RetrogeneDB ID:

retro_ecab_1101

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:X:18495456..18497640(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000003962
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SUPT20H
Ensembl ID:ENSECAG00000000116
Aliases:None
Description:suppressor of Ty 20 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20596]


Retrocopy-Parental alignment summary:






>retro_ecab_1101
ATGCAACACGCCTTAGAACGAGCTCTGGATCGCGCGGCGTGTGTCATCGAAAGTGCCCAACAGAGACCTCCTAAAAGGAA
GTACGCGTCTAGAGGGGAAAAATCGGTCTATGAGAAACTGTATGACATATATGTTGAAGAATGCGACAGAGAGCCTGAGG
TTGCGGAGGAATTACGAAGCAACGTGAACTTGCTAGAGAAGCTTGTTCAGAGAGAGTCGTTGTCGCGTTTAGTGGTCAAT
CTGCACCCAGGAGGGCAGGGATACTCGCTGATGCTCAGGGGAGAAAATGGCTCGTATTCGGAGACCATTCGGCTGTCTTA
TGAAGAGGGGGAACTGCTCCAGTACTTGGATGCAGAAGAATTACCTCCTGTTTTGGTGGGTCTCCTGGAAAAATCTCAGG
TGAACGTTTTTCACTGTGGATGCGTCATCGCAGAAATACGGGACTACAGGCAGTCCAGTGACGTGGAGGCCCCTGGTTAC
CAGAGCAGGTGCATTCTCTTACGACCAACCATGCAGACGTTAGCCTGCGACGTAGAGTCCCTAACCAGCGACAGCCAGAC
ATGGACCCAGGAGGACAAACTGTTGCTCGAGAGCCAGCTGATCTTAGCCACAGCTGAACCACTGTGTCTTGATCCTTCTG
TGTCAGTAGCCTGCACTGCAAACAGTCTGCTTTATAACAAACAAAAGATGAACACTGACCCAATGAAGCGCTGCTTCAAG
AGGTGCTCGAGCCCGGCTCTGAGTCGGCAGCAGGAGCTGTCTCATGGCCCACCTCCGCCCGAGCTAACGGTACTGACTTC
TTGCCAACCAAGCAAAGAGAGTAACGCAGGTGAGCAGTATGACCTCAAAATTTCTGGAGCAGGGAATTATGTGGATGTGT
GGGAACAGAGACCCTGTGACTTGGCCGTACCTTCTGAAGTGGATGTGGAGAAATATGCTACAGGGAAGAAGTCCGTGAGC
TCTGATGACTCCCAGCCAACAGGCTGGCCAGCCCATGAAGTCAGAGATGATTCTGTATTTGAATGGGAAGCAGGCGATCA
GTACCGGGATACAAAGATGTTCTTCATGCGCTCGCTTAATGATCCACTTATCTCTGGGAAAGAAATGTCACCTAAAAAAG
CCAGATATGAGAGACAGCTGTCTCCCCCCCACCCCTCCAGAGGTGACCATTCAAAGAGTTTCATGCCTGGGTCGAAGACT
GATGCTGGGACGGTAGTCATTCGGCCCGAGGAATTGGTCCAGAAGAACAGCAGTTGTCCAGTCAAGGTGTCACACAGCTC
CAGTGGCTCAGCCAGTCTCAGCCCACTTTCTCCAGGGAAGGAAACAGAACGGCCTAAGACCGTGCTGCTTCAGGCCTCAG
TCCTGGGGGAGGAAGTCCAACCTCCACCGCCGCCCGTCACGCTGCCCTCGAGCTCAGGCACGAGTTCCTCAGCCAGCAGT
TTTCCTCCACAGCAGGCAGGCGGCTTTCCTAAGTCTGCATCTCCTGCTCCTGCTTCTAAGCCACCAAGTCTTCCCCAGAA
TTCCCCTGTGGAAGTGAGTCGAGTTAGCACGCTTCCTGCAGCCGCCCAGTCCACTGCTGGCTCATCACAAACACAGGTGA
CCACCCAGGTCAGGGTCAGCCCCGTTGGTGTCAGGGTCATCAAAGTGGTGAATTCTGTTCCCGGAACCCACGCTTTGGTG
AGAGCTCCCAACCCCTCGCAGGGCTCTGCCACTCGGGCCACAGCTCCCGCGGGAATCTTGCCCAGCAACCTGCCCTTAAG
AGGCCAGCCACCAAAAGCGCCACCCACTGCCCTGCAAGCGAATTCTCAAGTAGGTGTTCGAGTGATTTTAAAAGATGCTC
CAGGTGCCAGGCCCTTAACTCTGCTCCAGTTTCCACCAGGTTCGCTCATTGTGAACACCCAGCAGCTGCCTGGGCAGCTG
CAGCAGCAGCACCTCTATCAGCTGATTCCAGAGCTACAGGGTCAGCAGCCCTCCACTTCGCATCCTCAGCAGCTAGTGTC
ACAGGGTGCAAGTGCACAAGGTTCAGCCAGTCAGAAAACGGCCTTCTGTGCCCAGCAAGCTGTTGTCGTTAACGTCAGTA
GAAGTTTTCTGCAGCCCCAGGTGATTGTGTTGTCTCCGCCTGTCCCTGCCCTGCAAAGACCTGGGCAAAGCCTTCCTCTG
CAGAGAGTCCAGCTCTCCTCCGCC

ORF - retro_ecab_1101 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.52 %
Parental protein coverage: 93.07 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQQALELALDRAEYVIESARQRPPKRKYLSSGRKSVFQKLYDLYIEECEKEPEV-KKLRRNVNLLEKLVM
MQ.ALE.ALDRA..VIESA.QRPPKRKY.S.G.KSV..KLYD.Y.EEC..EPEV...LR.NVNLLEKLV.
RetrocopyMQHALERALDRAACVIESAQQRPPKRKYASRGEKSVYEKLYDIYVEECDREPEVAEELRSNVNLLEKLVQ
ParentalQETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCG
.E.LS.LVVNL.PG..GYSLMLRG.NGS.SETIRL.YEEGELL.YLDAEELPP.LV.LLEKSQVN.FHCG
RetrocopyRESLSRLVVNLHPGGQGYSLMLRGENGSYSETIRLSYEEGELLQYLDAEELPPVLVGLLEKSQVNVFHCG
ParentalCVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCL
CVIAEIRDYRQSS....PGYQSR.ILLRPTMQTL.CDV.S.TSD...WTQEDKLLLESQLILATAEPLCL
RetrocopyCVIAEIRDYRQSSDVEAPGYQSRCILLRPTMQTLACDVESLTSDSQTWTQEDKLLLESQLILATAEPLCL
ParentalDPSIAVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPPPPQLKLLDFLQKRKERKAGQHY
DPS..V.CTAN.LLYNKQKMNT.PMKRCFKR.S...L.RQQ.LSH.PPPP.L..L...Q..KE..AG..Y
RetrocopyDPSVSVACTANSLLYNKQKMNTDPMKRCFKRCSSPALSRQQELSHGPPPPELTVLTSCQPSKESNAGEQY
ParentalDLKISKAGNCVDMWKQSPCNLAIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDVKDDYVFECEAGNQYQK
DLKIS.AGN.VD.W.Q.PC.LA.PSEVDVEKYA...KS..SDDSQPT.WPAH.V.DD.VFE.EAG.QY..
RetrocopyDLKISGAGNYVDVWEQRPCDLAVPSEVDVEKYATGKKSVSSDDSQPTGWPAHEVRDDSVFEWEAGDQYRD
ParentalTKLTILQSLGDPLYYGRIQPCKEDEESDSQMSPSHSSTDDHSNWFIIGSKTDAERVVNQYQELVQNEAKC
TK.....SL.DPL..G.....K.......Q.SP.H.S..DHS..F..GSKTDA..VV....ELVQ....C
RetrocopyTKMFFMRSLNDPLISGKEMSPKK-ARYERQLSPPHPSRGDHSKSFMPGSKTDAGTVVIRPEELVQKNSSC
ParentalPVKMSHSSSGSASLSQLSPGKDTEQPETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNYFTPQQTSSF
PVK.SHSSSGSASLS.LSPGK.TE.P.TV..Q.SVLG..V...PPP..LPSSSG.SSS...F.PQQ...F
RetrocopyPVKVSHSSSGSASLSPLSPGKETERPKTVLLQASVLGEEVQPPPPPVTLPSSSGTSSSASSFPPQQAGGF
ParentalLKSPTPPPASKPPSLSRKSSVDLNQVSMLSPAALSPASSSQRTTATQVMANSAGLNFINVVGSVCGAQAL
.KS..P.PASKPPSL...S.V....VS.L..AA.S.A.SSQ....TQV.....G...I.VV.SV.G..AL
RetrocopyPKSASPAPASKPPSLPQNSPVEVSRVSTLPAAAQSTAGSSQTQVTTQVRVSPVGVRVIKVVNSVPGTHAL
ParentalMSGSNPMLGCNTGAITPAGINLSGLLPSGSLLPNALPGAMQATSQAGVPFGLKNTSSLRPLNLLQLPGGS
....NP..G..T.A..PAGI.L...LP.....P.A.P.A.QA.SQ.GV...LK.....RPL.LLQ.P.GS
RetrocopyVRAPNPSQGSATRATAPAGI-LPSNLPLRGQPPKAPPTALQANSQVGVRVILKDAPGARPLTLLQFPPGS
ParentalLIFNTLQ---QQQQQ-LSQFTPQ-QPQQPTTSSPQQPGEQG-SEQGSTSQEQALSAQHAAVINLAGVGSF
LI.NT.Q...Q.QQQ.L.Q..P..Q.QQP.TS.PQQ...QG.S.QGS.SQ..A..AQ.A.V.N.....SF
RetrocopyLIVNTQQLPGQLQQQHLYQLIPELQGQQPSTSHPQQLVSQGASAQGSASQKTAFCAQQAVVVNVS--RSF
ParentalMQSQAAVLSQLGSAENRPEQSLPQQRFQLSSA
.Q.Q..VLS....A..RP.QSLP.QR.QLSSA
RetrocopyLQPQVIVLSPPVPALQRPGQSLPLQRVQLSSA

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






(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 0 .00 RPM 5 .96 RPM
SRP021940_cerebellum 0 .00 RPM 17 .86 RPM
SRP021940_embryo 0 .00 RPM 33 .81 RPM
SRP021940_placental_villous 0 .00 RPM 15 .20 RPM
SRP021940_synovial_membrane 0 .00 RPM 10 .76 RPM
SRP021940_testis 0 .13 RPM 93 .10 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1101 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1101 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_1101 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4794
Pan troglodytes retro_ptro_3189
Pongo abelii retro_pabe_3729
Macaca mulatta retro_mmul_2555

Parental genes homology:
Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG00000000116 2 retrocopies
retro_ecab_1052, retro_ecab_1101 ,
Homo sapiens ENSG000001027102 retrocopies
Loxodonta africana ENSLAFG000000275071 retrocopy
Macaca mulatta ENSMMUG000000035902 retrocopies
Pongo abelii ENSPPYG000000052882 retrocopies
Pan troglodytes ENSPTRG000000057912 retrocopies
Pteropus vampyrus ENSPVAG000000146091 retrocopy
Tarsius syrichta ENSTSYG000000132271 retrocopy
Vicugna pacos ENSVPAG000000072881 retrocopy



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