RetrogeneDB ID: retro_cjac_3233

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:82650005..82650403(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D3
• Ensembl ID: ENSCJAG00000017340
• Aliases: None
• Description: TM2 domain containing 3 [Source:HGNC Symbol;Acc:24128]

Sequence

>retro_cjac_3233
GAGTTAAAATCCCAAAGTAACTTTATAATCAACACGACTTGTAGATTTTGCTGGAAGCTTCCAAAACCAGAATATGAATG
TTCAATTCTACCAGCAGCATGAGGTCCTGTCCTCAATGGCATTACACCGCCAACTGCACGATAAACACATTCATGACTTG
GGTAACTACTTTTTACAAAACGCTGTACTAAAATTGGGCTGCAGGCTATAAGTGGTCTATTGCTCTGGCTCTAAGCATCA
CCCTTGGTGGCTTTGGAGCAGACCATTTCTACCAGGACCAGTGGCAAGAAGGCCTTGGCAAGCTCTTCAGCTTCAGTTGC
CTGGGAATATGGACACTAATAGACATCTTGCTAATTGGAGTTGGTTACATTGGACCAGCAGATGGCTCTTGATACATT

Alignment

ORF - retro_cjac_3233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.34 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFKSQKNFIINMTCRFCWQLPETDYECS-NSTSCMTVACPRQRYTANCTVRDHVHCLGNRTFPKMLYCNW
          ..KSQ.NFIIN.TCRFCW.LP...YECS.NSTS.M...CP...YTANCT...........TF.K.LY.NW
Retrocopy ELKSQSNFIINTTCRFCWKLPKPEYECS<NSTSSMR-SCPQWHYTANCTINTFMTWV--TTFYKTLY*NW

Parental  TGGYKWSTALALSITLGGFGADRFYLGQWREGLGKLFSFGGLGIWTLIDVLLIGVGYVGPADGSLYI
          ..GYKWS.ALALSITLGGFGAD.FY..QW.EGLGKLFSF..LGIWTLID.LLIGVGY.GPADGS.YI
Retrocopy AAGYKWSIALALSITLGGFGADHFYQDQWQEGLGKLFSFSCLGIWTLIDILLIGVGYIGPADGS*YI

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	6.81 RPM
SRP051959_heart	0.00 RPM	10.47 RPM
SRP051959_kidney	0.00 RPM	11.69 RPM
SRP051959_liver	0.00 RPM	8.69 RPM
SRP051959_lung	0.00 RPM	8.91 RPM
SRP051959_lymph_node	0.00 RPM	10.41 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.04 RPM
SRP051959_spleen	0.00 RPM	10.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3233 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3233 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017340	1 retrocopy	retro_cjac_3233 ,
Homo sapiens	ENSG00000184277	1 retrocopy	retro_hsap_1138,
Gorilla gorilla	ENSGGOG00000011598	1 retrocopy	retro_ggor_887,
Macaca mulatta	ENSMMUG00000000277	1 retrocopy	retro_mmul_884,
Mustela putorius furo	ENSMPUG00000010985	1 retrocopy	retro_mputfur_313,
Nomascus leucogenys	ENSNLEG00000000529	1 retrocopy	retro_nleu_937,
Pan troglodytes	ENSPTRG00000007515	1 retrocopy	retro_ptro_775,
Tarsius syrichta	ENSTSYG00000004536	1 retrocopy	retro_tsyr_1116,