RetrogeneDB ID:

retro_mmus_2234

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:3:35536881..35537800(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rpf2
Ensembl ID:ENSMUSG00000038510
Aliases:Rpf2, 2810470K21Rik, AU040229, AU043242, Bxdc1
Description:ribosome production factor 2 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914489]


Retrocopy-Parental alignment summary:






>retro_mmus_2234
ATGGATGCTTTGGACAAAGTTGTAAAGCCTAAAACTAAAAAGGCTAAGAGATTCCTTGAGAAGAGAGAACCGAAACTCAC
TGAGAACATTAAGAATACCATGCTGATTAAAGGCGGAAATGCAAATGCAACCGTGACACAAGTACTCAGAGACGTGTATG
CACTGAGGAAACCATATGGAGTTCTATATAAGAAGAAAAATATTACAAGACCATTTGAGGATTAGACATCACTGGAGTTC
TTTTCAAAGAAGTCAGACTGCTCTTTATTCATGTTTGGCTCCCATAACAAGAAGAGGCCAAATAACCTAGTAATAGGTTG
TATGTATGACTACCATGTGTTGGACATGATTGAATTAGGTATTGAGAAATTTGTGTCTCTAAAAGATGTTAAGACTAGTA
AGTGCCCCGAGGGAACAAAACCAATGTTGATATTTGCTGGTGATGATTTTGATGTAACAGAAGACTACAGAAGATTAAAA
AAATCTTCTTATTGATTTCTTCAGTGGCCCCACACTATTGAACGTCCAGCTGGATGGATTAGAGTATGTTCTGCAGTTCA
CTGCACTGAATGGGAAGGTTTACTTCCTAAGCTATAAGCTGCTGTTGAAGAAATCTGGGTGAAGAACACCACGAATTGAG
CTAGAAGAGATGGGACCATCACTGGACCTGGTTATGAGGAGGACACATCTAGCATCAGATGACCTTTATAAACTGTCCAT
GAAAGTGCCCAAGGCTCTCAAGCCAAAGAAGAGAAAGAATATCTCTCAGGATACTTTTGGCACAACATTTGGAAGGATTC
ATATGCAGAAGCAGGACTTAAGCAAACTACAAATGAGGAAAATGAAGTGGTTGAAGAAGCGACCTGCAGAGAATGGAGTA
GATGACCAGGGGGAAAAATCAAAGAGAATTAAGAAAAAT

ORF - retro_mmus_2234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.16 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMDALDKVLKPKTKRAKRFLEKREPKLTENIKNAMLIKGGNANATVTQVLRDMYALKKPYGVLYKKKNITR
MDALDKV.KPKTK.AKRFLEKREPKLTENIKN.MLIKGGNANATVTQVLRD.YAL.KPYGVLYKKKNITR
RetrocopyMDALDKVVKPKTKKAKRFLEKREPKLTENIKNTMLIKGGNANATVTQVLRDVYALRKPYGVLYKKKNITR
ParentalPFEDQTSLEFFSKKSDCSLFMFGSHNKKRPNNLVIGRMYDYHVLDMIELGIEKFVSLKDIKTSKCPEGTK
PFED.TSLEFFSKKSDCSLFMFGSHNKKRPNNLVIG.MYDYHVLDMIELGIEKFVSLKD.KTSKCPEGTK
RetrocopyPFED*TSLEFFSKKSDCSLFMFGSHNKKRPNNLVIGCMYDYHVLDMIELGIEKFVSLKDVKTSKCPEGTK
ParentalPMLIFAGDDFDVTEDFRRL-KNLLIDFFRGPTVSNVRLAGLEYVLHFTALNGKVYFRSYKLLLKKSGCRT
PMLIFAGDDFDVTED.RRL.KNLLIDFF.GPT..NV.L.GLEYVL.FTALNGKVYF.SYKLLLKKSG.RT
RetrocopyPMLIFAGDDFDVTEDYRRL>KNLLIDFFSGPTLLNVQLDGLEYVLQFTALNGKVYFLSYKLLLKKSG*RT
ParentalPRIELEEMGPSLDLVMRRTHLASDDLYKLSMKVPKALKPKKRKNISQDTFGTTFGRIHMQKQDLSKLQTR
PRIELEEMGPSLDLVMRRTHLASDDLYKLSMKVPKALKPKKRKNISQDTFGTTFGRIHMQKQDLSKLQ.R
RetrocopyPRIELEEMGPSLDLVMRRTHLASDDLYKLSMKVPKALKPKKRKNISQDTFGTTFGRIHMQKQDLSKLQMR
ParentalKMKGLKKRPAENGVDDQGKKSKRIKKN
KMK.LKKRPAENGVDDQG.KSKRIKKN
RetrocopyKMKWLKKRPAENGVDDQGEKSKRIKKN

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
SRP007412_brain 0 .00 RPM 8 .04 RPM
SRP007412_cerebellum 0 .04 RPM 5 .95 RPM
SRP007412_heart 0 .00 RPM 4 .95 RPM
SRP007412_kidney 0 .04 RPM 7 .99 RPM
SRP007412_liver 0 .03 RPM 5 .54 RPM
SRP007412_testis 0 .09 RPM 18 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_2234 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2234 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2234 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2234 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2234 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000039182 retrocopies
retro_cfam_1611, retro_cfam_903,
Callithrix jacchus ENSCJAG000000052126 retrocopies
retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473, retro_cjac_606, retro_cjac_933,
Cavia porcellus ENSCPOG000000067972 retrocopies
retro_cpor_332, retro_cpor_582,
Equus caballus ENSECAG000000171211 retrocopy
retro_ecab_782,
Erinaceus europaeus ENSEEUG000000061692 retrocopies
retro_eeur_454, retro_eeur_584,
Felis catus ENSFCAG000000015271 retrocopy
retro_fcat_1584,
Homo sapiens ENSG000001974981 retrocopy
retro_hsap_2425,
Gorilla gorilla ENSGGOG000000014691 retrocopy
retro_ggor_83,
Myotis lucifugus ENSMLUG000000056762 retrocopies
retro_mluc_485, retro_mluc_921,
Macaca mulatta ENSMMUG000000215321 retrocopy
retro_mmul_1903,
Mus musculus ENSMUSG00000038510 1 retrocopy
retro_mmus_2234 ,
Nomascus leucogenys ENSNLEG000000128543 retrocopies
retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus ENSOCUG000000160281 retrocopy
retro_ocun_831,
Pongo abelii ENSPPYG000000169252 retrocopies
retro_pabe_1788, retro_pabe_2464,
Pan troglodytes ENSPTRG000000185031 retrocopy
retro_ptro_1398,
Rattus norvegicus ENSRNOG000000005871 retrocopy
retro_rnor_2336,
Tupaia belangeri ENSTBEG000000171519 retrocopies
retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,


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