RetrogeneDB ID: retro_cjac_2992

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:77815149..77815737(-)
• Located in intron of: None

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_2992
ATGAAGCCACTGGTCGTGTTCATCCTCAGCGGCCCCAGCGCCGTCAAGGGGACACAGTGCACCCACATCGTCGAGAAATA
TGGCCACACACACCTTTCTGCATGAGAGCTGCTTCATGATGAAAGGAAGAACCCAGATTCACAGTATGGAGTACTTATTG
AAAAGTACATTAAAGAAGGAAAGATTGTACCAGTTGAGATAACCATCAGTTTATTAAAGAGGGAAATGGATCAGACAATG
GCTGCCAATGCTCAGAAGAATAAATTATTGATTGATGGGTTTCCAAGAAATCAAGACAACCTTCAAGGTTGGAACAAGAC
CATGGATGGGAAGGCAGATGTATCTTTCGTTCTGTTTTTTGACTGTAATAATGAGATCTGTATTGAACAATGTCTTGAGA
GGGGAAAGAGTAGTGGTGGGAGTGATGACAACAGAGAGAGCTTGTAAAAGAGAATTCAGACCTACCTTCACTCAACAAAA
CTGATTACTGACTTATATGAAGAAATGGGGAAAGTGAAGAAAATAGATGCTTCTAAATATGTTGATGAAGTTTTTGATGA
AGTTGTGAAGACTTTTGACAAGGAAGGC

Alignment

ORF - retro_cjac_2992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKPLVVFVLGGPGAGKGTQCARIVEKYGYTHLSAGELLRDERKNPDSQYGELIEKYIKEGKIVPVEITIS
          MKPLVVF.L.GP.A.KGTQC..IVEKYG.THLSA.ELL.DERKNPDSQYG.LIEKYIKEGKIVPVEITIS
Retrocopy MKPLVVFILSGPSAVKGTQCTHIVEKYGHTHLSA*ELLHDERKNPDSQYGVLIEKYIKEGKIVPVEITIS

Parental  LLKREMDQTMAANAQKNKFLIDGFPRNQDNLQGWNRTMDGKADVSFVLFFDCNNEICIERCLERGKSSGR
          LLKREMDQTMAANAQKNK.LIDGFPRNQDNLQGWN.TMDGKADVSFVLFFDCNNEICIE.CLERGKSSG.
Retrocopy LLKREMDQTMAANAQKNKLLIDGFPRNQDNLQGWNKTMDGKADVSFVLFFDCNNEICIEQCLERGKSSGG

Parental  SDDNRESLEKSRIQTYLQSTKPIIDLYEEMGKVKKIDASKSVDEVFDEVVKIFDKEG
          SDDNRESL.K.RIQTYL.STK.I.DLYEEMGKVKKIDASK.VDEVFDEVVK.FDKEG
Retrocopy SDDNRESL*K-RIQTYLHSTKLITDLYEEMGKVKKIDASKYVDEVFDEVVKTFDKEG

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	0.02 RPM	94.56 RPM
SRP051959_heart	0.00 RPM	23.63 RPM
SRP051959_kidney	0.00 RPM	41.71 RPM
SRP051959_liver	0.04 RPM	48.80 RPM
SRP051959_lung	0.02 RPM	30.36 RPM
SRP051959_lymph_node	0.00 RPM	23.99 RPM
SRP051959_skeletal_muscle	0.02 RPM	16.68 RPM
SRP051959_spleen	0.00 RPM	29.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2992 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2992 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2992 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,