RetrogeneDB ID:

retro_ecab_739

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:3:40366473..40367844(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000019082
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GSPT1
Ensembl ID:ENSECAG00000021195
Aliases:None
Description:G1 to S phase transition 1 [Source:HGNC Symbol;Acc:4621]


Retrocopy-Parental alignment summary:






>retro_ecab_739
CACCCGGAGGAAAGTGCCCAAGAAACGATGGAGGAGGAAGAGGAAATACCAAAACCTAACTCTGTGGTTGCACCGCCAGG
TGTGCCTAAAAAAGAACATGTACATGTAGTATTCATTGGGCGTGCAGATGTTGGCGAGTCAACCATGGGAGGACAAATAA
TGTCTTTGACTGGAATGCTTGACAAAAGACCTCTTGAGAAAGATGAAGGAGAAGCTAAAGAAAAACCGGGGAAACTTGGT
ACTTGTCTTGGGCCTTAGACACAAATCAGGAAGAACGAGACAAGGGTAAAACAGTAGAAGTGGGCCGTGCCTATTTTGAA
ACAGAAAAGAAGCATTTCGCAATTCTAGATGGCCCTGGCCACAAGAGTTTTGTCCCAGATATGATTGGTGGTGCTTCTCA
AGCTGATTTGGCTGTGTTGGTAATCTCTGCCAGGAAAGGAGAGTTTGAAACTAGATTTGAAAAAGGAGGGCAGAAAAGAG
AACATGCATTGTTGGCAAAGACAGCAGGGGTAAAACACTTAATTGTGCTGATCAATAAGATGGATGATCCAACAGTAAAC
TGAGCAAGGAGAGATATGAAGAATGTAAAGAGAAACTAGTGCCATTTTTGAAAAAAGTTGTCTTCAATCCCAAAAGGCAC
GTTCACTTTATGCCTGCTCAGGACTGACTGGAGCAAATGTTAAAGAGCAACCAGACTTCTGTCCTTGGTACATTGGATTA
CCATTTATTCCATATCTGGATAATTTGCCGAACTTCAATAGATCAGTTGATAGACCAATCAGGCTGCCAATTATGGATAA
ATACAAGGATATGGGCACTGTGGTGCTGGGAAAGCTGGGATCAGGATCTGCTTGCAAAGGCCAGCAGCTTGCAATGATGC
CAAATAAGCACAATGTGGAAGTTCTTGGAATCCTTTCCAACGATGTAGAAACGGATTCTGTAGCCCCAGGTGAAAACCTC
AAAATGAGACCGAAAGGAACTGAAGAAGAGGAGACTCTTCCAGGATTCATACTTTGTGATCCTAACAGTCTTTGTCATTC
TGGACGCACATTTGATGCCCAGATAGTGATTATAGAGCACAAATCCATCATCTGCCCAGGTTATAATGCGGTGCTGCGTA
TTCACACCTGTGTTGAAGAAGTCGAAACAACAGCCTTAATCTGCTTGGTATACAAAAAATCAGGAGAAAAAAGTAAGACT
TGGCCCCGTTTTGTGAAACAAGATCAAGCACGCATTGCTCGCTTAAGGACAGCAGGAACCAACTGCCTGGAGACCTTTAA
AGACTTCCCTCAGATGGGTCGTCTTACCTTACGAGATGAGGGTAAGACCATTGCAATTGGAAAAGTTCTGAAACTGGTTC
CAGAGAAAGAC

ORF - retro_ecab_739 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.29 %
Parental protein coverage: 87.74 %
Number of stop codons detected: 0
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalHPEESAQEMMEEEEEMPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYER
HPEESAQE.MEEEEE.PKP.SVVAPPG.PKKEHV.VVFIG..D.G.ST.GGQIM.LTGM.DKR.LEK.E.
RetrocopyHPEESAQETMEEEEEIPKPNSVVAPPGVPKKEHVHVVFIGRADVGESTMGGQIMSLTGMLDKRPLEKDEG
ParentalEAKEK-NRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAV
EAKEK...ETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHF.ILD.PGHKSFVP.MIGGASQADLAV
RetrocopyEAKEK<TGETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFAILDGPGHKSFVPDMIGGASQADLAV
ParentalLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVN-WSNERYEECKEKLVPFLKKVG
LVISARKGEFET.FEKGGQ.REHA.LAKTAGVKHLIVLINKMDDPTVN..S.ERYEECKEKLVPFLKKV.
RetrocopyLVISARKGEFETRFEKGGQKREHALLAKTAGVKHLIVLINKMDDPTVN<LSKERYEECKEKLVPFLKKVV
ParentalFNPKKDIHFMP-CSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYKDMGTVVL
FNPK...HFMP.CSGLTGAN.KEQ.DFCPWYIGLPFIPYLDNLPNFNRSVD.PIRLPI.DKYKDMGTVVL
RetrocopyFNPKRHVHFMP<CSGLTGANVKEQPDFCPWYIGLPFIPYLDNLPNFNRSVDRPIRLPIMDKYKDMGTVVL
ParentalGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDPNNLCH
GKL.SGS.CKGQQL.MMPNKHNVEVLGILS.DVETDSVAPGENLK.R.KG.EEEE.LPGFILCDPN.LCH
RetrocopyGKLGSGSACKGQQLAMMPNKHNVEVLGILSNDVETDSVAPGENLKMRPKGTEEEETLPGFILCDPNSLCH
ParentalSGRTFDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLR
SGRTFDAQIVIIEHKSIICPGYNAVL.IHTC.EEVE.TALICLV.KKSGEKSKT.PRFVKQDQ..IARLR
RetrocopySGRTFDAQIVIIEHKSIICPGYNAVLRIHTCVEEVETTALICLVYKKSGEKSKTWPRFVKQDQARIARLR
ParentalTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
TAGT.CLETFKDFPQMGR.TLRDEGKTIAIGKVLKLVPEKD
RetrocopyTAGTNCLETFKDFPQMGRLTLRDEGKTIAIGKVLKLVPEKD

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 .06 RPM 27 .80 RPM
SRP021940_cerebellum 0 .00 RPM 32 .41 RPM
SRP021940_embryo 0 .18 RPM 61 .94 RPM
SRP021940_placental_villous 0 .14 RPM 73 .61 RPM
SRP021940_synovial_membrane 0 .27 RPM 43 .81 RPM
SRP021940_testis 0 .00 RPM 48 .47 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_739 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_739 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_739 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095891 retrocopy
retro_amel_4,
Bos taurus ENSBTAG000000035772 retrocopies
retro_btau_1793, retro_btau_1840,
Canis familiaris ENSCAFG000000188561 retrocopy
retro_cfam_2072,
Callithrix jacchus ENSCJAG000000181911 retrocopy
retro_cjac_618,
Cavia porcellus ENSCPOG000000093811 retrocopy
retro_cpor_73,
Equus caballus ENSECAG00000021195 1 retrocopy
retro_ecab_739 ,
Echinops telfairi ENSETEG000000182491 retrocopy
retro_etel_1626,
Felis catus ENSFCAG000000222811 retrocopy
retro_fcat_1913,
Gorilla gorilla ENSGGOG000000040711 retrocopy
retro_ggor_2906,
Microcebus murinus ENSMICG000000141371 retrocopy
retro_mmur_28,
Myotis lucifugus ENSMLUG000000007921 retrocopy
retro_mluc_98,
Macaca mulatta ENSMMUG000000231781 retrocopy
retro_mmul_118,
Monodelphis domestica ENSMODG000000047281 retrocopy
retro_mdom_1420,
Mustela putorius furoENSMPUG000000145041 retrocopy
retro_mputfur_147,
Mus musculus ENSMUSG000000622031 retrocopy
retro_mmus_238,
Nomascus leucogenys ENSNLEG000000101991 retrocopy
retro_nleu_2705,
Oryctolagus cuniculus ENSOCUG000000047591 retrocopy
retro_ocun_1664,
Otolemur garnettii ENSOGAG000000070831 retrocopy
retro_ogar_100,
Pteropus vampyrus ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG000000059081 retrocopy
retro_shar_14,
Ictidomys tridecemlineatus ENSSTOG000000154061 retrocopy
retro_itri_109,
Tupaia belangeri ENSTBEG000000088732 retrocopies
retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta ENSTSYG000000138122 retrocopies
retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus ENSTTRG000000116301 retrocopy
retro_ttru_12,


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