RetrogeneDB ID:

retro_rnor_2135

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:5:29486003..29486846(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000031491
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Rnps1
Ensembl ID:ENSRNOG00000008703
Aliases:None
Description:RNA-binding protein with serine-rich domain 1 [Source:UniProtKB/Swiss-Prot;Acc:Q6AYK1]


Retrocopy-Parental alignment summary:






>retro_rnor_2135
GCTCCTTCTCCTACTAAACGAAAAGACCACTCTGATGAGAAGTCCAAGGATCGATCTAAAGATAAAGGGGCCACTACAGA
GTCCAGTGAGAAGGATTGTGGAAGAGATAAGACTCTGAAGAGACGCAGTGCTTCAAGCAGAAGCAGCAGCACCAGGTCTA
GGTCCAATTCGACCTCCAGCTCGGGCTCCAGCACCAGCACCGGCTCAAGCAGTGGGTCTAGCTTGTCCTCTGTATCCAGC
CGCTCAACAAGCTCCAGCACATCCCGAAGCTCCAGTTCTAGCAGCAGCTCCTGCTTCCCAAGCCCTTTTGGGCGCAGACA
TGACAAAAGGCGGAGCTCCGGCTCCAAATCCGAACCACCTAAAAGAGATGAAAAAGAGAGGAAAAGGCGGAGTCCTTCAC
CTAAACCTACCAAAGTGCACATTGGGAGGCTCAGCAGGAATGTGACCAAGGATCACATCATGGAAATATTTTCTACTTAC
GGGAAAATTAAAATGATTGACATGCCTGTAGAAAGGATGCATCCTCATCTATCCAAAGGCTATGCGTATGTGGAATTTGA
GAATCCAGATGAAGCAGAGAAGGCACTGAAACACATGGATGGAGGACAAATTGATGGCCAAGAGATCACTGCTACTGCGG
TGTTGGCACCCTGGCCTGGTCCACCGCTTCAGCTATTCAGCCAACCCAGGAGAAAGCTTCCACCACCTCCCATGTGGCAT
AGGTCACCCCCACGGATGAGGAGAAGGTCTCGATCCCCAAGACGCAGGTCCCCTGTGCGAAGGAGGTCTCGATCCCCCGG
CCACAGCCGACACAGGAGCCGATCCAGTTCCAATTCCTCCCGA

ORF - retro_rnor_2135 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.41 %
Parental protein coverage: 92.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAPSPTKRKDRSDEKSKDRSKDKGTTKESSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGSSTSTGSS
APSPTKRKD.SDEKSKDRSKDKG.T.ESSEKD.GRDKT.KRRSASS.SSSTRSRS.ST............
RetrocopyAPSPTKRKDHSDEKSKDRSKDKGATTESSEKDCGRDKTLKRRSASSRSSSTRSRSNSTXXXXXXXXXXXX
ParentalSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKVH
.GSS.SS.SSRS.SSSTSRSSSSSSSS..PSP..RRHD.RR.S.SKS.PPKRDEKERKRRSPSPKPTKVH
RetrocopyXGSSLSSVSSRSTSSSTSRSSSSSSSSCFPSPFGRRHDKRRSSGSKSEPPKRDEKERKRRSPSPKPTKVH
ParentalIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT
IGRL.RNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT
RetrocopyIGRLSRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT
ParentalATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRRRHRSRSSSNSS
ATAVLAPWP.PP...FS.PRR.LPPPPMW.RSPPRMRRRSRSPRRRSPVRRRSRSPG..RHRSRSSSNSS
RetrocopyATAVLAPWPGPPLQLFSQPRRKLPPPPMWHRSPPRMRRRSRSPRRRSPVRRRSRSPGHSRHRSRSSSNSS
ParentalR
R
RetrocopyR

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 .00 RPM 75 .71 RPM
SRP017611_kidney 0 .00 RPM 42 .29 RPM
SRP017611_liver 0 .00 RPM 21 .05 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_2135 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2135 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2135 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000178611 retrocopy
retro_amel_194,
Bos taurus ENSBTAG000000099697 retrocopies
retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris ENSCAFG000000193971 retrocopy
retro_cfam_449,
Choloepus hoffmanni ENSCHOG000000048664 retrocopies
retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Callithrix jacchus ENSCJAG000000149692 retrocopies
retro_cjac_2127, retro_cjac_3377,
Cavia porcellus ENSCPOG000000020662 retrocopies
retro_cpor_363, retro_cpor_953,
Equus caballus ENSECAG000000232881 retrocopy
retro_ecab_524,
Felis catus ENSFCAG000000076901 retrocopy
retro_fcat_248,
Homo sapiens ENSG000002059371 retrocopy
retro_hsap_2911,
Gorilla gorilla ENSGGOG000000142751 retrocopy
retro_ggor_2016,
Macropus eugenii ENSMEUG000000088821 retrocopy
retro_meug_1996,
Myotis lucifugus ENSMLUG000000168083 retrocopies
retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta ENSMMUG000000192381 retrocopy
retro_mmul_794,
Monodelphis domestica ENSMODG000000158911 retrocopy
retro_mdom_1171,
Mus musculus ENSMUSG000000346811 retrocopy
retro_mmus_173,
Oryctolagus cuniculus ENSOCUG000000043872 retrocopies
retro_ocun_1544, retro_ocun_1745,
Otolemur garnettii ENSOGAG000000315821 retrocopy
retro_ogar_3241,
Pan troglodytes ENSPTRG000000313101 retrocopy
retro_ptro_1967,
Pteropus vampyrus ENSPVAG000000051051 retrocopy
retro_pvam_296,
Rattus norvegicus ENSRNOG00000008703 4 retrocopies
retro_rnor_1537, retro_rnor_2135 , retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii ENSSHAG000000169511 retrocopy
retro_shar_390,
Ictidomys tridecemlineatus ENSSTOG000000132001 retrocopy
retro_itri_1160,
Tupaia belangeri ENSTBEG000000090988 retrocopies
retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta ENSTSYG000000016291 retrocopy
retro_tsyr_957,
Tursiops truncatus ENSTTRG000000082207 retrocopies
retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,


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