RetrogeneDB ID: retro_rnor_1940

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:167257603..167258029(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cmpk1
• Ensembl ID: ENSRNOG00000007775
• Aliases: Cmpk1, CK, Cmpk, RGD1310116
• Description: UMP-CMP kinase [Source:UniProtKB/Swiss-Prot;Acc:Q4KM73]

Sequence

>retro_rnor_1940
CTGCTCTAAGTCCTGGTCCTGATCTTCCCACTGCTGAATCCATGACTGTGGCTCTGCCCTCTCCACCTCATGAAGCAGCT
GGCCCCGTTTGTTTTGGGTGGGCCCGGTGTAGGCAAGGGGACCCAATGCATGTGCATTGCCGAGAAATATGGCTAAAAAC
ACCTTTCTATAGGATAGCTTCTTCCTGATGAAAGGAAGAATGCAGATTGACAGGATGGTGAACTTTTTATTGAAGAGCAC
ATTAAAGAAGGAAAGATTGTACCAGTTGAGATGACCATCGGCTTATTAAAGAGGAAAATGGACCCAACAATGGCTGCCAA
TGCTCAGAAGAATAAATTCTTGAGGGATGGATTTCCAAGAAATCCAGACGACCTTCAGGGTTGGAACAAGGCCATGGATG
GGAAAGCAGATGTATGTTTTGTTCTG

Alignment

ORF - retro_rnor_1940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.24 %
• Parental protein coverage: 62.11 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLHVLVPSFPPLTRGLRFFPLQLMKPLVVFVLGGPGAGKGTQCARIVEKYGYTHLSAGELLRDERKNPDS
          LL.VLV..FP.L...L...PL.LMK.L..FVLGGPG.GKGTQC..I.EKYG..HLS.G.LL.DERKN.D.
Retrocopy LL*VLVLIFPLLNP*LWLCPLHLMKQLAPFVLGGPGVGKGTQCMCIAEKYG*KHLSIG*LLPDERKNAD*

Parental  QYGEL-IEKYIKEGKIVPVEITISLLKREMDQTMAANAQKNKFLIDGFPRNQDNLQGWNKTMDGKADVSF
          Q.GEL.IE..IKEGKIVPVE.TI.LLKR.MD.TMAANAQKNKFL.DGFPRN.D.LQGWNK.MDGKADV.F
Retrocopy QDGELFIEEHIKEGKIVPVEMTIGLLKRKMDPTMAANAQKNKFLRDGFPRNPDDLQGWNKAMDGKADVCF

Parental  VL
          VL
Retrocopy VL

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
SRP017611_brain	0.00 RPM	48.60 RPM
SRP017611_kidney	0.00 RPM	128.33 RPM
SRP017611_liver	0.00 RPM	57.15 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1940 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1940 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004030	1 retrocopy	retro_cfam_1729,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Cavia porcellus	ENSCPOG00000014747	4 retrocopies	retro_cpor_1070, retro_cpor_1295, retro_cpor_417, retro_cpor_799,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Mustela putorius furo	ENSMPUG00000012394	1 retrocopy	retro_mputfur_1061,
Mus musculus	ENSMUSG00000028719	1 retrocopy	retro_mmus_2576,
Rattus norvegicus	ENSRNOG00000007775	1 retrocopy	retro_rnor_1940 ,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,