RetrogeneDB ID:

retro_pabe_60

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:40765856..40767710(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000019179
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL13
Ensembl ID:ENSPPYG00000020658
Aliases:None
Description:kelch-like family member 13 [Source:HGNC Symbol;Acc:22931]


Retrocopy-Parental alignment summary:






>retro_pabe_60
ATGAAAGTGTCCCTTGGTAACGGCGAAATGGGCGTCTCTGCCCATTTGCAGCCTTGTAAGGCAGGAACCACACGCTTTTT
TACCAGCAATACTCACAGTTCGGTGGTACTGCAAGGCTTTGATCAGCTTAGAATAGAGGGATTGCTTTGTGATGTGACCC
TGGTACCAGGTGATGGAGATGAAATCTTCCCTGTTCACAGAGCTATGATGGCGTCTGCTAGTGATTATTTCAAAGCCATG
TTCACAGGTGGAATGAAAGAACAAGATTTGATGTGCATTAAGCTTCATGGGGTGAACAAGGTTGGTCTGAAGAAAATCAT
TGATTTTATTTATACTGCAAAACTTTCTCTTAATATGGACAATCTTCAGGACACACTTGAAGCTGCTAGCTTTTTACAAA
TATTACCCGTTTTGGATTTCTGTAAAGTATTCCTTATATCAGGAGTCTCTTTGGATAACTGTGTTGAGGTTGGACGAATT
GCTAACACCTACAATCTTATAGAAGTGGATAAATATGTTAATAATTTCATCCTGAAGAACTTTCCTGCTTTATTGAGTAC
TGGGGAGTTTCTAAAACTCCCTTTTGAACGGCTTGCATTTGTGCTTTCCAGTAATAGTCTTAAGCACTGTACCGAACTTG
AACTCTTTAAGGCAGCCTGTCGCTGGCTAAGGTTGGAAGACCCTCGGATGGATTATGCTGCAAAATTAATGAAGAATATT
CGATTTCCACTGATGACACCACAGGATCTCATCAATTACGTGCAGACAGTAGATTTCATGAGAACAGACAATACCTGCGT
GAATTTGCTTTTGGAAGCTAGCAATTACCAAATGATGCCATATATGCAGCCAGTGATGCAGTCAGATAGAACTGCCATTC
GATCTGACTCCACTCACTTGGTTACCTTAGGAGGAGTTTTGAGGCAGCAGCTGGTTGTCAGTAAAGAGTTACGGATGTAT
GATGAAAGGGCACAAGAATGGAGATCTTTAGCCCCAATGGATGCTCCCCGTTACCAGCATGGTATTGCTGTCATTGGAAA
CTTTCTTTATGTAGTTGGTGGTCAGAGTAATTATGATACAAAAGGAAAAACTGCTGTTGATACAGTTTTCAGATTTGATC
CTCGGTATAATAAATGGATGCAGGTTGCATCATTAAATGAGAAGCGCACATTCTTTCACTTGAGTGCCCTCAAAGGACAT
TTGTATGCAGTTGGTGGGCGCAGTGCAGCTGGTGAACTGGCCACAGTAGAATGTTACAACCCAAGAATGAATGAGTGGAG
CTATGTTGCAAAAATGAGTGAACCCCACTATGGTCATGCTGGAACAGTTTATGGAGGCTTAATGTATATTTCAGGAGGAA
TTACCCATGACACTTTCCAAAATGAGCTCATGTGTTTTGACCCAGATACAGATAAATGGATGCAAAAGGCTCCAATGACT
ACAGTCAGAGGTCTGCATTGCATGTGTACAGTTGGAGATAAGCTCTATGTCATTGGTGGCAATCACTTCAGAGGAACAAG
TGATTATGATGATGTTCTAAGCTGTGAATACTATTCACCAACCCTTGACCAGTGGACCCCAATTGCCGCAATGTTAAGAG
GCCAAAGTGATGTTGGAGTTGCCGTCTTTGAAAATAAAATCTATGTTGTTGGTGGATATTCTTGGAATAATCGTTGTATG
GTAGAAATTGTCCAGAAATATGACCCAGAAAAAGATGAGTGGCATAAAGTTTTTGATCTTCCAGAGTCACTTGGTGGCAT
TCGAGCCTGTACACTCACAGTTTTTCCACCTGAAGAAAACCCTGGGTCACCTTCTAGAGAATCACCTCTTTCAGCACCTT
CAGATCATTCTTAG

ORF - retro_pabe_60 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.49 %
Parental protein coverage: 94.2 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKLSLGGSEMGLSSHLQSSKAGPTRIFTSNTHSSVVLQGFDQLRLEGLLCDVTLMPGDTDDAFPVHRVMM
MK.SLG..EMG.S.HLQ..KAG.TR.FTSNTHSSVVLQGFDQLR.EGLLCDVTL.PGD.D..FPVHR.MM
RetrocopyMKVSLGNGEMGVSAHLQPCKAGTTRFFTSNTHSSVVLQGFDQLRIEGLLCDVTLVPGDGDEIFPVHRAMM
ParentalASASDYFKAMFTGGMKEQDLMCIKLHGVSKVGLRKIIDFIYTAKLSLNMDNLQDTLEAASFLQILPVLDF
ASASDYFKAMFTGGMKEQDLMCIKLHGV.KVGL.KIIDFIYTAKLSLNMDNLQDTLEAASFLQILPVLDF
RetrocopyASASDYFKAMFTGGMKEQDLMCIKLHGVNKVGLKKIIDFIYTAKLSLNMDNLQDTLEAASFLQILPVLDF
ParentalCKVFLISGVTLDNCVEVGRIANTYNLTEVDKYVNNFVLKNFPALLSTGEFLKLPFERLAFVLSSNSLKHC
CKVFLISGV.LDNCVEVGRIANTYNL.EVDKYVNNF.LKNFPALLSTGEFLKLPFERLAFVLSSNSLKHC
RetrocopyCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLSTGEFLKLPFERLAFVLSSNSLKHC
ParentalTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQTVDFMRTDNTCVNLLLEASNYQMMP
TELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVDFMRTDNTCVNLLLEASNYQMMP
RetrocopyTELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVDFMRTDNTCVNLLLEASNYQMMP
ParentalYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKAHEWKSLAPMDAPRYQHGIAVIGNFLY
YMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE.A.EW.SLAPMDAPRYQHGIAVIGNFLY
RetrocopyYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWRSLAPMDAPRYQHGIAVIGNFLY
ParentalVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGYLYAVGGRNAAGELPTVECYN
VVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKG.LYAVGGR.AAGEL.TVECYN
RetrocopyVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGHLYAVGGRSAAGELATVECYN
ParentalPRTNEWTYVAKMSEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDPDADKWIQKAPMTTVRGLHCMCT
PR.NEW.YVAKMSEPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDPD.DKW.QKAPMTTVRGLHCMCT
RetrocopyPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDPDTDKWMQKAPMTTVRGLHCMCT
ParentalVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQSDVGVAVSKIKSMWLGG
VG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQSDVGVAV...K....GG
RetrocopyVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDVGVAVFENKIYVVGG

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 15 .70 RPM 5 .09 RPM
SRP007412_cerebellum 26 .51 RPM 8 .63 RPM
SRP007412_heart 9 .69 RPM 2 .47 RPM
SRP007412_kidney 14 .39 RPM 7 .19 RPM
SRP007412_liver 13 .13 RPM 0 .58 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_60 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_60 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_60 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017821 retrocopy
retro_amel_749,
Bos taurus ENSBTAG000000005011 retrocopy
retro_btau_44,
Canis familiaris ENSCAFG000000182721 retrocopy
retro_cfam_422,
Callithrix jacchus ENSCJAG000000024471 retrocopy
retro_cjac_3406,
Cavia porcellus ENSCPOG000000112681 retrocopy
retro_cpor_590,
Equus caballus ENSECAG000000082371 retrocopy
retro_ecab_622,
Loxodonta africana ENSLAFG000000081221 retrocopy
retro_lafr_1018,
Myotis lucifugus ENSMLUG000000273931 retrocopy
retro_mluc_204,
Macaca mulatta ENSMMUG000000022931 retrocopy
retro_mmul_42,
Mustela putorius furoENSMPUG000000017301 retrocopy
retro_mputfur_169,
Mus musculus ENSMUSG000000367821 retrocopy
retro_mmus_121,
Nomascus leucogenys ENSNLEG000000147361 retrocopy
retro_nleu_1031,
Oryctolagus cuniculus ENSOCUG000000019931 retrocopy
retro_ocun_254,
Pongo abelii ENSPPYG00000020658 1 retrocopy
retro_pabe_60 ,
Pteropus vampyrus ENSPVAG000000159891 retrocopy
retro_pvam_1485,
Rattus norvegicus ENSRNOG000000140291 retrocopy
retro_rnor_154,
Sus scrofa ENSSSCG000000126371 retrocopy
retro_sscr_51,
Ictidomys tridecemlineatus ENSSTOG000000120351 retrocopy
retro_itri_124,
Tarsius syrichta ENSTSYG000000025211 retrocopy
retro_tsyr_19,
Tursiops truncatus ENSTTRG000000140981 retrocopy
retro_ttru_26,
Vicugna pacos ENSVPAG000000030911 retrocopy
retro_vpac_8,


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