RetrogeneDB ID: retro_cjac_2652

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:107734741..107735328(-)
• Located in intron of: ENSCJAG00000007037

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSCJAG00000021250
• Aliases: None
• Description: cytidine monophosphate (UMP-CMP) kinase 1, cytosolic [Source:HGNC Symbol;Acc:18170]

Sequence

>retro_cjac_2652
ATGAAGCCGCTGGTCGTGTTTGTCCTCGGCGGCCCTGGTTCCGGCAAGGGGCCACAGTGTGCCCACATCGTTGAGAAATA
CGGCTATACACACCTTTCTGCAGGAGAGCTGCTTTGTGATGAAAGGAAGAACCCAGATTTACAGTATGGTGAACTTATTG
AAAAGTACATTAAAGAAGGAAAAATTGTACCAGTTGAGATAACCATCAGTTTATTAAAGAGGGAAATGGATCAAACAATG
GCTGCCAATGCTCAGAAGAATAAATTCTTGATTGATGGGTTTCCAAGAAATCAAGACAACCTTCAAGGTTGGAACAAGAC
CATAGATGGGAAGGCAGATGTATCTTTCGTTCTGTTTTTTGACTGTAATAATGAGATCTGTATTGAATGATGTCTGAGAG
GGGAAAGAGTAGTGGTGGGAGTGATGACAGCAGAGAGAGCTTGGAAAAGAGAATTCAGACCTACCTTCAGTCAACAAAGC
TGATTACTGACTTACATGAAGAAATGGGGAAAGTGAAGAAAATAGATGCTTCTAAATCTATTGATGAAGTTTTTGATGAA
GTTGTAAAGATTTTTGACAAGGAAGGC

Alignment

ORF - retro_cjac_2652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKPLVVFVLGGPGAGKGTQCARIVEKYGYTHLSAGELLRDERKNPDSQYGELIEKYIKEGKIVPVEITIS
          MKPLVVFVLGGPG.GKG.QCA.IVEKYGYTHLSAGELL.DERKNPD.QYGELIEKYIKEGKIVPVEITIS
Retrocopy MKPLVVFVLGGPGSGKGPQCAHIVEKYGYTHLSAGELLCDERKNPDLQYGELIEKYIKEGKIVPVEITIS

Parental  LLKREMDQTMAANAQKNKFLIDGFPRNQDNLQGWNRTMDGKADVSFVLFFDCNNEICIERCL-ERGKSSG
          LLKREMDQTMAANAQKNKFLIDGFPRNQDNLQGWN.T.DGKADVSFVLFFDCNNEICIE.CL.ERGKSSG
Retrocopy LLKREMDQTMAANAQKNKFLIDGFPRNQDNLQGWNKTIDGKADVSFVLFFDCNNEICIE*CL<ERGKSSG

Parental  RSDDNRESLEKSRIQTYLQSTKPIIDLYEEMGKVKKIDASKSVDEVFDEVVKIFDKEG
          .SDD.RESLEK.RIQTYLQSTK.I.DL.EEMGKVKKIDASKS.DEVFDEVVKIFDKEG
Retrocopy GSDDSRESLEK-RIQTYLQSTKLITDLHEEMGKVKKIDASKSIDEVFDEVVKIFDKEG

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	1.02 RPM	94.56 RPM
SRP051959_heart	1.14 RPM	23.63 RPM
SRP051959_kidney	0.93 RPM	41.71 RPM
SRP051959_liver	0.76 RPM	48.80 RPM
SRP051959_lung	1.12 RPM	30.36 RPM
SRP051959_lymph_node	1.62 RPM	23.99 RPM
SRP051959_skeletal_muscle	0.63 RPM	16.68 RPM
SRP051959_spleen	1.13 RPM	29.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2652 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2652 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000012	2 retrocopies	retro_amel_1074, retro_amel_1711,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Callithrix jacchus	ENSCJAG00000021250	2 retrocopies	retro_cjac_2652 , retro_cjac_2992,
Felis catus	ENSFCAG00000025426	1 retrocopy	retro_fcat_1259,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Otolemur garnettii	ENSOGAG00000026904	2 retrocopies	retro_ogar_1589, retro_ogar_3204,
Pongo abelii	ENSPPYG00000001380	1 retrocopy	retro_pabe_1369,
Sorex araneus	ENSSARG00000009745	2 retrocopies	retro_sara_199, retro_sara_294,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,
Tupaia belangeri	ENSTBEG00000017494	2 retrocopies	retro_tbel_3597, retro_tbel_691,
Tarsius syrichta	ENSTSYG00000007511	1 retrocopy	retro_tsyr_319,
Vicugna pacos	ENSVPAG00000004127	2 retrocopies	retro_vpac_345, retro_vpac_373,