RetrogeneDB ID:

retro_xtro_12

Retrocopy
location
Organism:Xenopus (Xenopus tropicalis)
Coordinates:GL173226.1:17573..19127(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSXETG00000014720
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:aldh2
Ensembl ID:ENSXETG00000020930
Aliases:None
Description:aldehyde dehydrogenase 2 family (mitochondrial) [Source:Jamboree;Acc:XB-GENE-490836]


Retrocopy-Parental alignment summary:






>retro_xtro_12
ATGCAACGCTCTTTTAGTCATCACTATATTGGCACCATATGGCAAATGGGTGCACGATTTTCCACAGCAATAATCCCTAA
GCCTTTATCAAATCCTGAAGTATTTTACACCAAGCTGTTTATAAACAACGAATGGCGTGATGCAGTAAGCGGAAGAAGAT
TTCCAACAGTGGATCCATGTACTGGAGAAGTGATTACACATGTAGCTGAGGCTGACAAGGCCGATATTGATGCTGCAGTT
AAAGCAGCAAGAGAAGCCTTTAAGCAGGGGTCTCCATGGCGAAGTATGGATGCATCACAGCGTGGGCAGTTGCTTCACCG
CCTTGCAGATCTTATTGAAAGAGATAAAATCTATCTAGCATCTTTGGAAACCATGGATAATGGCAAGCCGTTTGCTGACA
GTTTTGCAATAGATCTAAGTACAGTCGTTAAGGTGTATAGATATTATGCAGGCTTTGCAGACAAGGTCCATGGAAAAACT
ATACCCCTGGATGGTAACTACTTTTGCTATACAAGACATGAACCTGTTGGGGTCTGTGGCCAGATTATTCCATGGAATTT
CCCATTGGTAATGCAGGGGTGGAAGCTGGGCCCTGCACTTGCCACTGGAAATACAGTTGTAATGAAGGTTGCTGAGCAGA
CACCGCTCTCTGCATTGTACATTGCATCCTTGATAAAAGAAGCTGGATATCCTCCAGGCGTTGTGAATATATTAACAGGT
TTTGGGCCTACGGCTGGAGCAGCTTTAGCACAACATATGGATGTTGACAAAATAGCTTTCACTGGCTCTACTGAGGTTGG
CAGATTGATTCAGAAAGCAGCAGGTTCAACTAACCTGAAAAGAGTGACCCTTGAACTGGGTGGTAAAAGTCCATGCATTG
TCATGGCAGATGCAGACCTAGAGCAAGCTGTGGAACAGTGTCATGAGGCTTTGTTTTTTAACATGGGTCAGTGTTGCGCT
GCAGGTTCCAGAACATTTGTGGAGGAAAATGTCTACGATGAATTTCTTGAAAGAACCGTGGAGAAAGCAAAATTAAGAAA
AGTGGGCAACCCGTTTGACCTAGACACAAAGCATGGCCCTCAGATAAATAAGGAACAATTTGACAAGATCCTTGGCTATA
TTAAAAGCGGCAAAACAGAAGGTGCTAAACTTATGTGCGGTGGGGAGCGCTATGGAGATAAAGGCTTTTTCATCAAACCC
ACTGTCTTTGCCAATGTTCAGGACAATATGAAAATCGCAAGGGAAGAAATATTTGGCCCAGTGCAGCCAGTGTTTAAGTT
TAAATCAATAAAGGAAGTTATTGAAAGAGCCAATAACACAAGCTATGGGCTAGCAGCTGGCATATTTACAAGAGACTTAG
ATAAAGCAATGCTTCTTACACAGGCACTGCGAGCTGGGACAGTATGGGTTAATACTTACAACATTGTGACCTGTCAGACA
CCATTTGGAGGCTTTAAAGAATCTGGTAATGGACGAGAACTTGGTGAAGATGGGCTGAAAGCATACACAGAAGTGAAAAC
AGTCACAATGAAAATATCTCATAAGAAATCCTAA

ORF - retro_xtro_12 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.14 %
Parental protein coverage: 95.58 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRYSVAI-PTPNPKPDVHFNQLFINNEWHDAASKKTFPTINPSTGEVICHVAEGDKADVDKAVKAAREAFR
R.S.AI.P.P...P.V....LFINNEW.DA.S...FPT..P.TGEVI.HVAE.DKAD.D.AVKAAREAF.
RetrocopyRFSTAIIPKPLSNPEVFYTKLFINNEWRDAVSGRRFPTVDPCTGEVITHVAEADKADIDAAVKAAREAFK
ParentalLGSPWRRMDASQRGVLLNRLADLIERDRAILATLETLDNGKPYAISYAVDLDLVVKCLRYYAGWADKCHG
.GSPWR.MDASQRG.LL.RLADLIERD...LA.LET.DNGKP.A.S.A.DL..VVK..RYYAG.ADK.HG
RetrocopyQGSPWRSMDASQRGQLLHRLADLIERDKIYLASLETMDNGKPFADSFAIDLSTVVKVYRYYAGFADKVHG
ParentalKTIPIDGDYFTYTRHEPVGVCGQIIPWNFPLLMLAWKFGPALATGNVIVMKVAEQTPLTALHVASLVKEA
KTIP.DG.YF.YTRHEPVGVCGQIIPWNFPL.M..WK.GPALATGN..VMKVAEQTPL.AL..ASL.KEA
RetrocopyKTIPLDGNYFCYTRHEPVGVCGQIIPWNFPLVMQGWKLGPALATGNTVVMKVAEQTPLSALYIASLIKEA
ParentalGFPPGVVNIITGMGPTAGAAISSHMDVDKVAFTGSTEVGRLIQQAAGKSN-KKVTLELGGKSPNIIFSDA
G.PPGVVNI.TG.GPTAGAA...HMDVDK.AFTGSTEVGRLIQ.AAG..N.K.VTLELGGKSP.I...DA
RetrocopyGYPPGVVNILTGFGPTAGAALAQHMDVDKIAFTGSTEVGRLIQKAAGSTNLKRVTLELGGKSPCIVMADA
ParentalDLDWAVEQAHFALFFNQGQCCCAGSRTYVQEDIYNEFVERSIQRAKNRIVGNPFDFKTEQGPQVDEEQFN
DL..AVEQ.H.ALFFN.GQCC.AGSRT.V.E..Y.EF.ER....AK.R.VGNPFD..T..GPQ...EQF.
RetrocopyDLEQAVEQCHEALFFNMGQCCAAGSRTFVEENVYDEFLERTVEKAKLRKVGNPFDLDTKHGPQINKEQFD
ParentalKVLGYIKSGKKEGAKLLYGGNPAADRGYFIQPTVFGDVTDNMTIAREEIFGPVMQILKFKSIEEVIDRAN
K.LGYIKSGK.EGAKL..GG....D.G.FI.PTVF..V.DNM.IAREEIFGPV....KFKSI.EVI.RAN
RetrocopyKILGYIKSGKTEGAKLMCGGERYGDKGFFIKPTVFANVQDNMKIAREEIFGPVQPVFKFKSIKEVIERAN
ParentalNSMYGLAAAVFTKDIDKAHYVSQSVRAGTVWINCYDVFGAQAPFGGFKASGIGRELGEYGLEAYTEVKNV
N..YGLAA..FT.D.DKA....Q..RAGTVW.N.Y.....Q.PFGGFK.SG.GRELGE.GL.AYTEVK.V
RetrocopyNTSYGLAAGIFTRDLDKAMLLTQALRAGTVWVNTYNIVTCQTPFGGFKESGNGRELGEDGLKAYTEVKTV
ParentalTIKIPQKNS
T.KI..K.S
RetrocopyTMKISHKKS

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 6 .02 RPM 40 .92 RPM
SRP007412_heart 0 .19 RPM 157 .04 RPM
SRP007412_kidney 0 .19 RPM 157 .04 RPM
SRP007412_liver 0 .17 RPM 303 .31 RPM
SRP007412_skeletal_muscle 0 .00 RPM 177 .23 RPM

ChIP-Seq - click to see more details

Xenopus tropicalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xtro_12 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_12 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 22 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136641 retrocopy
retro_amel_51,
Bos taurus ENSBTAG000000087431 retrocopy
retro_btau_48,
Canis familiaris ENSCAFG000000086831 retrocopy
retro_cfam_1493,
Equus caballus ENSECAG000000176732 retrocopies
retro_ecab_1054, retro_ecab_1061,
Felis catus ENSFCAG000000220001 retrocopy
retro_fcat_1590,
Homo sapiens ENSG000001112751 retrocopy
retro_hsap_19,
Gorilla gorilla ENSGGOG000000071081 retrocopy
retro_ggor_33,
Latimeria chalumnae ENSLACG000000117981 retrocopy
retro_lcha_108,
Microcebus murinus ENSMICG000000034871 retrocopy
retro_mmur_19,
Myotis lucifugus ENSMLUG000000170841 retrocopy
retro_mluc_1918,
Macaca mulatta ENSMMUG000000083361 retrocopy
retro_mmul_247,
Mustela putorius furoENSMPUG000000022821 retrocopy
retro_mputfur_27,
Mus musculus ENSMUSG000000294551 retrocopy
retro_mmus_222,
Nomascus leucogenys ENSNLEG000000000161 retrocopy
retro_nleu_22,
Otolemur garnettii ENSOGAG000000330931 retrocopy
retro_ogar_203,
Pongo abelii ENSPPYG000000049661 retrocopy
retro_pabe_32,
Pteropus vampyrus ENSPVAG000000131891 retrocopy
retro_pvam_163,
Rattus norvegicus ENSRNOG000000013441 retrocopy
retro_rnor_307,
Sus scrofa ENSSSCG000000098891 retrocopy
retro_sscr_9,
Ictidomys tridecemlineatus ENSSTOG000000150091 retrocopy
retro_itri_33,
Xenopus tropicalis ENSXETG000000133041 retrocopy
retro_xtro_56,
Xenopus tropicalis ENSXETG00000020930 1 retrocopy
retro_xtro_12 ,


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