E...AY.M..QTRSADEP.TTFY..C.AQCGH..R.
Retrocopy RGELLHAYCM*PQTRSADEPKTTFYQRCRAQCGHHRRE

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	4.70 RPM
SRP051959_heart	0.00 RPM	2.65 RPM
SRP051959_kidney	0.00 RPM	2.88 RPM
SRP051959_liver	0.00 RPM	2.45 RPM
SRP051959_lung	0.00 RPM	3.71 RPM
SRP051959_lymph_node	0.02 RPM	3.95 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.73 RPM
SRP051959_spleen	0.00 RPM	3.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2660 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019715	1 retrocopy	retro_cfam_1881,
Callithrix jacchus	ENSCJAG00000011568	1 retrocopy	retro_cjac_2660 ,
Echinops telfairi	ENSETEG00000009989	2 retrocopies	retro_etel_1166, retro_etel_1543,
Felis catus	ENSFCAG00000009110	2 retrocopies	retro_fcat_1978, retro_fcat_409,
Homo sapiens	ENSG00000161980	1 retrocopy	retro_hsap_1861,
Myotis lucifugus	ENSMLUG00000015593	3 retrocopies	retro_mluc_1565, retro_mluc_1943, retro_mluc_341,
Oryctolagus cuniculus	ENSOCUG00000013608	1 retrocopy	retro_ocun_145,
Otolemur garnettii	ENSOGAG00000002526	2 retrocopies	retro_ogar_1101, retro_ogar_254,
Pan troglodytes	ENSPTRG00000007525	1 retrocopy	retro_ptro_1241,
Pteropus vampyrus	ENSPVAG00000000530	1 retrocopy	retro_pvam_928,
Sus scrofa	ENSSSCG00000007970	1 retrocopy	retro_sscr_1141,