RetrogeneDB ID:

retro_pvam_1426

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_8364:50545..52330(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPVAG00000011322
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GSPT1
Ensembl ID:ENSPVAG00000005009
Aliases:None
Description:G1 to S phase transition 1 [Source:HGNC Symbol;Acc:4621]


Retrocopy-Parental alignment summary:






>retro_pvam_1426
TCCTCGGCAGTGGCCGAGACCCAGCGTGAGCACATTAGCTCGGCCTTCAGCCGTCAGCTCAACGTCAACGCCAAACCCAT
CGTGCCAAACGTACACGCCGCGGAGTTCGTCCCGTCCTTCCTACGGAGCCCAGCCCAGCCGCAGACCCCCGGGGCGGATG
CCACCAGCATCGAGGAAACCTGTGCCGGTGCGGGCGACCCTCAAGGTAAAAGGCTGGGACGGGGGGCACCTGTGGAACAT
TCCAAAGAGGAACAGATAGTGTTGCGTGAAGGTTCCAATTCAGCCGTTACCATGGAACTTTCAGAACCTGTTGTAGAAAA
TGGAGAGGTGGAGATGGTCCTAGAGGAGTCATGGGAGCACAATAAAGAAGTAAGTGAAGCTGAGCCAGGGGGTAGTTCCT
TGGGAGATTCAGGGCCCCCAGAAGAAAGTGGCCAGGAAATGATGGAGAAAGAGGGAATGAGGAAATCTAAATCTGTGGTC
GTACCCTCAGGTGCTCCTAAAAAAGAACACGTAAATGTGGTATTCATTGGGCATGTAGATGCTGGCAAGTCAACCATTGG
AGGACAGATAATGTTTTTGACAGGAATGGTTGACAAAAGAACACTTGAGAAATATGAAAGAGAAGCTAAAGAAAAAAACA
GAGAAACTTGGTATTTGTCCTGGGCATTAGATACAAATCAGGAAGAACGAGAAAAGGGTAAAACAGTAGAAGTGGGTCGT
GCCTATTTTGAAACAGAAAAGAAACATTTCACAATTTTAGATGCCCCTGGCCACAAAAGTTTTGTCCCAAATATGATTGG
TGGTGCTTCTCAAGCTGATTTGGCTGTACTGGTCATTTCTGCCAGGAAAGGAGAGTTTGAAACTGGCTTTGAAAAAGGTG
GACAGACAAGAGAACATGCGATGTTGGCAAAAACAGCAGGGGTAAAATATTTAATAGTGCTTATTAATAAGATGGATGAC
CCCACCGTAAATTGGAGCAGCGAGAGATATGAAGAATGTAAAGAAAAATTGATGCCTTTTTTGAAAAGAGTTGGCTTCAG
TCCCAAAAAGGACATTCACTTTATGCCCTGCTCAGGGCTAACCGGGGCAAATATTAAAGAGCAATCAGATTTCTGCCCTT
GGTACACTGGGTTACCATTTATTCCATATTTGGATAATATGCCAAACTTCAGCAGATCAATCGATGGACCAATTAGACTG
CCAATTGTGGATAAGTACAAGGATATGGGCATTGTGGTTCTGGGAAAGCTGGAATCAGGATCTATTTTTAAAGGCCAGCA
GCTCGTGATGATGCCAAACAAGCACAATGTGGAAGTTCTTGGAATACTTTCTGATGATGCTGAAACTGATTATGTAGCCC
CCGGTGAAAATCTTAAAATCCGACTGAAGGGAATTGAAGAAGAAGAGATTCTTCCAGGATTCATACTTTGTGACCCTACT
AATCTTTGTCATTCTGGACGCACATTTGATGTTCAGATAGTGATTATTGAACACAAGTCCATCATCTGCCCAGGTTATAA
TGCGGTGCTGCACATACATACTTGTATTGAGGAAGTTGAGATAACAGCCTTAATCTCCTTGATAGATAAAAAATCTGGAG
AAAAAAGTAAGACGCGGCCCCGTTTCGTGAAACAAGATCAAGTGTGCATTGCCCGTTTAAGGACAGCGGGAACTATCTGC
CTTGAGACATTCAAAGATTTTCCTCAGATGGGTCGTTTTATTTTAAGAGATGAGGGTAAGACCATTGCAATTGGAAAAGT
TTTGAAACTGGTCCCAGAGAAAGAC

ORF - retro_pvam_1426 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.58 %
Parental protein coverage: 82.63 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalATAAAEAQREHLSAAFSRQLNVNAKPFVPNVHAAEFVPSFLRGPAQPAAPPAGAAANNH---GAGSGAG-
..A.AE.QREH.S.AFSRQLNVNAKP.VPNVHAAEFVPSFLR.PAQP..P.A.A........GAG...G.
RetrocopySSAVAETQREHISSAFSRQLNVNAKPIVPNVHAAEFVPSFLRSPAQPQTPGADATSIEETCAGAGDPQGK
Parental--GPSAPVEPSQEEQSLLCEGSNSAVSMELSEPVVENGETEMSPEESWEHKEEISEAEPGGGSLGDGRPP
..G..APVE.S.EEQ..L.EGSNSAV.MELSEPVVENGE.EM..EESWEH..E.SEAEPGG.SLGD..PP
RetrocopyRLGRGAPVEHSKEEQIVLREGSNSAVTMELSEPVVENGEVEMVLEESWEHNKEVSEAEPGGSSLGDSGPP
ParentalEENAQEMMEEEEEIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREA
EE..QEMME.E....K.KSVV.P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.LTGMVDKRTLEKYEREA
RetrocopyEESGQEMMEKEG-MRKSKSVVVPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMFLTGMVDKRTLEKYEREA
ParentalKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVI
KEKNRETWYLSWALDTNQEER.KGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVI
RetrocopyKEKNRETWYLSWALDTNQEEREKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVI
ParentalSARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPK
SARKGEFETGFEKGGQTREHAMLAKTAGVK.LIVLINKMDDPTVNWS.ERYEECKEKL.PFLK.VGF.PK
RetrocopySARKGEFETGFEKGGQTREHAMLAKTAGVKYLIVLINKMDDPTVNWSSERYEECKEKLMPFLKRVGFSPK
ParentalKDIHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYKDMGTVVLGKLES
KDIHFMPCSGLTGAN.KEQSDFCPWY.GLPFIPYLDN.PNF.RS.DGPIRLPIVDKYKDMG.VVLGKLES
RetrocopyKDIHFMPCSGLTGANIKEQSDFCPWYTGLPFIPYLDNMPNFSRSIDGPIRLPIVDKYKDMGIVVLGKLES
ParentalGSICKGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTF
GSI.KGQQLVMMPNKHNVEVLGILSDD.ETD.VAPGENLKIRLKGIEEEEILPGFILCDP.NLCHSGRTF
RetrocopyGSIFKGQQLVMMPNKHNVEVLGILSDDAETDYVAPGENLKIRLKGIEEEEILPGFILCDPTNLCHSGRTF
ParentalDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTI
D.QIVIIEHKSIICPGYNAVLHIHTCIEEVEITALI.L.DKKSGEKSKTRPRFVKQDQVCIARLRTAGTI
RetrocopyDVQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALISLIDKKSGEKSKTRPRFVKQDQVCIARLRTAGTI
ParentalCLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
CLETFKDFPQMGRF.LRDEGKTIAIGKVLKLVPEKD
RetrocopyCLETFKDFPQMGRFILRDEGKTIAIGKVLKLVPEKD

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






RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_1426 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSECAG000000211951 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 ENSPVAG00000005009 1 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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