RetrogeneDB ID:

retro_ecab_622

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:23:40217664..40219548(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000005817
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL13
Ensembl ID:ENSECAG00000008237
Aliases:None
Description:kelch-like family member 13 [Source:HGNC Symbol;Acc:22931]


Retrocopy-Parental alignment summary:






>retro_ecab_622
CCCCTGCCTCCGGCGTACGTCTTTGTGCAAGAGGAAAGCTTTCACATGAAAGTGTCTCTTGGTAACGGCGATATGGGCGT
CTCTGCCCATTTGCAGCCTTGCAAAGCAGGAACCACACGTTTCTTTACCAGCAATACTCACAGTTCGGTGGTGTTGCAAG
GCTTTGATCAGCTTAGAATAGAAGGATTGCTTTGTGATGTGACTCTGGTCCCGGGTGATGGAGATGAAATCTTCCCTGTT
CACAGAGCTATGATGGCATCTGCTAGTGATTATTTCAAGGCTATGTTCACAGGGGGAATGAAAGAACAAGATTTAATGTG
CATTAAGCTTCATGGAGTGAACAAGGTTGGTCTGAAGAAAATAATTGATTTTATTTATACTGCAAAACTTTCTCTTAATA
TGGACAATCTTCAGGACACACTTGAAGCTGCCAGCTTTTTACAAATTTTACCTGTTTTGGATTTCTGTAAAGTGTTTCTT
ATTTCAGGAGTCTCTTTAGATAACTGTGTTGAAGTTGGGCGAATTGCTAACACCTATAATCTCATAGAAGTGGATAAATA
TGTCAATAATTTCATCCTGAAGAATTTTCCTGCGTTATTGAGTACTGGGGAGTTTCTAAAACTCCCTTTTGAACGGCTCG
CCTTTGTGCTTTCCAGCAATAGTCTTAAGCACTGTACCGAACTCGAGCTGTTCAAGGCTGCCTGTCGCTGGCTAAGGTTG
GAAGACCCTCGGATGGAATGTGCTGCAAAATTAATGAAGAATATTCGATTTCCACTGATGACACCACAGGACCTCATCAA
TTATGTGCAGACAGTAGATTTCATGAGAACAGACAATACCTGTGTGAATTTGCTTTTGGAAGCCAGCAATTACCAAATGA
TGCCGTATATGCAACCAGTGATGCAGTCAGATAGAACTGCCATTCGATCTGACTCAACGCACTTGGTTACATTAGGAGGA
GTTTTGAGGCAGCAGCTGGTTGTCAGTAAAGAATTACGGATGTATGATGAAAGGGCACAAGAGTGGAGATCTTTAGCCCC
CATGGATGCTCCTCGTTACCAGCATGGCATTGCTGTCATTGGAAACTTTCTTTATGTAGTTGGTGGTCAAAGTAATTACG
ATACGAAAGGAAAAACTGCCGTCGATACAGTTTTCAGATTTGATCCTCGGTATAATAAATGGATGCAGGTTGCATCATTA
AATGAAAAGCGCACATTCTTCCACTTGAGTGCCCTCAAAGGACATTTGTATGCTGTTGGTGGGCGAAGTGCAGCTGGTGA
ACTGGCTACAGTAGAATGTTACAACCCAAGAATGAATGAGTGGAGTTATGTCGCAAAAATGTGCGAACCCCACTATGGCC
ATGCTGGAACAGTGTATGGAGGCTTAATGTATATTTCAGGAGGAATTACTCACGACACTTTCCAAAACGAGCTCATGTGT
TTTGACCCAGATACAGACAAATGGACACAAAAGGCTCCAATGACTACAGTCAGAGGTCTGCATTGCATGTGTACAGTTGG
AGACAAGCTCTATGTCATTGGTGGCAATCACTTCAGAGGAACAAGTGATTATGATGATGTTCTAAGCTGTGAATACTATT
CGCCGACCCTTGACCAGTGGACACCAATTGCTGCTATGTTAAGAGGTCAAAGTGATGTTGGAGTTGCTGTCTTTGAAAAT
AAAATCTATGTTGTAGGTGGATATTCTTGGAATAATCGTTGTATGGTTGAAATTGTCCAGAAATATGACCCAGAAAAGGA
TGAGTGGCATAAAGTTTTTGACCTTCCAGAGTCACTTGGTGGCATTCGAGCTTGTACTCTCACAGTTTTTCCACCTGAAG
AAAACCCTGGGTCACCTTCTAGAGAGTCACCTCTTTCAGCACCT

ORF - retro_ecab_622 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.41 %
Parental protein coverage: 96.03 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPLSPAYISLVEEEDQHMKLSLGSSEMGLSSHLQSSKAGATRIFTSNTHSSVVLQGFDQLRLEGLLCDVTL
PL.PAY...V.EE..HMK.SLG...MG.S.HLQ..KAG.TR.FTSNTHSSVVLQGFDQLR.EGLLCDVTL
RetrocopyPLPPAYV-FVQEESFHMKVSLGNGDMGVSAHLQPCKAGTTRFFTSNTHSSVVLQGFDQLRIEGLLCDVTL
ParentalMPGDTDDAFPVHRVMMASASDYFKAMFTGGMKEQDLMCIKLHGVSKVGLRKIIDFIYTAKLSLNMDNLQD
.PGD.D..FPVHR.MMASASDYFKAMFTGGMKEQDLMCIKLHGV.KVGL.KIIDFIYTAKLSLNMDNLQD
RetrocopyVPGDGDEIFPVHRAMMASASDYFKAMFTGGMKEQDLMCIKLHGVNKVGLKKIIDFIYTAKLSLNMDNLQD
ParentalTLEAASFLQILPVLDFCKVFLISGVTLDNCVEVGRIANTYNLTEVDKYVNSFVLKNFPALLSTGEFLKLP
TLEAASFLQILPVLDFCKVFLISGV.LDNCVEVGRIANTYNL.EVDKYVN.F.LKNFPALLSTGEFLKLP
RetrocopyTLEAASFLQILPVLDFCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLSTGEFLKLP
ParentalFERLAFVLSSNSLKHCTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQTVDFMRTDN
FERLAFVLSSNSLKHCTELELFKA.CRWLRLE.PRM..AAKLMKNIRFPLMTPQ.LINYVQTVDFMRTDN
RetrocopyFERLAFVLSSNSLKHCTELELFKAACRWLRLEDPRMECAAKLMKNIRFPLMTPQDLINYVQTVDFMRTDN
ParentalTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKAHEWKSLAPMD
TCVNLLLEASNYQMMPYMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE.A.EW.SLAPMD
RetrocopyTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWRSLAPMD
ParentalAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGYLYAV
APRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKG.LYAV
RetrocopyAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGHLYAV
ParentalGGRNAAGELPTVECYNPRTNEWTYVAKMSEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDPDTDKWI
GGR.AAGEL.TVECYNPR.NEW.YVAKM.EPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDPDTDKW.
RetrocopyGGRSAAGELATVECYNPRMNEWSYVAKMCEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDPDTDKWT
ParentalQKAPMTTVRGLHCMCTVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQSDVGVAVFE
QKAPMTTVRGLHCMCTVG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQSDVGVAVFE
RetrocopyQKAPMTTVRGLHCMCTVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDVGVAVFE
ParentalNKIYVVGGYSWNNRCMVEIVQKYDPDKDEWHKVFDLPESLGGIRACTLTVFPPEETTPSPSRESPLSAP
NKIYVVGGYSWNNRCMVEIVQKYDP.KDEWHKVFDLPESLGGIRACTLTVFPPEE...SPSRESPLSAP
RetrocopyNKIYVVGGYSWNNRCMVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSRESPLSAP

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
SRP021940_articular_cartilage 23 .38 RPM 0 .83 RPM
SRP021940_cerebellum 41 .65 RPM 24 .30 RPM
SRP021940_embryo 53 .63 RPM 30 .56 RPM
SRP021940_placental_villous 21 .60 RPM 6 .59 RPM
SRP021940_synovial_membrane 24 .13 RPM 14 .52 RPM
SRP021940_testis 10 .04 RPM 3 .20 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_622 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_622 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_622 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 20 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 ENSECAG00000008237 1 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 ENSPPYG000000206581 retrocopy
retro_pabe_60,
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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