RetrogeneDB ID: retro_cjac_656

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:202785070..202785494(-)
• Located in intron of: ENSCJAG00000009771

Retrocopy information

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

Parental gene information

• Parental gene symbol: COA1
• Ensembl ID: ENSCJAG00000007826
• Aliases: None
• Description: cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21868]

Sequence

>retro_cjac_656
CAAAAGTATCCAGGAAGCAGGATGCCAGTGCCTCAAGGAAAATGGTCCTTTTCAGCAGTATATTTGGTACCTGGGGCTTG
GCCCTTGTGTATTACCTCACACAAAAGACTTTTCCAGGGCTTCGTTTTACTAGTTGGCATTGGAGCATGTGCGTAGCCAT
CCCAAGGCACGGGGAGCTCTGGGCCCTCCTTCAACATTTACATTCTCAAACTCAGTGACAAGCAAGACTTTGTGGACATT
GCTGATGCCAAGTTGAAGATTTCCTATCTCTGGATCCAAGTCAGAGGGCCATCTCCAGGTCAGCTCATCCAGAAGTGGCC
CCATTCAGAGGTGTTGCCTTGATGATATCTTCTTAGAGCTCAAGGATGGTCAACAGATTCCCATGTTCAAGCTCAGTGGG
GAGAATGGTGAAGAAGTGAGAAAG

Alignment

ORF - retro_cjac_656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.9 %
• Parental protein coverage: 97.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QTHPRSRMSM-SPAKMIIYGSVLCTGGFSLAYFIIQKTY-SRSLYYQLALEQLQIHPGAQEALGPP-VSV
          Q..P.SRM......KM....S...T.G..L.Y...QKT..SR...Y.LALE....HP.A..ALGPP....
Retrocopy QKYPGSRMPV<ASRKMVLFSSIFGTWGLALVYYLTQKTF<SRASFY*LALEHVRSHPKARGALGPP<FNI

Parental  HHLKLTGKDNFVDIADAKLKI-PVSGSKSEGHLHVHSTRSGPFQRWHLDEVFLELKDGQQIPVFNLSGEN
          ..LKL..K..FVDIADAKLKI.P.SGSKSEGHL.V.S.RSGP.QR..LD..FLELKDGQQIP.F.LSGEN
Retrocopy YILKLSDKQDFVDIADAKLKI>PISGSKSEGHLQVSSSRSGPIQRCCLDDIFLELKDGQQIPMFKLSGEN

Parental  GDEVKK
          G.EV.K
Retrocopy GEEVRK

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	0.42 RPM	2.46 RPM
SRP051959_heart	0.33 RPM	3.51 RPM
SRP051959_kidney	0.49 RPM	3.37 RPM
SRP051959_liver	0.39 RPM	2.62 RPM
SRP051959_lung	0.24 RPM	6.78 RPM
SRP051959_lymph_node	0.18 RPM	11.96 RPM
SRP051959_skeletal_muscle	0.24 RPM	2.66 RPM
SRP051959_spleen	0.38 RPM	7.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_656 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_656 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2595
Pan troglodytes	retro_ptro_1520
Gorilla gorilla	retro_ggor_1624
Pongo abelii	retro_pabe_1914

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009377	1 retrocopy	retro_amel_1871,
Canis familiaris	ENSCAFG00000031110	1 retrocopy	retro_cfam_2115,
Callithrix jacchus	ENSCJAG00000007826	1 retrocopy	retro_cjac_656 ,
Homo sapiens	ENSG00000106603	1 retrocopy	retro_hsap_2595,
Gorilla gorilla	ENSGGOG00000034928	1 retrocopy	retro_ggor_1624,
Macaca mulatta	ENSMMUG00000019023	1 retrocopy	retro_mmul_653,
Mustela putorius furo	ENSMPUG00000018149	1 retrocopy	retro_mputfur_1572,
Nomascus leucogenys	ENSNLEG00000003316	1 retrocopy	retro_nleu_1527,
Pongo abelii	ENSPPYG00000017606	1 retrocopy	retro_pabe_1914,
Pan troglodytes	ENSPTRG00000019125	1 retrocopy	retro_ptro_1520,