RetrogeneDB ID: retro_xtro_68

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL187071.1:2688..4077(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: atp5b
• Ensembl ID: ENSXETG00000024665
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide [Source:Jamboree;Acc:XB-GENE-943110]

Sequence

>retro_xtro_68
GGCAAGATTGTTCAATGTATCGGCGCCGTGGTGGACGTGGAGTTTCCGCGCGACCAGATGCCCAAGGTGTACGACGCGCT
CAAGCTCGACGGCTCGGCCCTGACGCTGGAAGTGCAACAGCAGCTCGGCGACGGCGTGGTGCGTACCATCGCCCTGGGGT
CGTCCGACGGCCTCAAGCGCGGCATCATGGTGACGAACACCGCCAACCCCATCACCGTGCCCGTAGGCAAGGCCACCCTG
GGCCGCATCATGGACGTGCTGGGCAACCCCATCGACGAGCGCGGCCCCGTGGACCAGACCCTGAGGGCCTCCATCCACCG
CAAGGCACCCGCCTATGACGAACTGAGCCCCTCGCAAGAACTGCTCGAAACCGGTATCAAGGTGATCGACCTGGTCTGCC
CGTTCGCCAAGGGCGGCAAAGTGGGCCTGTTCGGCGGCGCTGGCGTGGGCAAAACCGTCAACATGATGGAGCTCATCAAC
AACATCGCCAAGGCGCACTCGGGCCTGTCCGTGTTCGCTGGCGTGGGCGAGCGCACCCGTGAGGGCAACGACTTCTACCA
CGAGATGGCTGACTCCGGCGTCGTGAATCTGGAAAACCTGGGCGAATCCAAAGTATCCATGGTGTACGGCCAGATGAACG
AACCCCCGGGCAACCGTTTGCGCGTGGCGCTGACCGGTCTGACCATCGCCGAGTCGTTCCGCGACGAAGGCCGCGACGTG
CTGTTCTTCGTGGACAACATCTACCGCTACACGCTGGCCGGTACCGAAGTATCCGCCCTGTTGGGCCGCATGCCCTCCGC
CGTGGGCTACCAGCCGACGCTGGCCGAGGAAATGGGTCGCCTGCAAGAGCGGATTACCTCCACCAAGGTTGGCTCGATCA
CCTCCATCCAGGCCGTGTACGTGCCTGCCGATGACTTGACCGACCCGTCGCCCGCCACGACCTTCGCCCACCTGGACTCC
ACCGTGGTGTTGTCGCGTGACATCGCTGCCCTGGGCATCTACCCCGCCGTGGACCCGCTGGACTCCACCAGCCGCCAGCT
CGACCCGCAGGTGGTGGGCGAAGAGCACTACAGGGTGGCCCGCGACGTGCAGGGCACGCTGCAGCGCTACAAGGAACTGC
GCGACATCATCTCCATTCTGGGCATGGACGAACTGGCGCCCGAGGACAAACTCGTCGTGGCCCGTGCGCGCAAGATACAG
CGTTTTCTGTCGCAGCCGTTCCACGTGGCCGAAGTGTTCACGGGCTCGCCGGGCAAGTACGTGCCGCTGTCGGAAACCAT
CCGTGGCTTCAAGATGATCGTCAACGGCGAATGCGACCACCTGCCCGAACAGGCTTTCTACATGGTCGGCACCATCGACG
AAGCCTTCGAAAAGGCCAAGCAGCTGGCA

Alignment

ORF - retro_xtro_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.74 %
• Parental protein coverage: 86.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRIVAVIGAVVDVQFD-EGLPPILNALEVQGRDTRLVLEVAQHLGENTVRTIAMDGTEGLVRGQKVLDAG
          G.IV..IGAVVDV.F.....P....AL...G....L.LEV.Q.LG...VRTIA.....GL.RG..V....
Retrocopy GKIVQCIGAVVDVEFPRDQMPKVYDALKLDG--SALTLEVQQQLGDGVVRTIALGSSDGLKRGIMVTNTA

Parental  TPIRIPVGPETLGRIMNVIGEPIDERGPITTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKG
          .PI..PVG..TLGRIM.V.G.PIDERGP......A.IH..AP...E.S..QE.L.TGIKV.DL..P.AKG
Retrocopy NPITVPVGKATLGRIMDVLGNPIDERGPVDQTLRASIHRKAPAYDELSPSQELLETGIKVIDLVCPFAKG

Parental  GKIGSLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDT-TSKVAL
          GK.G.LFGGAGVGKTV..MELINN.AKAH.G.SVFAGVGERTREGND.YHEM..SGV.NL.....SKV..
Retrocopy GKVG-LFGGAGVGKTVNMMELINNIAKAHSGLSVFAGVGERTREGNDFYHEMADSGVVNLENLGESKVSM

Parental  VYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLAT
          VYGQMNEPPG.R.RVALTGLT.AE.FRD.EG.DVL.F.DNI.R.T.AG.EVSALLGR.PSAVGYQPTLA.
Retrocopy VYGQMNEPPGNRLRVALTGLTIAESFRD-EGRDVLFFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAE

Parental  DMGTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRI
          .MG..QERIT.TK.GSITS.QA.YVPADDLTDP.PATTFAHLD.T.VLSR.IA.LGIYPAVDPLDSTSR.
Retrocopy EMGRLQERITSTKVGSITSIQAVYVPADDLTDPSPATTFAHLDSTVVLSRDIAALGIYPAVDPLDSTSRQ

Parental  MDPNIVGLEHYEVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGH
          .DP..VG.EHY.VAR.VQ..LQ.YK.L.DII.ILGMDEL..EDKL.VARARKIQRFLSQPF.VAEVFTG.
Retrocopy LDPQVVGEEHYRVARDVQGTLQRYKELRDIISILGMDELAPEDKLVVARARKIQRFLSQPFHVAEVFTGS

Parental  LGKLVPLKDTIKGFKQILHGGYDNLPEQAFYMVGPIEEAVTKAEKLA
          .GK.VPL..TI.GFK.I..G..D.LPEQAFYMVG.I.EA..KA..LA
Retrocopy PGKYVPLSETIRGFKMIVNGECDHLPEQAFYMVGTIDEAFEKAKQLA

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	0.00 RPM	483.74 RPM
SRP007412_heart	0.00 RPM	2580.30 RPM
SRP007412_kidney	0.00 RPM	2580.30 RPM
SRP007412_liver	0.00 RPM	522.66 RPM
SRP007412_skeletal_muscle	0.00 RPM	2290.65 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_68 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_68 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Latimeria chalumnae	ENSLACG00000009340	1 retrocopy	retro_lcha_27,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Xenopus tropicalis	ENSXETG00000024665	1 retrocopy	retro_xtro_68 ,