RetrogeneDB ID:

retro_itri_109

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393719.1:436240..438127(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000008532
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GSPT1
Ensembl ID:ENSSTOG00000015406
Aliases:None
Description:G1 to S phase transition 1 [Source:HGNC Symbol;Acc:4621]


Retrocopy-Parental alignment summary:






>retro_itri_109
ATGGATCCCGGCAGCAGCAGCAGCGATTCAGCACCCGACTGCTGGGATCAGGTGGACATGGAAGCCCCGGGTTCGGCCCC
GAGCGGGGATGGAATCTCCTCGGCAGTGGCCGAGGCCCCGCGCGAGCATCTCAGCTCGGCCTTCAGCCGCCAGCTCAACG
TCAACGCCAAACCCTTCGTGCCTAATGTACACGCCGCGGAGTTCGTGCCGTCCTTCCTGCGGGGTTCGGCACAGCCGCCC
ACCCCCCTGGCCGGCTCCAACAGCATTGACGAAATCTGCATCAGCGCGGGAGACCCTCAAGGTAAAAGCCTGGGACGGGG
GGCACCTGTGGAACCTTCCAAAGATGAACCTTTAGTGTCGTGTGAAGGTTCCAGTTCAGGCGTTACCATGGAACTTTCAG
AACCTGTTGTAGAAAATGGAGAGGTGGAAATGGTCCTAGAAGAATCATGGGAGCACAGTAAAGAAGTAAGTGAAGCAGAG
CCTGGGGGTTGTTCCTTGGGAGATTCAGGGCCCCCTGAAGAAAGTGGTCAGGAAATGATGGAGGAGAAAGAGGAAATAAG
AAAATCAAAATCTGTGGTCGTACCCTCAGGTGCTCCTAAGAAAGAACACGTAAACGTGGTCTTCATTGGGCATGTAGATG
CTGGCAAGTCAACCATTGGAGGACAGATCATGTTTTTAACTGGAATGGTTGACAAAAGGACACTTGAGAAATATGAACGA
GAAGCTAAGGAGAAAAACAGAGAAACTTGGTATTTGTCCTGGGCCTTAGATACAAATCAGGAAGAACGAGACAAGGGTAA
AACAGTAGAAGTGGGTCGTGCCTATTTTGAAACAGAAAAGAAACATTTCACAATTTTAGATGCTCCTGGCCACAAGAGTT
TTGTCCCAAATATGATTGGTGGTGCTTCTCAAGCTGATTTGGCTGTGCTAGTAATTTCTGCCAGAAAAGGAGAGTTTGAA
ACAGGATTTGAAAAAGGTGGACAGACGAGAGAACATGCAATGCTAGCCAAAACGGCAGGTGTGAAACATTTAATAGTGCT
TATTAATAAGATGGATGATCCCACGGTAAATTGGAGCAGCGAGAGATATGAAGAATGTAAAGAAAAACTGGTGCCCTTTT
TGAAAAAAGTCGGCTTCAGTCCGAAAAAGGACATTCACTTTATGCCCTGCTCAGGACTGACCGGAGCAAATATTAAAGAG
CAATCAGATTTCTGCCCTTGGTACACTGGATTACCATTTATTCCATATTTAGATAATTTGCCAAACTTCAACAGATCAAT
TGATGGACCAATTAGACTGCCAATTGTGGATAAGTACAAGGATATGGGCACCGTGGTCCTGGGAAAGCTGGAATCAGGAT
CCATTTTTAAAGGCCAGCAACTTGTGATGATGCCAAACAAGCACAGTGTAGAAGTTCTTGGAATACTTTCTGATGATACT
GAAACTGATTTTGTAGCCCCAGGTGAAAACCTGAAAATCAGACTGAAAGGAATTGAAGAAGAGGAGATTCTTCCAGGCTT
CATACTTTGTGACCCCAGTAATCTTTGCCATTCTGGACGCACATTTGATGTTCAGATAGTGATCATTGAGCACAAATCTA
TCATCTGCCCAGGTTATAATGCGGTGCTGCACATTCATACTTGTATTGAGGAAGTTGAGATAACAGCCTTAATCTCCTTG
GTAGACAAAAAATCAGGAGAAAAAAGTAAGACACGACCCCGTTTTGTGAAGCAAGATCAAGTGTGCATTGCCCGTTTAAG
GACAGCAGGAACTATTTGCCTCGAGACATTTAAAGATTTTCCTCAGATGGGTCGTTTTACCTTAAGAGATGAGGGTAAGA
CCATTGCAATTGGAAAAGTTCTGAAACTAGTCCCAGAAAAGGACTAA

ORF - retro_itri_109 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.51 %
Parental protein coverage: 99.81 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAPVEPSQEEQSL-CEGSNSSVSMELSEPVVENGETEMSPEESWEHKEEISEAEPGG---GDGRPPEESAQ
APVEPS..E....CEGS.S.V.MELSEPVVENGE.EM..EESWEH..E.SEAEPGG...GD..PPEES.Q
RetrocopyAPVEPSKDEPLVSCEGSSSGVTMELSEPVVENGEVEMVLEESWEHSKEVSEAEPGGCSLGDSGPPEESGQ
ParentalEMMEEEEEIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREAKEKNR
EMMEE.EEI.K.KSVV.P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.LTGMVDKRTLEKYEREAKEKNR
RetrocopyEMMEEKEEIRKSKSVVVPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMFLTGMVDKRTLEKYEREAKEKNR
ParentalETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKG
ETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKG
RetrocopyETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKG
ParentalEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHF
EFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWS.ERYEECKEKLVPFLKKVGF.PKKDIHF
RetrocopyEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSSERYEECKEKLVPFLKKVGFSPKKDIHF
ParentalMPCSGLTGANLKEQSDFCPWYNGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYKDMGTVVLGKLESGSICK
MPCSGLTGAN.KEQSDFCPWY.GLPFIPYLDNLPNFNRS.DGPIRLPIVDKYKDMGTVVLGKLESGSI.K
RetrocopyMPCSGLTGANIKEQSDFCPWYTGLPFIPYLDNLPNFNRSIDGPIRLPIVDKYKDMGTVVLGKLESGSIFK
ParentalGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIV
GQQLVMMPNKH.VEVLGILSDD.ETD.VAPGENLKIRLKGIEEEEILPGFILCDP.NLCHSGRTFD.QIV
RetrocopyGQQLVMMPNKHSVEVLGILSDDTETDFVAPGENLKIRLKGIEEEEILPGFILCDPSNLCHSGRTFDVQIV
ParentalIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
IIEHKSIICPGYNAVLHIHTCIEEVEITALI.LVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
RetrocopyIIEHKSIICPGYNAVLHIHTCIEEVEITALISLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETF
ParentalKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
KDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
RetrocopyKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_109 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_109 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG000000059081 retrocopy
retro_shar_14,
Ictidomys tridecemlineatus ENSSTOG00000015406 1 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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