RetrogeneDB ID:

retro_rnor_459

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:1:90017381..90018499(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000020844
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Actb
Ensembl ID:ENSRNOG00000034254
Aliases:Actb, Actx
Description:Actin, cytoplasmic 1 Actin, cytoplasmic 1, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:P60711]


Retrocopy-Parental alignment summary:






>retro_rnor_459
ATGGAAGAAGAAATCGCCGCCCTCGTCATTGACAATGGCTCTGGCATGTGCAAAGCTGGCTTTACTGGGGACGACACCCT
CAGGGCCGTGTTTCCTTCCATCGTTGTGCGCCCCCGACACCAGGGCGTCATGGTGGGCATGGGCCAGAAAGACTCGTACG
TGGGTGATGAGGCCCAGAGCAAGAGGGGTATCCTGACCCTGAAGTACCCTATCGAGCACGGCATTGTCACCAACTGGGAT
GATGTGGAGAAGATCTGGCACCGCACCTACAACGAGCTGCGTGTGGCCCCTGAGGAGCACCCGGTGCTTCTGACCGAGGC
CCCCCTGAACCCTAAAGCTAACCGAGAGATGACGCAGATAATGTACGAAACCTTCAATACCCCGGCCATGTACGTGGCCG
TTCAGGCGGTGCTCTCCTTGTATGCATCTGGGCACACCACTGGCATTTTCATAGACTCTGGTGACGGGGTCACACACACA
GTGCCTATCTATAAGGGCTACGCCCTTCCCCACGCCATCTTGCGTCTGGACCTGGCTGGCTGGGACCTGACAGACTACCT
CATGAAGATCCTGACTGAACCGGACTACAGCTTTACCACCACTGCTGAGAGGGAAATTGTTCGTGACATAAAGGAGAACC
TGTGCTATGTTGCCCTGGATTTTGAGCAAGAAATGGCTACTGCTGCATTATCTTCCTCCTTGGAGAAGAGTTACGAGCTG
CCTGATGGTCAGGTGATCACCATCGGCAATGAGCGCTTCCGGTGTCCAGAGGCTCTCTTCCAGCCTTCCTTCCTGGGCAT
GGAGTCCTGTGGCATCCACGAGACCACCTTCAACTCCATCATGAAGTGCGATGTGGACATAGCAAAGACCTGTATGCCAA
CACAGTGCTGTCTGGTGGTAGCACCATGTATCCAGGCATTGCTGACAGGATGCAGAAGGAGATCACAGCCCTGGCACCCA
GCACAATGAAGATTAAGATCATTGCTCCCCCTGAGCGCAAGCACTCAGTCTGGATTGGCGGCTCCATCCTGGCCTCACTG
TCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATGACGAGTCAGGCCCCTCCATCGTCCACCGCAAATGCTTC

ORF - retro_rnor_459 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.82 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
M...IAALV.DNGSGMCKAGF.GDD..RAVFPSIV.RPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
RetrocopyMEEEIAALVIDNGSGMCKAGFTGDDTLRAVFPSIVVRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
ParentalIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
IEHGIVTNWDD.EKIWH.T.YNELRVAPEEHPVLLTEAPLNPKANRE.MTQIM.ETFNTPAMYVA.QAVL
RetrocopyIEHGIVTNWDDVEKIWHRT-YNELRVAPEEHPVLLTEAPLNPKANRE-MTQIMYETFNTPAMYVAVQAVL
ParentalSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
SLYASG.TTGI..DSGDGVTHTVPIY.GYALPHAILRLDLAG.DLTDYLMKILTE..YSFTTTAEREIVR
RetrocopySLYASGHTTGIFIDSGDGVTHTVPIYKGYALPHAILRLDLAGWDLTDYLMKILTEPDYSFTTTAEREIVR
ParentalDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
DIKE.LCYVALDFEQEMATAA.SSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
RetrocopyDIKENLCYVALDFEQEMATAALSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
ParentalSIMKCDVDI-RKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASL
SIMKCDVDI..KDLYANTVLSGG.TMYPGIADRMQKEITALAPSTMKIKIIAPPERK.SVWIGGSILASL
RetrocopySIMKCDVDI<SKDLYANTVLSGGSTMYPGIADRMQKEITALAPSTMKIKIIAPPERKHSVWIGGSILASL
ParentalSTFQQMWISKQEYDESGPSIVHRKCF
STFQQMWISKQEYDESGPSIVHRKCF
RetrocopySTFQQMWISKQEYDESGPSIVHRKCF

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 .22 RPM 855 .93 RPM
SRP017611_kidney 0 .07 RPM 1102 .49 RPM
SRP017611_liver 0 .00 RPM 363 .62 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_459 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_459 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_459 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 89 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066011 retrocopy
retro_amel_11,
Cavia porcellus ENSCPOG000000134671 retrocopy
retro_cpor_60,
Homo sapiens ENSG000000756246 retrocopies
retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus ENSGALG000000096211 retrocopy
retro_ggal_4,
Gorilla gorilla ENSGGOG0000000113318 retrocopies
retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Meleagris gallopavo ENSMGAG000000039602 retrocopies
retro_mgal_5, retro_mgal_6,
Macaca mulatta ENSMMUG000000111531 retrocopy
retro_mmul_135,
Mustela putorius furoENSMPUG000000166122 retrocopies
retro_mputfur_440, retro_mputfur_461,
Mus musculus ENSMUSG000000295807 retrocopies
retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
retro_oana_4, retro_oana_8,
Otolemur garnettii ENSOGAG000000083481 retrocopy
retro_ogar_2637,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000001733623 retrocopies
retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus ENSRNOG00000034254 10 retrocopies
retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459 , retro_rnor_935,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa ENSSSCG000000075851 retrocopy
retro_sscr_548,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


Copyright © RetrogeneDB 2014-2017