RetrogeneDB ID: retro_cjac_2364

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:106422077..106422455(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC6A
• Ensembl ID: ENSCJAG00000012869
• Aliases: None
• Description: trafficking protein particle complex 6A [Source:HGNC Symbol;Acc:23069]

Sequence

>retro_cjac_2364
GGACAGAAGATGAGCCTGTTGATCCTGGAGAGCATGGATTTCTGCGTGAGCCAGGTTCTAGGCGAGAGACTGCCCCAGGA
GATGCTCATCTCAGGGAGGAGCTATGTGGCCTCAAATTCCTATGCAAAACCCTGTGGGTGGCTGTGTTCCAACAGCTGAA
CGGCCTGTGCACCAATTACATACTTTTTGCAGGACAACAGCTTCCCCTCCTCATCCCGATGGCCTTGGGCCTGCAGAATC
TGGAGTAAGCACCCAAGTTCCTGGCTTCACTTGTGGCCTGTGCGTGGCACCCTCAGTACCCTGGGCATAGAGAGTTTGGT
CACTGCCCCTGTGGCAACCCTGACTGCTTGTAAGCTCCCAGTGATAATCTGGAAATCT

Alignment

ORF - retro_cjac_2364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.7 %
• Parental protein coverage: 75.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GQNMNLSVLESVGFRVGQALGERLPREMLA-FREELDVLKFLCKDLWLAIFQKQMDSLRTNHQGTYVLQD
          GQ.M.L..LES..F.V.Q.LGERLP.EML...REEL..LKFLCK.LW.A.FQ.Q...L.TN.........
Retrocopy GQKMSLLILESMDFCVSQVLGERLPQEMLI<LREELCGLKFLCKTLWVAVFQ-QLNGLCTNY---ILFAG

Parental  NSFPLLLPMAAGLQYLEEAPKFLA-FTCGL-LRGALCTLGIESVVTASVAALPGCKFQVVIQNS
          ...PLL.PMA.GLQ.LE.APKFLA.FTCGL..RG.L.TLGIES.VTA.VA.L..CK..V.I..S
Retrocopy QQLPLLIPMALGLQNLE*APKFLA<FTCGL<VRGTLSTLGIESLVTAPVATLTACKLPVIIWKS

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	0.04 RPM	1.84 RPM
SRP051959_heart	0.00 RPM	0.77 RPM
SRP051959_kidney	0.09 RPM	10.87 RPM
SRP051959_liver	0.00 RPM	1.91 RPM
SRP051959_lung	0.05 RPM	1.25 RPM
SRP051959_lymph_node	0.00 RPM	2.65 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.22 RPM
SRP051959_spleen	0.00 RPM	1.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2364 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2364 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012869	1 retrocopy	retro_cjac_2364 ,
	ENSG00000007255	0 retrocopies
Macaca mulatta	ENSMMUG00000022932	1 retrocopy	retro_mmul_686,
Pongo abelii	ENSPPYG00000010109	1 retrocopy	retro_pabe_2899,