RetrogeneDB ID: retro_tbel_3597

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_145828:225169..225620(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSTBEG00000017494
• Aliases: None
• Description: cytidine monophosphate (UMP-CMP) kinase 1, cytosolic [Source:HGNC Symbol;Acc:18170]

Sequence

>retro_tbel_3597
AAATCCGGCTACACATAGCTCTCTGCAGGAGAACTTTGTGATGAAAGAAAGAACTCAAATTCACAGTATGGTGAACTCAT
TAAAAAGTACATTAAAGAAGCAAAGATTGTGCCAGTTGAGATAACCATCAGTTTATTGAAGAGGGAAATGGATCACTCAG
TGGTTGCCAGTGCTTAGAAGAATAAATTCTTGATCAATGGGTTTCCAAGAAAGCAGGACAGCCTTCAAGGTTGGAACAAG
ACCATGCATGGGAAAGTAGATGCATCTTCATTCTGTTTTTTGACTGCAATAGCGAGATCTGTATTGATGCCTTGAGAGAG
GAGAGAGTAGTGGTACGAGTGATGACAACAGAGAGAGCTCGGAAAAGAGAATTGAGACCTATCCTCAGTCATCCGAGCCA
GTTACTGACTTAGATGAAGAAGTGGGGAAAGTCAAGAAAATAGATGCTTCT

Alignment

ORF - retro_tbel_3597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.03 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KYGYTHLSAGELLRDERKNPDSQYGELIEKYIKEGKIVPVEITISLLKREMDQTMAANAQKNKFLIDGFP
          K.GYT.LSAGEL..DERKN..SQYGELI.KYIKE.KIVPVEITISLLKREMD....A.A.KNKFLI.GFP
Retrocopy KSGYT*LSAGELC-DERKNSNSQYGELIKKYIKEAKIVPVEITISLLKREMDHSVVASA*KNKFLINGFP

Parental  RNQDNLQGWNKTMDGKADVS-FVLFFDCNNEICIERCLER-GKSSGRSDDNRESLEKRIQTYLQSTKPII
          R.QD.LQGWNKTM.GK.D.S.F.LFFDCN.EICI....E....S....D....S.EKRI.TY.QS..P..
Retrocopy RKQDSLQGWNKTMHGKVDAS<FILFFDCNSEICIDALREE<ESSGTSDDNRESS-EKRIETYPQSSEPVT

Parental  DLYEEMGKVKKIDAS
          DL.EE.GKVKKIDAS
Retrocopy DLDEEVGKVKKIDAS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3597 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3597 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,