RetrogeneDB ID: retro_cjac_810

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:98833481..98833874(-)
• Located in intron of: ENSCJAG00000009911

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C
• Ensembl ID: ENSCJAG00000014578
• Aliases: None
• Description: 5', 3'-nucleotidase, cytosolic [Source:HGNC Symbol;Acc:17144]

Sequence

>retro_cjac_810
GGCCTCCTGCGGGTCTTCAGATGCGGCTTCTCAGGGAGCTGCGTGTGACACTGCAGCAACACCGCAGCTTCCTGGCCTGG
GAGCAGTACCGTACCCTGCTGCCCGACCTGGCTGATAAAGTGGCCCATGGATGTGAAGCTCTAAGCTTTTCCCGAGGCTT
GGAGCCCAACCCGGGAGGGCCTTGTGTGAGATGAAGCACATGTAAAACACCGAGGTCTTCATACTGCACCAGCCCCTGTG
GAAGTATGACCACTGTGTGGGTGAGAAGCACCGCTGGCTAGAGCAGCACCTGGAGCCCTGGAGGATAACTGAATTATCCT
CACAATGGACAAGACTGTGATCTTTGGGGACCTGACCAATGATGACAAAGACACCATTAGAGGCCACAATCAA

Alignment

ORF - retro_cjac_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.85 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLLRGFRDRFPG-EPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGF-FLDLEPIPGALDAVREMN
          GLLR.FR..F.G.E..V.L.Q.R.FLA.EQYR.L.PDLADKVA...EA..F.F..L...PG...A..EM.
Retrocopy GLLRVFRCGFSG<ELRVTLQQHRSFLAWEQYRTLLPDLADKVAHGCEALSF<FPRLGAQPGR--ALCEMK

Parental  DLPDTEVFICTSPLLKYDHCVGEKYRWVEQHLGPQFLER-IILTRDKTVVLGDLLIDDKDTIRGHEE
          ....TEVFI...PL.KYDHCVGEK.RW.EQHL.P......IILT.DKTV..GDL..DDKDTIRGH..
Retrocopy HM*NTEVFILHQPLWKYDHCVGEKHRWLEQHLEPWRITE<IILTMDKTVIFGDLTNDDKDTIRGHNQ

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	5.59 RPM
SRP051959_heart	0.05 RPM	4.39 RPM
SRP051959_kidney	0.09 RPM	6.88 RPM
SRP051959_liver	0.02 RPM	9.05 RPM
SRP051959_lung	0.00 RPM	7.60 RPM
SRP051959_lymph_node	0.07 RPM	11.62 RPM
SRP051959_skeletal_muscle	0.02 RPM	8.47 RPM
SRP051959_spleen	0.02 RPM	7.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_810 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_810 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1109

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009175	1 retrocopy	retro_amel_1684,
Callithrix jacchus	ENSCJAG00000014578	1 retrocopy	retro_cjac_810 ,
Felis catus	ENSFCAG00000031408	2 retrocopies	retro_fcat_1016, retro_fcat_606,
Homo sapiens	ENSG00000125458	2 retrocopies	retro_hsap_1441, retro_hsap_1442,
Gorilla gorilla	ENSGGOG00000004740	2 retrocopies	retro_ggor_1061, retro_ggor_1109,
Microcebus murinus	ENSMICG00000017488	1 retrocopy	retro_mmur_1088,
Mustela putorius furo	ENSMPUG00000013985	1 retrocopy	retro_mputfur_1352,
Nomascus leucogenys	ENSNLEG00000000601	2 retrocopies	retro_nleu_1083, retro_nleu_1416,
Pongo abelii	ENSPPYG00000008619	1 retrocopy	retro_pabe_1195,