RetrogeneDB ID: retro_cjac_814

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:106797108..106797417(-)
• Located in intron of: ENSCJAG00000017200

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSCJAG00000032182
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 variant 2 [Source:HGNC Symbol;Acc:12495]

Sequence

>retro_cjac_814
CTTACAAGGTAGACAGGCATGATTATTGGGCCACCAAGGACAAATTATGAAAACAGAATATATAGCCTGAAAGTAGAATG
TGGACCTTTATACCCCAAAGCTCCTCCGTCAGTTAGATTTGTAACAAAAATTAATATGAATGGAGTAAATAATTCCAGTG
GGATGGTGGATGCCCAGAGCATACCAGTGTTAGCAAAATGGCAACATTCATATAGCATTAAAGTTGTACTTCAAGAGCTA
AGACGTCTAATAATGTCCAAAGAAAATATGAAGCTTCCACAGCCACCAGAAGGACAAACATACAACAAT

Alignment

ORF - retro_cjac_814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.17 %
• Parental protein coverage: 71.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGVNNSSGMVDARSIPVLAKWQNS
          LTR.TGMIIGPPRTNYENRIYSLKVECGP.YP.APPSVRFVTKINMNGVNNSSGMVDA.SIPVLAKWQ.S
Retrocopy LTR*TGMIIGPPRTNYENRIYSLKVECGPLYPKAPPSVRFVTKINMNGVNNSSGMVDAQSIPVLAKWQHS

Parental  YSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN
          YSIKVVLQELRRL.MSKENMKLPQPPEGQTYNN
Retrocopy YSIKVVLQELRRLIMSKENMKLPQPPEGQTYNN

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	0.38 RPM	8.12 RPM
SRP051959_heart	0.44 RPM	9.89 RPM
SRP051959_kidney	0.47 RPM	9.01 RPM
SRP051959_liver	0.37 RPM	8.27 RPM
SRP051959_lung	0.23 RPM	8.90 RPM
SRP051959_lymph_node	0.05 RPM	6.39 RPM
SRP051959_skeletal_muscle	0.44 RPM	10.31 RPM
SRP051959_spleen	0.74 RPM	7.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_814 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_814 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032182	1 retrocopy	retro_cjac_814 ,
Callithrix jacchus	ENSCJAG00000036984	10 retrocopies	retro_cjac_1076, retro_cjac_1952, retro_cjac_2810, retro_cjac_2865, retro_cjac_3081, retro_cjac_3140, retro_cjac_3258, retro_cjac_4089, retro_cjac_462, retro_cjac_974,
Loxodonta africana	ENSLAFG00000017749	1 retrocopy	retro_lafr_1168,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mus musculus	ENSMUSG00000022674	4 retrocopies	retro_mmus_1385, retro_mmus_189, retro_mmus_2048, retro_mmus_2770,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Procavia capensis	ENSPCAG00000000293	1 retrocopy	retro_pcap_138,
Sus scrofa	ENSSSCG00000022190	1 retrocopy	retro_sscr_524,
Tursiops truncatus	ENSTTRG00000008325	1 retrocopy	retro_ttru_1623,