RetrogeneDB ID: retro_cjac_1057

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:93933355..93933573(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC1
• Ensembl ID: ENSCJAG00000014756
• Aliases: None
• Description: trafficking protein particle complex 1 [Source:HGNC Symbol;Acc:19894]

Sequence

>retro_cjac_1057
ACTGTCCACACCTCTACCTGTTTGACCAGAATGAAGTGTGTCTACACCAGAGCAAATGGCACCACAAGAAGCAAGCAGAG
ATCCCCAAGGAGGAGGATTATAAGCTGATGTACAGTATGCTCTTCTCTATCCGCTTATTTGTCAGCAAGATATCTCAGCT
AGACATGAAGAACAGCTTCCTGGCTTTCCATATTAGCCATGAAAAACTTCATTACTGG

Alignment

ORF - retro_cjac_1057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 50.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVH-NLYLFDRNGVCLHYSEWHRKKQAGIPKEEEYKLMYGMLFSIRSFVSKMSPLDMKDGFLAFQTSRYK
          TVH..LYLFD.N.VCLH.S.WH.KKQA.IPKEE.YKLMY.MLFSIR.FVSK.S.LDMK..FLAF..S..K
Retrocopy TVH<HLYLFDQNEVCLHQSKWHHKKQAEIPKEEDYKLMYSMLFSIRLFVSKISQLDMKNSFLAFHISHEK

Parental  LHYY
          LHY.
Retrocopy LHYW

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	1.46 RPM
SRP051959_heart	0.00 RPM	1.30 RPM
SRP051959_kidney	0.00 RPM	1.86 RPM
SRP051959_liver	0.00 RPM	1.34 RPM
SRP051959_lung	0.00 RPM	2.18 RPM
SRP051959_lymph_node	0.00 RPM	3.40 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.66 RPM
SRP051959_spleen	0.00 RPM	2.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1057 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1057 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047214	1 retrocopy	retro_btau_280,
Callithrix jacchus	ENSCJAG00000014756	1 retrocopy	retro_cjac_1057 ,
Erinaceus europaeus	ENSEEUG00000004320	1 retrocopy	retro_eeur_665,
Sorex araneus	ENSSARG00000010582	1 retrocopy	retro_sara_590,
Tursiops truncatus	ENSTTRG00000010306	1 retrocopy	retro_ttru_403,