RetrogeneDB ID: retro_xtro_9

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172975.1:741990..742776(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000019642
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: dck.2
• Ensembl ID: ENSXETG00000018331
• Aliases: None
• Description: deoxycytidine kinase, gene 2 [Source:Jamboree;Acc:XB-GENE-5727742]

Sequence

>retro_xtro_9
ATCTCCAAGCCACTTCAACAGTCCATTTCTCCAGACCCTAATTCCAGGAAAGAAATGCAAGTGAAAAAATTATCCGTGGA
AGGAAATATAGCGGTAGGAAAATCCACCTTTCTCAAATTGCTATCCAATACATTTCAAGAATGGAGTTTTGCTACAGAGC
CTCTGAAGAAATGGCAGAATGTTCAATCTACTTCATTCCAAACAATGACTTCCTCAAAGCCGCCTATGGACAACCTGCTA
CAACTGATGTATGATGATCCTACACGATGGTCTTACACGTTCCAGACATTTTCTTGTATGAGTCGATTTAAAATACAAAT
TCAGCCACTTTCAGAGCAAGTATTACATCAGCAGGAGCCTGTTCAGATATTTGAGAGATCTGTTTATAGTGACAGATATA
TATTTGCTAAAACTCTTTATGAACTCCAACACTTAAATGAAATTGAGTGGACTTTGTATCAGGAATGGCACACTTTTCTT
ATTGAAGAATTTTCCAGAAGAGTTGCATTGGATGGAATTATTTACCTACGGGCATCTCCAGAAAAATGTTTTCAGAGACT
ACAAAAAAGAGCTAGAAAGGAGGAAAAGACTCTGCAATGTGAATACCTTGAGAAGTTGCATGATCAGCATGAAAGTTGGC
TGACAAAGAAGACAACTGAGGTCCATTTTGAAAACATGAAAAATATTCCAGTTTTGCTGTTAGATGTTGAAGAAGACTTT
GAAAACAATTCTGCAGCAGGTGATGATCTCAACAGCAGAGTTAAAGCCTTTGTTGCTGGACTGTGA

Alignment

ORF - retro_xtro_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.77 %
• Parental protein coverage: 98.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKRMCHSPVFNNSFEKRFKKLSVEGNIAAGKSTFVRILEKANDEWEVVPEPIAKWCNVQTTGNEDEELST
          P.....SP..N...E...KKLSVEGNIA.GKSTF...L.....EW....EP..KW.NVQ.T.........
Retrocopy PLQQSISPDPNSRKEMQVKKLSVEGNIAVGKSTFLKLLSNTFQEWSFATEPLKKWQNVQSTSFQT--MTS

Parental  SQKSGGNLLQMLYDKPTRWAYTFQTYACLSRVRAQLNPPSHKLREAEHPVQFFERSVYSDRYVFASSLFE
          S.....NLLQ..YD.PTRW.YTFQT..C.SR...Q..P.S........PVQ.FERSVYSDRY.FA..L.E
Retrocopy SKPPMDNLLQLMYDDPTRWSYTFQTFSCMSRFKIQIQPLSEQVLHQQEPVQIFERSVYSDRYIFAKTLYE

Parental  SQNINETEWAIYQDWHTWLLNQFESDIDLDGIIYLRATPEKCMDRIHTRGRDEEQGIELEYLESLHYKHE
          .Q..NE.EW..YQ.WHT.L...F.....LDGIIYLRA.PEKC..R...R.R.EE.....EYLE.LH..HE
Retrocopy LQHLNEIEWTLYQEWHTFLIEEFSRRVALDGIIYLRASPEKCFQRLQKRARKEEKTLQCEYLEKLHDQHE

Parental  SWLYDRTIQVDFENLQHMPVLVLDVNEDFKNDKIKQEALLDKVKEFLASL
          SWL...T..V.FEN....PVL.LDV.EDF.N.......L...VK.F.A.L
Retrocopy SWLTKKTTEVHFENMKNIPVLLLDVEEDFENNSAAGDDLNSRVKAFVAGL

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
SRP007412_brain	4.43 RPM	0.00 RPM
SRP007412_heart	4.11 RPM	0.06 RPM
SRP007412_kidney	4.11 RPM	0.06 RPM
SRP007412_liver	2.26 RPM	0.63 RPM
SRP007412_skeletal_muscle	1.42 RPM	0.00 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_9 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_9 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022606	1 retrocopy	retro_fcat_1830,
Myotis lucifugus	ENSMLUG00000005844	1 retrocopy	retro_mluc_2007,
Mus musculus	ENSMUSG00000029366	1 retrocopy	retro_mmus_2735,
Oryctolagus cuniculus	ENSOCUG00000001265	1 retrocopy	retro_ocun_1247,
Pan troglodytes	ENSPTRG00000016139	1 retrocopy	retro_ptro_427,
Pteropus vampyrus	ENSPVAG00000004341	1 retrocopy	retro_pvam_32,
Rattus norvegicus	ENSRNOG00000003296	1 retrocopy	retro_rnor_1026,
Xenopus tropicalis	ENSXETG00000018331	1 retrocopy	retro_xtro_9 ,