RetrogeneDB ID:

retro_pabe_32

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:23179159..23180713(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000019051
Aliases:ALDH1B1, ALDHX
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ALDH2
Ensembl ID:ENSPPYG00000004966
Aliases:None
Description:aldehyde dehydrogenase, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001124747]


Retrocopy-Parental alignment summary:






>retro_pabe_32
ATGCTGCGCTTCCTGGCACCCCGGCTGCTTAGCCTCCAGGGCAGGACCGCCCGCTACTCCTCGGCAGCAGCGCTCCCAAG
CCCCATTCTGAACCCAGACATCCCCTACAACCAGCTGTTCATCAACAACGAATGGCAAGATGCAGTCAGCAAGAAGACCT
TCCCGACGGTCAACCCTACCACCGGGGAGGTCATCGGGCACGTGGCTGAAGGTGACCGGGCTGATGTGGATCGGGCTGTG
AAAGCAGCCCGGGAAGCCTTCCGCCTGGGGTCCCCATGGCGCCGGATGGATGCCTCTGAGCGGGGCCGGCTGCTGAACTG
CCTGGCAGACCTAGTGGAGCGGGATCGAGTCTACTTGGCCTCACTGGAGACCTTGGACAATGGGAAGCCTTTCCAAGAGT
CTTACGCCTTGGACTTGGATGAGGTCATCAAGGTGTATCGGTACTTTGCTGGCTGGGCTGACAAGTGGCATGGCAAGACC
ATCCCCATGGATGGCCAGCATTTCTGCTTCACCCGGCATGAGCCCATTGGTGTCTGTGGCCAGATCATCCCATGGAACTT
CCCCTTGGTCATGCAGGGTTGGAAACTTGCCCCGGCACTCGCCACAGGCAACACTGTGGTTATGAAGGTGGCAGAGCAGA
CCCCCCTCTCTGCCCTGTATTTGGCCTCCCTCATCAAGGAGGCGGGCTTTCCCCCTGGGGTGGTGAACATCATTACGGGC
TATGGCCCAACAGCAGGTGCGGCCATTGCACAGCACATGGATGTTGACAAAGTTGCCTTCACCGGTTCCACCGAGGTGGG
CCATCTGATCCAGAAAGCAGCTGGTGATTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGTAAGAGCCCCAGCATCG
TGCTGGCCGATGCTGACATGGAGCATGCCGTGGAGCAGTGCCACGAAGCCCTGTTCTTCAACATGGGCCAGTGCTGCTGT
GCTGGCTCCCGGACCTTCGTGGAAGAATCCATCTACAATGAGTTTCTCGAGAGAACCGTGGAGAAAGCAAAGCAGAGGAA
AGTGGGGAACCCCTTTGAGCTGGACACCCAGCAGGGGCCTCAGGTGGACAAGGAGCAGTTTGAACGAGTCCTAGGCTACA
TCCAGCTTGGCCAGAAGGAGGGCGCAAAACTCCTCTGTGGCGGAGAGCGTTTCGGGGAGCGTGGTTTCTTCATCAAGCCT
ACTGTCTTTGGTGGCGTGCAGGATGACATGAGAATTGCCAAAGAGGAGATCTTTGGGCCTGTGCAGCCCCTGTTCAAGTT
CAAGAAGATGGAGGAGGTGATTGAGAGGGCCAACAACACCAGGTATGGCCTGGCTGCGGCTGTGTTCACCCGGGATCTGG
ACAAGGCCATGTACTTCACCCAGGCACTCCAGGCCGGGACCGTGTGGGTAAACACCTACAACATCGTCACCTGCCACACG
CCATTTGGAGGGTTTAAGGAATCTGGAAATGGGAGGGAGCTGGGTGAGGATGGGCTTAAGGCCTACACAGAGGTGAAGAC
GGTCACCATCAAGGTTCCTCAGAAGAACTCGTAA

ORF - retro_pabe_32 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.76 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMLRAAARFGPRLGRRLLSAAATQAVPAPNQQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAE
MLR..A.....L..R........A.P.P...P....NQ.FINNEW.DAVS.KTFPTVNP.TGEVI..VAE
RetrocopyMLRFLAPRLLSLQGRTARYSSAAALPSPILNPDIPYNQLFINNEWQDAVSKKTFPTVNPTTGEVIGHVAE
ParentalGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLD
GD..DVD.AVKAAR.AF.LGSPWRRMDAS.RGRLLN.LADL.ERDR.YLA.LETLDNGKP...SY..DLD
RetrocopyGDRADVDRAVKAAREAFRLGSPWRRMDASERGRLLNCLADLVERDRVYLASLETLDNGKPFQESYALDLD
ParentalMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKV
.V.K..RY.AGWADK.HGKTIP.DG..F..TRHEP.GVCGQIIPWNFPL.MQ.WKL.PALATGN.VVMKV
RetrocopyEVIKVYRYFAGWADKWHGKTIPMDGQHFCFTRHEPIGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKV
ParentalAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLK
AEQTPL.ALY.A.LIKEAGFPPGVVNI..G.GPTAGAAIA.H.DVDKVAFTGSTE.G..IQ.AAG.SNLK
RetrocopyAEQTPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVGHLIQKAAGDSNLK
ParentalRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGN
RVTLELGGKSP.I...DADM..AVEQ.H.ALFFN.GQCCCAGSRTFV.E.IY.EF.ER.V..AK.R.VGN
RetrocopyRVTLELGGKSPSIVLADADMEHAVEQCHEALFFNMGQCCCAGSRTFVEESIYNEFLERTVEKAKQRKVGN
ParentalPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDV-DGMTIAKEEIFGP
PF...T.QGPQVD..QF...LGYI..G..EGAKLLCGG.....RG.FI.PTVFG.V.D.M.IAKEEIFGP
RetrocopyPFELDTQQGPQVDKEQFERVLGYIQLGQKEGAKLLCGGERFGERGFFIKPTVFGGVQDDMRIAKEEIFGP
ParentalVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGS
V....KFK..EEV..RANN..YGLAAAVFT.DLDKA.Y..QALQAGTVWVN.Y.......PFGG.K.SG.
RetrocopyVQPLFKFKKMEEVIERANNTRYGLAAAVFTRDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGN
ParentalGRELGEYGLQAYTEVKTVTVKVPQKNS
GRELGE.GL.AYTEVKTVT.KVPQKNS
RetrocopyGRELGEDGLKAYTEVKTVTIKVPQKNS

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_prefrontal_cortex 3 .82 RPM 125 .57 RPM
SRP007412_cerebellum 1 .70 RPM 32 .95 RPM
SRP007412_heart 1 .14 RPM 74 .63 RPM
SRP007412_kidney 11 .37 RPM 545 .66 RPM
SRP007412_liver 11 .23 RPM 643 .06 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_32 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_32 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_32 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_19
Pan troglodytes retro_ptro_118
Gorilla gorilla retro_ggor_33
Macaca mulatta retro_mmul_247
Mus musculus retro_mmus_222
Rattus norvegicus retro_rnor_307
Bos taurus retro_btau_48
Sus scrofa retro_sscr_9
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 ENSPPYG00000004966 1 retrocopy
retro_pabe_32 ,
Pongo abelii ENSPPYG000000259271 retrocopy
retro_pabe_2651,
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 ENSXETG000000209301 retrocopy
retro_xtro_12,




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