RetrogeneDB ID:

retro_ecab_962

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:8:488206..489866(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000012704
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CNOT6
Ensembl ID:ENSECAG00000019325
Aliases:None
Description:CCR4-NOT transcription complex, subunit 6 [Source:HGNC Symbol;Acc:14099]


Retrocopy-Parental alignment summary:






>retro_ecab_962
GGCATGCCCAAAGACAAATGCGAGCCCCCTGACCCTGGGAGGATGTACACAATTATGTCCTCTGAGGAAGCAGCAAATGG
AAAGAAATCACATTGGGCAGAGCTTGAAATAAGTGGAAAAGTAAGAAGCTTAAGCTCATCTTTGTGGTCACTAACTCACC
TGACAGCTTTGCATCTGAGTGACAATTCCCTGTCCCGTATTCCTTCAGACATTGCCAAGCTTCACAATCTGGTGTATCTG
GACCTGTCTTCTAATAAAATCCGGAGTTTACCGGCAGAACTCGGAAACATGGTATCACTCAGGGAACTCCATTTAAATAA
CAACCTGTTACGAGTTCTACCTTTTGAGCTGGGAAAACTGTTTCAGTTGCAGACTTTAGGCCTGAAAGGAAATCCACTTA
CCCAAGATATATTGAACCTCTATTTGGAACTAGATGGAACAAGAAGGCTACTGAACTATTTGCTTGATAATTTGGCAGTT
TCAACAGAACAACCACCTCCAAGATCTTGGATTATGTTACAAGAACCAGACAGAACAAGGCCTTCTGCCTTGTTTTCTTT
CATGTGCTACAATGTTCTTTGTGATAAATATGCGACCCGGCAGTTATACGGCTACTGTCCGTCATGGGTGCTAAACTGGG
ACTACAGGAAAAAGGCCATTATTCAAGAAATCTTGAGCTGCAATGCTGATATCATAAGTCTTAAGGAGGTTGAAACAGAA
CAGTATTACAGTTTTTTTTCTGGTAGAACTGAAAGAACGTGGCTATAATGGATTCTTTAGTCCTAAATCTAGAGCTGGGA
CAATGTCAGAACAAGAAAGAAAACATGTTGATGGCTGTGCAATATTCTTCAAGACAGAAAAATTTACTTTGGTTCAGAAA
CACACTGTTGAATTTAATCAGCTAGCGATGGCAAATTCAGAAGGGTCTGAAGCTATGCTGAACAGAGTCATGACAAAAGA
TAACATTGGAGTTGCAGTACTGCTAGAACTTCGAAAGGAATTGATTGAAATGTCATCTGGAAAGCCACGTCTTGGAACAG
AAAAACAACTGATTCTCGTGCCTAATGCTCATATGCATTGGGACCCTGAATACTCTGATGTGAAGTTGGTTCAGACAATG
ATGTTCCTCTCAGAAGTGACGAACATTATTGACAAAGCCTCACGGAGCCTCCAGTCCAGTGTCTTGGGAGAGTTTGGAGC
TATTCCATTGGTGGTGTGTGCAGATCTTAATTCTTTGCCAGACTCTGGTGATGTAGAATATTTGAGCACTGGTGGAGTAG
AAACAAACCATAAAGACTTTAAGGAGCTGAGATATAATGAAAGTCTCACAAACTTCAGCTGCAATGGGAAAAATGGGACG
ACCAATGGCAGGATCACGCATGGGTTCAAGTTAAAGAGTGCCTACGAGAGTGGCCTGATGCCTTACACGAACTACACCTT
CGATTTCAAGGGTATAATTGACTACATCTTCTACTCTAAACCTCAGCTGAACACTTTAGGCATCCTGGGACCTCTGGACC
ACCATTGGCTAGTTGAGAATAATATCAGTGGTGGCCCACACCCACTCATCCCCTCTGATCACTGCTCACTTTTTGCACAA
CTGGAGCTCTTACTGCCTTTCCTGCCCCAAGTAAACGGCATTCACCTTCCCAGCAGGAGG

ORF - retro_ecab_962 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.28 %
Parental protein coverage: 99.82 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGMPKEKYEPPDPRRMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLSRIPSD
GMPK.K.EPPDP.RMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLSRIPSD
RetrocopyGMPKDKCEPPDPGRMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLSRIPSD
ParentalIAKLHNLVYLDLSSNKIRSLPAELGNMVSLRELHLNNNLLRVLPFELGKLFQLQTLGLKGNPLTQDILNL
IAKLHNLVYLDLSSNKIRSLPAELGNMVSLRELHLNNNLLRVLPFELGKLFQLQTLGLKGNPLTQDILNL
RetrocopyIAKLHNLVYLDLSSNKIRSLPAELGNMVSLRELHLNNNLLRVLPFELGKLFQLQTLGLKGNPLTQDILNL
ParentalYLEPDGTRRLLNYLLDNLAGTAKRISTEQPPPRSWIMLQEPDRTRPTALFSVMCYNVLCDKYATRQLYGY
YLE.DGTRRLLNYLLDNLA..........PP.RSWIMLQEPDRTRP.ALFS.MCYNVLCDKYATRQLYGY
RetrocopyYLELDGTRRLLNYLLDNLAVSTE----QPPP-RSWIMLQEPDRTRPSALFSFMCYNVLCDKYATRQLYGY
ParentalCPSWALNWDYRKKAIIQEILSCNADIVSLQEVETEQYY-SFFLVELKERGYNGFFSPKSRARTMSEQERK
CPSW.LNWDYRKKAIIQEILSCNADI.SL.EVETEQYY....LVELKERGYNGFFSPKSRA.TMSEQERK
RetrocopyCPSWVLNWDYRKKAIIQEILSCNADIISLKEVETEQYY>XXXLVELKERGYNGFFSPKSRAGTMSEQERK
ParentalHVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAVLLELRKELIEMSSGKPHL
HVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAVLLELRKELIEMSSGKP.L
RetrocopyHVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAVLLELRKELIEMSSGKPRL
ParentalGTEKQLILVANAHMHWDPEYSDVKLVQTMMFLSEVKNIIDKASRSLQSSVLGEFGAIPLVLCADLNSLPD
GTEKQLILV.NAHMHWDPEYSDVKLVQTMMFLSEV.NIIDKASRSLQSSVLGEFGAIPLV.CADLNSLPD
RetrocopyGTEKQLILVPNAHMHWDPEYSDVKLVQTMMFLSEVTNIIDKASRSLQSSVLGEFGAIPLVVCADLNSLPD
ParentalSGVVEYLSTGGVETNHKDFKELRYNESLTNFSCNGKNGTTNGRITHGFKLKSAYESGLMPYTNYTFDFKG
SG.VEYLSTGGVETNHKDFKELRYNESLTNFSCNGKNGTTNGRITHGFKLKSAYESGLMPYTNYTFDFKG
RetrocopySGDVEYLSTGGVETNHKDFKELRYNESLTNFSCNGKNGTTNGRITHGFKLKSAYESGLMPYTNYTFDFKG
ParentalIIDYIFYSKPQLNTLGILGPLDHHWLVENNISGCPHPLIPSDHFSLFAQLELLLPFLPQVNGIHLPSRR
IIDYIFYSKPQLNTLGILGPLDHHWLVENNISG.PHPLIPSDH.SLFAQLELLLPFLPQVNGIHLPSRR
RetrocopyIIDYIFYSKPQLNTLGILGPLDHHWLVENNISGGPHPLIPSDHCSLFAQLELLLPFLPQVNGIHLPSRR

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 0 .24 RPM 6 .38 RPM
SRP021940_cerebellum 0 .21 RPM 9 .04 RPM
SRP021940_embryo 0 .31 RPM 16 .16 RPM
SRP021940_placental_villous 0 .00 RPM 8 .08 RPM
SRP021940_synovial_membrane 0 .05 RPM 6 .40 RPM
SRP021940_testis 0 .00 RPM 4 .99 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_962 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_962 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_962 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG00000019325 1 retrocopy
retro_ecab_962 ,
Microcebus murinus ENSMICG000000130181 retrocopy
retro_mmur_1392,
Oryctolagus cuniculus ENSOCUG000000110831 retrocopy
retro_ocun_1589,


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