RetrogeneDB ID:

retro_itri_1168

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393392.1:1220635..1221910(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000029243
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP4
Ensembl ID:ENSSTOG00000012011
Aliases:None
Description:retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]


Retrocopy-Parental alignment summary:






>retro_itri_1168
ATGGCTGACAAGGAAGCAGCCTTTGACCACACAGTGGAAGAACGTGTGATCAATGAGGAGTACAAAATATGGAAAAAGAA
CACCCCTTTTCTTTACGATTTGTTGATGACCCATGCTCTGGAGTGGTCCAGCCTAACAGCACAGTGGCTTCCAGATGTAA
CCAGACCAGAAGGAAAAGATTTCAGCATTCATCCACTTGTCCTGGGGACATCCACATCAGATGAGCAAAACCACCTTGTG
ATAGCCAGTGTACAGCTCCCTAATGATGATGCTCAATTTGATGTATCACACTACGACAGTGAGAAAGGAGAATTAGGAGG
TTTTGGCTCAGTTAGTGGGAAAATTGAAATAGAAATCAAGATCAACCAGGAAGGAGAAGTAAATAGGGCTCATTATATGC
CCCAGAACCCTTGCATCATTGCAACAAAGACTCCATCCAGTGATGTTCTTGTTTTTGACTATACAAAACATCCTTCTAAA
CCAGACCCTTCTGGAGAGTGCAACCCAGATTTGCGTCTCCGTGGACATCAGAAGGAAGGGTATGGGCTTTCTTGGAACCC
AAATCTCAGTGGGCACTTACTTAGTGCTTTAGATGACCATGCCATCTGCCTATGGGATATCAGTGTCATCCCAAAGGAAG
GAAAAGTGGTTGATGCGAAGACCATCTTTACAGGGCACACAGCAGAAGTAGAAGATGTTTCCTGGCATCTGCTCCATGAG
TCCCTGTTTGGGTCAGTTGCTGATGATCAGAAACTTATGATTTGGAATATTCGTTCAAACAATACTTCCAAACCAAGCCA
CTCAGTAGATGCTCACACTGCTGAAGTGAACTGCCTCTCTTTCAATCCTTATAGTGAGTTCATACTTGCCACAGGATCAG
CTGATAAGACTGTTGCCTTGTGGGATCTGAGAAATCTGAAACTTAAGTTGCATTCCTTTGAATCACATAAGGATGAAATA
TTTCAGGTTCAATGGTCACCTCACAATGAGACTATTCTGGCTTCTAGTGGTACTGATTGTAGACTGCATGTCTGGGATTT
AAGTAAAATTGGAGAAGAACAATCCCCAGAAGATGCAGAAGATGGCCCACCAGAAGTATTGTTTATTCATGGTGGTCACA
CTGCCAAGATATCTGATTTCTCCTGGAATCCCAATGAACCTTGGGTGATTTGTTCTGTATCAGAAGACAATATCATGCAA
GTGTGGAAGATGGCAGAGAACATCTATAATGATGAAGATCCTGAAGGAAGTGTGGATCCTGAAGGACAAGGATCC

ORF - retro_itri_1168 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.06 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGT
MADKEAAFD..VEERVINEEYKIWKKNTPFLYDL.MTHALEW.SLTAQWLPDVTRPEGKDFSIH.LVLGT
RetrocopyMADKEAAFDHTVEERVINEEYKIWKKNTPFLYDLLMTHALEWSSLTAQWLPDVTRPEGKDFSIHPLVLGT
ParentalHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCII
.TSDEQNHLVIASVQLPNDDAQFD.SHYDSEKGE.GGFGSVSGKIEIEIKIN.EGEVNRA.YMPQNPCII
RetrocopySTSDEQNHLVIASVQLPNDDAQFDVSHYDSEKGELGGFGSVSGKIEIEIKINQEGEVNRAHYMPQNPCII
ParentalATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAV
ATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSA.DDH.ICLWDIS..
RetrocopyATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSALDDHAICLWDISVI
ParentalPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLS
PKEGKVVDAKTIFTGHTA.VEDVSWHLLHESLFGSVADDQKLMIW..RSNNTSKPSHSVDAHTAEVNCLS
RetrocopyPKEGKVVDAKTIFTGHTAEVEDVSWHLLHESLFGSVADDQKLMIWNIRSNNTSKPSHSVDAHTAEVNCLS
ParentalFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKI
FNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTD.RL.VWDLSKI
RetrocopyFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDCRLHVWDLSKI
ParentalGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDP
GEEQSPEDAEDGPPE.LFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVW.MAENIYNDEDPEGSVDP
RetrocopyGEEQSPEDAEDGPPEVLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWKMAENIYNDEDPEGSVDP
ParentalEGQGS
EGQGS
RetrocopyEGQGS

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_1168 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1168 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 21 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000059042 retrocopies
retro_btau_1610, retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG000000010217 retrocopies
retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG000001625216 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000572361 retrocopy
retro_mmus_356,
Nomascus leucogenys ENSNLEG000000028056 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Petromyzon marinus ENSPMAG000000071891 retrocopy
retro_pmar_26,
Pongo abelii ENSPPYG000000015886 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG00000012011 1 retrocopy
retro_itri_1168 ,


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