RetrogeneDB ID: retro_cjac_4063

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:51153698..51154248(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPV17L2
• Ensembl ID: ENSCJAG00000014104
• Aliases: None
• Description: MPV17 mitochondrial membrane protein-like 2 [Source:HGNC Symbol;Acc:28177]

Sequence

>retro_cjac_4063
CTGCATGGCCTGTGGACTATGGGGCAGTCCCTGTTCCAGGGTTGTGTGCTGCTGGTCATCAACACACTGGGCTGTGGTGT
GCTTATGGTGGCCCGGGATGGCGTGTGACAGTCCTGGGAGGTCTTACACCCAGCTGGACCAGATGTTCCACTGGTGGCAC
TCAGCGAGCACGTTTGCAGCGGGCAGCAGTGTGGATCCCTCCCTGCACTACTGGTACCTCTGGTTGGACTGCCTACTCCC
TGTGTCTGGCCTCTGAGGCCTCCCAAATGCTCTCAGGAAGATCTCTGTGGATCAGCTGGTAGCGTCTCCCATGCTGGGCA
TCTGGTACTTCTTGGGCCTTGGCTGCCTGGAAGGCCAGACGCTGGGAGAGAGCTGCCAGGAGCTGCAGGACAAGTTATGG
GAATTCTACAAGGCTGACTGGTGCATGTGGCCGGCGACATGCTGGTGAACTTTCTCTTTGTGTCCCTCCCTCCTTCCCCA
GTTCCGAGTCACCTACATCAATGGCCTGCCATTGGGCTGGGGCACATACCTGTCCTACCTGAAGTACCAG

Alignment

ORF - retro_cjac_4063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.39 %
• Parental protein coverage: 87.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LHRLLSAGQLLFQGRALLVTNTLGCGALMAAGDGVRQSWEIRSRPG-QVFDPRRSASMFAVGCSMGPFLH
          LH.L...GQ.LFQG..LLV.NTLGCG.LM.A.DGV.QSWE.....G.Q.F....SAS.FA.G.S..P.LH
Retrocopy LHGLWTMGQSLFQGCVLLVINTLGCGVLMVARDGV*QSWEVLHPAG>QMFHWWHSASTFAAGSSVDPSLH

Parental  YWYLSLDRLFPASGLRGFPNVLKKVLVDQLVASPVLGVWYFLGLGCLEGQTLAESFQELRDKFWEFYKAD
          YWYL.LD.L.P.SGL.G.PN.L.K..VDQLVASP.LG.WYFLGLGCLEGQTL.ES.QEL.DK.WEFYKAD
Retrocopy YWYLWLDCLLPVSGL*GLPNALRKISVDQLVASPMLGIWYFLGLGCLEGQTLGESCQELQDKLWEFYKAD

Parental  WCVWPAAQLVNFLFVP---PQFRVTYINGLTLGWDTYLSYLKYR
          WC.WPA.....F...P...PQFRVTYINGL.LGW.TYLSYLKY.
Retrocopy WCMWPATCW*TFSLCPSLLPQFRVTYINGLPLGWGTYLSYLKYQ

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	2.91 RPM
SRP051959_heart	0.00 RPM	3.00 RPM
SRP051959_kidney	0.00 RPM	4.93 RPM
SRP051959_liver	0.00 RPM	3.40 RPM
SRP051959_lung	0.00 RPM	2.13 RPM
SRP051959_lymph_node	0.00 RPM	1.67 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.32 RPM
SRP051959_spleen	0.00 RPM	2.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4063 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4063 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4063 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2493

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000027644	1 retrocopy	retro_acar_180,
Bos taurus	ENSBTAG00000025788	1 retrocopy	retro_btau_306,
Callithrix jacchus	ENSCJAG00000014104	1 retrocopy	retro_cjac_4063 ,
Echinops telfairi	ENSETEG00000013840	1 retrocopy	retro_etel_1446,
Macropus eugenii	ENSMEUG00000016379	2 retrocopies	retro_meug_223, retro_meug_943,
Macaca mulatta	ENSMMUG00000005025	1 retrocopy	retro_mmul_2493,
Nomascus leucogenys	ENSNLEG00000005944	1 retrocopy	retro_nleu_2666,
Pteropus vampyrus	ENSPVAG00000002028	1 retrocopy	retro_pvam_1254,