RetrogeneDB ID:

retro_rnor_1289

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:17:23118341..23118763(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Pomp
Ensembl ID:ENSRNOG00000048470
Aliases:Pomp, RGD1305831
Description:proteasome maturation protein [Source:RefSeq peptide;Acc:NP_001094412]


Retrocopy-Parental alignment summary:






>retro_rnor_1289
ATGGATGCCAGAGGCCTTGGGTCGCAGCTGAAGGACAGGATTCCAGTTGCAGAACTCTCAGCCAGTGGACCCTTTGAGAG
TCATGATCTTCTCCGGAAAGGGTTTTCTTGTGTGCAAAGTGAACTTTTGCCCAGTCACCCTCTTGAATTATTCAAGAAAA
AAATTTCCAGCTCAACCAGGACAAGATGAACTTTTCCACCCTGAGGAACATCCAGGGTGTGTTTGCTCCCCTGAAGTGAC
AGATGGAGTTCAAGGCAGTGCAACAGGTTCAGCGTCTTCCGTTTCTTCCGAGCTCAAACCTCTTGCTGGATATTTTGAGG
GGCAACGATGAGACCACTGGTTTTGAGGATATTCTTAAGGATCCATCACAGAGTGAACTGATGGGCGAGCCTCACTTGAT
GGAATATAAGCTGGGCTTGCTG

ORF - retro_rnor_1289 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.22 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMNARGLGSQLKDSIPVTELSASGPFESHDLLR-KGFSCVKNELLPSHPLELS-EKNFQLNQDKMNFSTLR
M.ARGLGSQLKD.IPV.ELSASGPFESHDLLR.KGF...K....P...L..S.EKNFQLNQDKMNFSTLR
RetrocopyMDARGLGSQLKDRIPVAELSASGPFESHDLLR>KGFLVCKVNFCPVTLLNYS>EKNFQLNQDKMNFSTLR
ParentalNIQGLFAPLKLQMEFKAVQQVQRLPFLPSSNLSLDILRGNDETIGFEDILNDPSQSELMGEPHMMVEYKL
NIQG.FAPLK.QMEFKAVQQVQRLPFLPSSNL.LDILRGNDET.GFEDIL.DPSQSELMGEPH.M.EYKL
RetrocopyNIQGVFAPLK*QMEFKAVQQVQRLPFLPSSNLLLDILRGNDETTGFEDILKDPSQSELMGEPHLM-EYKL
ParentalGLL
GLL
RetrocopyGLL

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
SRP017611_brain 0 .07 RPM 0 .00 RPM
SRP017611_kidney 0 .00 RPM 0 .00 RPM
SRP017611_liver 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1289 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1289 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1289 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 34 parental genes, and 100 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000096711 retrocopy
retro_acar_56,
Ailuropoda melanoleuca ENSAMEG000000089611 retrocopy
retro_amel_965,
Bos taurus ENSBTAG000000140243 retrocopies
retro_btau_1392, retro_btau_1563, retro_btau_755,
Choloepus hoffmanni ENSCHOG0000001280712 retrocopies
retro_chof_1473, retro_chof_1715, retro_chof_1767, retro_chof_2191, retro_chof_2256, retro_chof_2360, retro_chof_2479, retro_chof_442, retro_chof_658, retro_chof_738, retro_chof_739, retro_chof_924,
Callithrix jacchus ENSCJAG000000194733 retrocopies
retro_cjac_2947, retro_cjac_3177, retro_cjac_4191,
Cavia porcellus ENSCPOG000000017103 retrocopies
retro_cpor_1465, retro_cpor_411, retro_cpor_630,
Dasypus novemcinctus ENSDNOG000000088484 retrocopies
retro_dnov_1744, retro_dnov_1919, retro_dnov_2264, retro_dnov_2301,
Equus caballus ENSECAG000000119511 retrocopy
retro_ecab_329,
Echinops telfairi ENSETEG000000124482 retrocopies
retro_etel_1043, retro_etel_718,
Felis catus ENSFCAG000000082355 retrocopies
retro_fcat_2020, retro_fcat_266, retro_fcat_525, retro_fcat_742, retro_fcat_834,
Homo sapiens ENSG000001329632 retrocopies
retro_hsap_2261, retro_hsap_4866,
Gorilla gorilla ENSGGOG000000153162 retrocopies
retro_ggor_1684, retro_ggor_3038,
Loxodonta africana ENSLAFG000000036651 retrocopy
retro_lafr_1113,
Macropus eugenii ENSMEUG000000154162 retrocopies
retro_meug_1570, retro_meug_1571,
Myotis lucifugus ENSMLUG000000103221 retrocopy
retro_mluc_53,
Macaca mulatta ENSMMUG000000000972 retrocopies
retro_mmul_1027, retro_mmul_2603,
Mustela putorius furoENSMPUG000000046903 retrocopies
retro_mputfur_1023, retro_mputfur_1447, retro_mputfur_366,
Mus musculus ENSMUSG000000296493 retrocopies
retro_mmus_1417, retro_mmus_2356, retro_mmus_3300,
Nomascus leucogenys ENSNLEG000000005723 retrocopies
retro_nleu_1285, retro_nleu_1440, retro_nleu_1998,
Oryctolagus cuniculus ENSOCUG000000101371 retrocopy
retro_ocun_1377,
Otolemur garnettii ENSOGAG000000060441 retrocopy
retro_ogar_1672,
Ochotona princeps ENSOPRG000000165172 retrocopies
retro_opri_459, retro_opri_833,
Procavia capensis ENSPCAG000000096801 retrocopy
retro_pcap_178,
Pongo abelii ENSPPYG000000052471 retrocopy
retro_pabe_3783,
Pan troglodytes ENSPTRG000000057451 retrocopy
retro_ptro_1601,
Pteropus vampyrus ENSPVAG000000000323 retrocopies
retro_pvam_262, retro_pvam_551, retro_pvam_813,
Rattus norvegicus ENSRNOG00000048470 2 retrocopies
retro_rnor_1289 , retro_rnor_2020,
Rattus norvegicus ENSRNOG000000492294 retrocopies
retro_rnor_1590, retro_rnor_1843, retro_rnor_2325, retro_rnor_625,
Sorex araneus ENSSARG000000011345 retrocopies
retro_sara_184, retro_sara_371, retro_sara_423, retro_sara_57, retro_sara_64,
Ictidomys tridecemlineatus ENSSTOG000000136872 retrocopies
retro_itri_1612, retro_itri_614,
Tupaia belangeri ENSTBEG0000001214913 retrocopies
retro_tbel_1015, retro_tbel_1278, retro_tbel_193, retro_tbel_2264, retro_tbel_3135, retro_tbel_3412, retro_tbel_3437, retro_tbel_346, retro_tbel_3491, retro_tbel_3861, retro_tbel_4172, retro_tbel_4342, retro_tbel_4708,
Tarsius syrichta ENSTSYG000000051214 retrocopies
retro_tsyr_1002, retro_tsyr_1693, retro_tsyr_1887, retro_tsyr_1984,
Tursiops truncatus ENSTTRG000000129244 retrocopies
retro_ttru_1166, retro_ttru_1465, retro_ttru_374, retro_ttru_577,
Vicugna pacos ENSVPAG000000013152 retrocopies
retro_vpac_266, retro_vpac_284,


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