RetrogeneDB ID: retro_cjac_3333

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:102260101..102260347(-)
• Located in intron of: ENSCJAG00000012100

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004610
• Aliases: None
• Description: None

Sequence

>retro_cjac_3333
ATGGCCTTTACTCTGTATTCACTGCTAGAGGCAGCCCTGCTCTTCGTCAGCGCTATTGCCATGCTGCACAAAGAGAGATT
CCTCAAGAACATTGGCTGGAGAACAGACCAGGGAATTGGTATATTTGGGGAGGAGCCAGGAATTAAATCTCGGCTAATGA
ACCGTATTTGATCTGTAACAACTGTGATGAGAATGCCATTAATAATGGTAAACTCAATTGTAGTTGTGTTACTTTTATTA
TTTGGA

Alignment

ORF - retro_cjac_3333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFTLYSLLQAALLCVNAIAVLHEERFLKNIGWGTDQGIGGFGEEPGIKSQLMNLIRSVRTVMRVPLIIV
          MAFTLYSLL.AALL.V.AIA.LH.ERFLKNIGW.TDQGIG.FGEEPGIKS.LMN.I.SV.TVMR.PLI.V
Retrocopy MAFTLYSLLEAALLFVSAIAMLHKERFLKNIGWRTDQGIGIFGEEPGIKSRLMNRI*SVTTVMRMPLIMV

Parental  NSIAIVLLLLFG
          NSI..VLLLLFG
Retrocopy NSIVVVLLLLFG

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	0.67 RPM
SRP051959_heart	0.02 RPM	0.70 RPM
SRP051959_kidney	0.09 RPM	1.69 RPM
SRP051959_liver	0.00 RPM	1.19 RPM
SRP051959_lung	0.23 RPM	0.70 RPM
SRP051959_lymph_node	0.00 RPM	0.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.16 RPM
SRP051959_spleen	0.00 RPM	0.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3333 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3333 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032961	1 retrocopy	retro_btau_13,
Callithrix jacchus	ENSCJAG00000004610	1 retrocopy	retro_cjac_3333 ,
Echinops telfairi	ENSETEG00000000303	1 retrocopy	retro_etel_1526,
Homo sapiens	ENSG00000134049	1 retrocopy	retro_hsap_1156,
Gorilla gorilla	ENSGGOG00000027939	1 retrocopy	retro_ggor_903,
Mus musculus	ENSMUSG00000090000	1 retrocopy	retro_mmus_150,
Nomascus leucogenys	ENSNLEG00000011450	1 retrocopy	retro_nleu_2504,
Otolemur garnettii	ENSOGAG00000016626	1 retrocopy	retro_ogar_2152,
Pongo abelii	ENSPPYG00000009141	3 retrocopies	retro_pabe_2850, retro_pabe_2851, retro_pabe_962,
Pan troglodytes	ENSPTRG00000010002	1 retrocopy	retro_ptro_791,
Tupaia belangeri	ENSTBEG00000001443	4 retrocopies	retro_tbel_1530, retro_tbel_2783, retro_tbel_3343, retro_tbel_3429,
Tursiops truncatus	ENSTTRG00000001019	1 retrocopy	retro_ttru_1930,