RetrogeneDB ID:

retro_rnor_1456

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:19:40711196..40712293(-)
Located in intron of:ENSRNOG00000018382
Retrocopy
information
Ensembl ID:ENSRNOG00000018377
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Smarce1
Ensembl ID:ENSRNOG00000010676
Aliases:Smarce1, BAF57, RGD1304726
Description:SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 [Source:RefSeq peptide;Acc:NP_001020164]


Retrocopy-Parental alignment summary:






>retro_rnor_1456
CCGGGCACCAACAGCCGGGTCACGGCGTCCTCCGGCATTACAATCCCAAAGCCTCCAAAGCCACCAGATAAGCCGCTCAT
GCCCTACATGAGGTACAGCAGAAAGGTCTGGGACCAAGTAAAGCTTCCAACTCTGACCTAAAGTTGTGGGAGATTGGCAA
GATTATTGGTGGCATGTGGCGAGATCTCACTGATGAAGAGAAACAAGAATATGTAAACGAGCACGAAGCAGAAAAGATAG
AGTACAATGAATCTATGAAGGCCTATCACAATTCCCCTGCATACCTTGCGTATATTAATGCAAAAAGTCGTGCGGAAGCT
GCATTAGAGGAAGAAAGCCGACAGAGACAGTCGCGCATGGAGAAAGGAGAGCCTTACATGAGCATTCAGCCTGCTGAGGA
CCCAGACGATTATGATGATGGCTTTTCAATGAAGCATACAGCCACTGCCCGTTTCCAGAGAAACCACCGCCTCATCAGTG
AGATCCTCAGTGAGAGTGTGGTACCTGATGTGCGGTCGGTTGTCACAACAGTTAGAATGCAGGTCCTCAAGCGACAGGTC
CAGTCTTTAATGGTTCATCAGCGGAAACTAGAAGCAGAGCTTCTTCAGATAGAGGAACGACACCAGGAAAAGAAGAGGAA
ATTCCTGGAAAGCACAGACTCCTTTAACAATGAACTTAAAAGGCTGTGTGGTCCGCAGGTGGAAGTGGACATGGAGAAGA
TTGCAGCAGAGATCGCACAGGCGGAGGAGCAGGCCCGCAAAAGGCAGGAGGAGAGGGAGAAGGAGGCAGCCGAGCAAGCT
GAGCGCAGCCAGGGCAGCATCGCCCCCGAGGAAGAGCAAGTGGCGAACAAAGCTGAGGAGAAGGATGAGAGGAACATCCG
GATGGAGACAGAGGAGACACATCTTGAAGACACTGCGGAGAACCAGCAGAATGGTGAAGAAGGCATGTCTACTCCTGAGG
ACAAGGAGAGTGGGCAGGAGGGGGTTGACAGCATGGAGGTGGAAGGGACCAGTGACAGTAACACCGGCTCAGTGAGCAAC
AGCGCAACGGTGGAGGAGCAGCCCACAGACCCTGTGCCAGAAGATGAGAAGAAGGAG

ORF - retro_rnor_1456 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.57 %
Parental protein coverage: 97.6 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPPTPAPATASSGITIPKPPKPPDKPLMPYMRYSRKVWDQVK-ASNPDLKLWEIGKIIGGMWRDLTDEEKQ
P.T....TASSGITIPKPPKPPDKPLMPYMRYSRKVWDQVK.ASN.DLKLWEIGKIIGGMWRDLTDEEKQ
RetrocopyPGTNSRVTASSGITIPKPPKPPDKPLMPYMRYSRKVWDQVK<ASNSDLKLWEIGKIIGGMWRDLTDEEKQ
ParentalEYLNEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYD
EY.NE.EAEKIEYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYD
RetrocopyEYVNEHEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYD
ParentalDGFSMKHTATARFQRNHRLISEILSESVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQ
DGFSMKHTATARFQRNHRLISEILSESVVPDVRSVVTT.RMQVLKRQVQSLMVHQRKLEAELLQIEERHQ
RetrocopyDGFSMKHTATARFQRNHRLISEILSESVVPDVRSVVTTVRMQVLKRQVQSLMVHQRKLEAELLQIEERHQ
ParentalEKKRKFLESTDSFNNELKRLCGLKVEVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQGSIAPEEE
EKKRKFLESTDSFNNELKRLCG..VEVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQGSIAPEEE
RetrocopyEKKRKFLESTDSFNNELKRLCGPQVEVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQGSIAPEEE
ParentalQVANKAEEKKDEENIPMETEETHLEDTAENQQNGEEGTSTPEDKESGQEGVDSMEVEGTSDSNTGSESNS
QVANKAEE.KDE.NI.METEETHLEDTAENQQNGEEG.STPEDKESGQEGVDSMEVEGTSDSNTGS.SNS
RetrocopyQVANKAEE-KDERNIRMETEETHLEDTAENQQNGEEGMSTPEDKESGQEGVDSMEVEGTSDSNTGSVSNS
ParentalATVEEPPTDP-PEAEKKE
ATVEE.PTDP.PE.EKKE
RetrocopyATVEEQPTDPVPEDEKKE

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 .93 RPM 33 .29 RPM
SRP017611_kidney 2 .30 RPM 37 .26 RPM
SRP017611_liver 1 .21 RPM 18 .76 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_1456 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1456 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1456 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 82 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000160258 retrocopies
retro_cfam_1057, retro_cfam_1131, retro_cfam_1134, retro_cfam_1300, retro_cfam_1412, retro_cfam_1803, retro_cfam_2063, retro_cfam_2127,
Choloepus hoffmanni ENSCHOG000000087273 retrocopies
retro_chof_1245, retro_chof_482, retro_chof_573,
Callithrix jacchus ENSCJAG000000135734 retrocopies
retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Felis catus ENSFCAG000000096462 retrocopies
retro_fcat_234, retro_fcat_513,
Homo sapiens ENSG000000735845 retrocopies
retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla ENSGGOG000000118032 retrocopies
retro_ggor_1020, retro_ggor_931,
Microcebus murinus ENSMICG000000098214 retrocopies
retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus ENSMLUG000000046091 retrocopy
retro_mluc_1209,
Macaca mulatta ENSMMUG000000040053 retrocopies
retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furoENSMPUG000000146604 retrocopies
retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus ENSMUSG000000379355 retrocopies
retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys ENSNLEG000000019574 retrocopies
retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus ENSOCUG000000089811 retrocopy
retro_ocun_59,
Otolemur garnettii ENSOGAG000000016527 retrocopies
retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps ENSOPRG000000009851 retrocopy
retro_opri_731,
Pongo abelii ENSPPYG000000084564 retrocopies
retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes ENSPTRG000000229025 retrocopies
retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus ENSPVAG000000113551 retrocopy
retro_pvam_237,
Rattus norvegicus ENSRNOG00000010676 7 retrocopies
retro_rnor_1278, retro_rnor_1311, retro_rnor_1456 , retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri ENSTBEG0000000077010 retrocopies
retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,
Tursiops truncatus ENSTTRG000000138851 retrocopy
retro_ttru_1217,


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