RetrogeneDB ID:

retro_ecab_557

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:20:47802180..47803368(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000003389
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PGK1
Ensembl ID:ENSECAG00000014984
Aliases:None
Description:phosphoglycerate kinase 1 [Source:HGNC Symbol;Acc:8896]


Retrocopy-Parental alignment summary:






>retro_ecab_557
AGAGTAGACTTCAACGTTCCCATGAAGAAGAACCAGATTACAAACAACCAGAGAATCAAGGCTTCCATCCCAAGCATCAA
GTACTGCCTGGATAATGGAGCCAGGTCAGTAGTTCTTATGAGTCATTTAGGTCGACCTGATGGTGTTCCCATGCCTGATA
AATACTCTTTAGAGCCTGTTGCTGCTGAGCTCAAATCCTTGCTGGGCAAGGATGTTCTGTTCCTGAAGGACTGTGTGGGC
TCAGAAGTGGAGAAAGCCTGTGCCAACCCAGCTACTGGTTCAGTTATCCTGCTGGAGAACCTGCGCTTTCATGTGGAGGA
AGAAGGGAAGGGCCAAGATCCTTCTGGAAATAAGCTTAAAGCTGAGGCAGGTAAAATAGAAGCCTTCCGGGCATCACTGT
CCAAGCTCGGGGATGTCTATGTCAATGATGCTTTTGGCACTGCTCACCGAGCCCACAGTTCCATGGTGGGAATAAATCTG
CCCCAGAAGGCATCTGGATTTCTGATGAAGAAGGAGCTGGAGTACTTTGCCAAAGCCTTGGAAAACCCAGAGAGACCCTT
TCTGGCTATACTTGGTGGAGCCAAAGTGGCAGACAAGATCCAACTCATCAAAAATATGCTGGACAAGGTCAATGAGATGA
TTATTGGTGGTGGAATGGCTTATACCTTCCTTAAGGTACTTAACAACATGGAGATTGGTGCTTCCCTGTTTGATGAAGAG
GGAGCCAAGATTGTCAAAGATATCATGGCCAAAGCCAATAAGAATGGTGTGCGCATTACATTTCCTGTTGATTTTGTTAC
TGCTGACAAGTTTGAGGAGAATGCTAAGGTTGGCCAAGCCACTGTAGCATCAGGCATACCTGCCGGCTGGATGGGTTTGG
ACTGCGGTCCTGAGACTAATAAGAAGTATGCTCAAGTGATGGCCCAAGCCAAACTAATTGTGTGGAATGGACCTGTAGGG
GTATTTGAATGGGATGCCTTTGCTAAGGGAACCAAAGCCCTCATGGATGAAATTGTGAAAGCCACTTCCAGGGGCTGTAT
CACCATTATAGGAGGTGGAGACACTGCTACTTGCTGTGCTAAATGGAACACCGAAGATAAAGTCAGTCATGTGAGCACTG
GAGGAGGTGCCAGTCTAGAGCTTCTGGAAGGTAAAATCCTTCCTGGAGTGGATGCTCTCAGCAACCTG

ORF - retro_ecab_557 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.89 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLQPVAVELKSLLGK
RVDFNVPMK.NQITNNQRIKA..PSIK.CLDNGA.SVVLMSHLGRPDGVPMPDKYSL.PVA.ELKSLLGK
RetrocopyRVDFNVPMKKNQITNNQRIKASIPSIKYCLDNGARSVVLMSHLGRPDGVPMPDKYSLEPVAAELKSLLGK
ParentalDVLFLKDCVGPEVEKACADPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIETFRASLSKLGDVY
DVLFLKDCVG.EVEKACA.PA.GSVILLENLRFHVEEEGKG.D.SGNK.KAE..KIE.FRASLSKLGDVY
RetrocopyDVLFLKDCVGSEVEKACANPATGSVILLENLRFHVEEEGKGQDPSGNKLKAEAGKIEAFRASLSKLGDVY
ParentalVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKV
VNDAFGTAHRAHSSMVG.NLPQKA.GFLMKKEL.YFAKALE.PERPFLAILGGAKVADKIQLI.NMLDKV
RetrocopyVNDAFGTAHRAHSSMVGINLPQKASGFLMKKELEYFAKALENPERPFLAILGGAKVADKIQLIKNMLDKV
ParentalNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDEHAKTGQA
NEMIIGGGMA.TFLKVLNNMEIG.SLFDEEGAKIVKD.M.KA.KNGV.IT.PVDFVTADKF.E.AK.GQA
RetrocopyNEMIIGGGMAYTFLKVLNNMEIGASLFDEEGAKIVKDIMAKANKNGVRITFPVDFVTADKFEENAKVGQA
ParentalTVASGIPAGWMGLDCGTESSKKYAEAVARAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITII
TVASGIPAGWMGLDCG.E..KKYA...A.AK.IVWNGPVGVFEW.AFA.GTKALMDE.VKATSRGCITII
RetrocopyTVASGIPAGWMGLDCGPETNKKYAQVMAQAKLIVWNGPVGVFEWDAFAKGTKALMDEIVKATSRGCITII
ParentalGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV
GGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGK.LPGVDALSN.
RetrocopyGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKILPGVDALSNL

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 .00 RPM 240 .61 RPM
SRP021940_cerebellum 0 .00 RPM 383 .78 RPM
SRP021940_embryo 0 .00 RPM 125 .66 RPM
SRP021940_placental_villous 0 .14 RPM 225 .30 RPM
SRP021940_synovial_membrane 0 .00 RPM 116 .18 RPM
SRP021940_testis 168 .43 RPM 122 .77 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_557 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_557 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_557 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_90
Pan troglodytes retro_ptro_2
Gorilla gorilla retro_ggor_2420
Pongo abelii retro_pabe_134
Macaca mulatta retro_mmul_144
Callithrix jacchus retro_cjac_137
Bos taurus retro_btau_1021
Sus scrofa retro_sscr_933
Canis familiaris retro_cfam_510
Parental genes homology:
Parental genes homology involve 29 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000176191 retrocopy
retro_amel_117,
Bos taurus ENSBTAG000000008941 retrocopy
retro_btau_1021,
Canis familiaris ENSCAFG000000172702 retrocopies
retro_cfam_1194, retro_cfam_510,
Callithrix jacchus ENSCJAG000000210823 retrocopies
retro_cjac_1367, retro_cjac_137, retro_cjac_4171,
Cavia porcellus ENSCPOG000000237851 retrocopy
retro_cpor_102,
Equus caballus ENSECAG00000014984 1 retrocopy
retro_ecab_557 ,
Felis catus ENSFCAG000000132092 retrocopies
retro_fcat_123, retro_fcat_316,
Homo sapiens ENSG000001021442 retrocopies
retro_hsap_1966, retro_hsap_90,
Gorilla gorilla ENSGGOG000000171113 retrocopies
retro_ggor_1429, retro_ggor_2420, retro_ggor_3026,
Loxodonta africana ENSLAFG000000119541 retrocopy
retro_lafr_13,
Macropus eugenii ENSMEUG000000047793 retrocopies
retro_meug_11, retro_meug_1649, retro_meug_400,
Myotis lucifugus ENSMLUG000000177912 retrocopies
retro_mluc_1657, retro_mluc_2159,
Macaca mulatta ENSMMUG000000128741 retrocopy
retro_mmul_144,
Monodelphis domestica ENSMODG000000040552 retrocopies
retro_mdom_140, retro_mdom_170,
Mus musculus ENSMUSG000000620702 retrocopies
retro_mmus_29, retro_mmus_9,
Nomascus leucogenys ENSNLEG000000014233 retrocopies
retro_nleu_2372, retro_nleu_2610, retro_nleu_79,
Oryctolagus cuniculus ENSOCUG000000147261 retrocopy
retro_ocun_171,
Otolemur garnettii ENSOGAG000000111041 retrocopy
retro_ogar_73,
Procavia capensis ENSPCAG000000021171 retrocopy
retro_pcap_17,
Pongo abelii ENSPPYG000000204963 retrocopies
retro_pabe_134, retro_pabe_1624, retro_pabe_3770,
Pan troglodytes ENSPTRG000000220522 retrocopies
retro_ptro_2, retro_ptro_3229,
Rattus norvegicus ENSRNOG000000024677 retrocopies
retro_rnor_1526, retro_rnor_1527, retro_rnor_2603, retro_rnor_3, retro_rnor_462, retro_rnor_590, retro_rnor_611,
Sorex araneus ENSSARG000000039561 retrocopy
retro_sara_14,
Sarcophilus harrisii ENSSHAG000000018531 retrocopy
retro_shar_11,
Sus scrofa ENSSSCG000000124401 retrocopy
retro_sscr_933,
Ictidomys tridecemlineatus ENSSTOG000000019721 retrocopy
retro_itri_65,
Tupaia belangeri ENSTBEG000000103091 retrocopy
retro_tbel_35,
Tarsius syrichta ENSTSYG000000079171 retrocopy
retro_tsyr_40,
Vicugna pacos ENSVPAG000000012081 retrocopy
retro_vpac_21,


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