RetrogeneDB ID:

retro_rnor_1673

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:2:210108093..210110219(-)
Located in intron of:ENSRNOG00000047767
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Zc3h11a
Ensembl ID:ENSRNOG00000002993
Aliases:Zc3h11a, RGD1308290
Description:zinc finger CCCH domain-containing protein 11A [Source:RefSeq peptide;Acc:NP_001041367]


Retrocopy-Parental alignment summary:






>retro_rnor_1673
ATACCTAATCAGGGAGAAGACTGCTATTTTTATTTCTATTCTACATGCACCAAGGGTGACAGCTGCCCATTCCGTCACTG
TGAAGCTGCACTAGGAAATGAAACTGTTTGCACACTGTGGCAGGAAGGTCATTGTTTTCGACAGGTGTGCAAATTTCGCC
ACATGGAAATTGACAAAAAACGAAGTGAAATTCCTTGTTATTGGGAAAACCAGCCAATGGGATGTCAAAAATTAAATTGC
ACTTTCCATCACAACAGAAGTCGTTATGTCGATGGACTGTTCCTACTTCCAAGCAAAACTGTGTTACCCACTGTGCCTGA
GTCACAAGAAGAGGAAGTAAAGACCGGCCAGCTCACGGTTCAACAGAACAAATTGTCTGTTCAGTCCAACCCCTCCCCTC
AGCTGCGGAGCGTGATGAAAGTGGAGAGTTCGGAAAACGTTCCCAGCCCCACATACCCTCCTGTCGTGATCAATGCTGCC
GATGATGATGAAGATGACAATGTTTTCTGAGGAGGGTGATGAGAGCAAAACACCTGCCCTGCAGCCAACAACTGACGCCC
ATAATGGACTACAAGTGGCCTCTACCCGCAAACCTGGAGCCAGTTTAAAGCCAGGTGACTCTTTGAATTTTGGAATAAAA
ACGCTTGAGGAAATTAAATCAAAGAAAATGAAGGAAAAATCCAAGAAGCAAGGTGAAGGCTCCTCGGGAATTTCCAGTGT
TTTACATCAGCCTTAGCCCAATCCAGGCCCTGAGGAGAATGTTCGGACTGTGGTGAGAACCGTAACTCTGTCAAGCAAAC
AAGAAGAGCCCTTGGTTAGACTGAGTCTTACTGAGAGACTGGGGAAACGAAAACTTCCAGGAGATGGTGACAGTGATCCC
CCATTAAAGCGAAGTCTTGCACAGAGACTGGGAAAAAAAAGTGGAAGCACCAGAAACTAACATTGATAAAGCACCAAAGA
AAGAGAGAGTTAATAAAACTGGTGAGATCCATGTTAAGACACTGGAAGAAATTCTTCTTGAAAGAGCCAGTCAGAAACGT
GGAGAATTGCAAACTAAACTAAAGACAGAAGAACCTTCAGGAGCTGAGGATTCTCCATCAGGAACAAAAAGTTCTTCAGT
GCGCATCAAAACCTTCTCTGAGGTCCTGGCTGAAAAGAAACATCGGCAGCAGGAAATGGAAAGACAGAAATCCAAAAAGG
ATACAAGTTGCCTCATGCTAACAGAAGATTCTGAAGTGAAAAAGACTGTGAGCCTGCCGACTGTTGCTGTTAGCAAAGGA
CAGCTTGAGGAGGAGCCTGCAGACAGAGCCAGGCCTATGCAGGAGGTGCATATTAAGACGCTAGAGGAAATTAAGCTGGA
AAAGGCCCTGAGGGTGCAGCAAAGCGCTGAGAGGAGTGGCAGCTCCCGGCCTCAAGCGGAGGCTGCCCCAGTGGCCAAGA
GGCTGCTGCGCATCACCAAGAGATCAGGTGCAAGAGAAGAGAAAAAACTTGAACTTGAGGACAGTGGTGGCGCTCCCTCT
CAGAGCAGTGTGACTAAGATGGGACTTAGTGAGACTTCAGATGAGACCATAAGTGATCCCACAAAACTTCCAGTCAACAG
ATGTGACATTGTCAAAGAGAAACACACACAGAGACAGCAAGAGAGAGGAGCATCACAAAAGGAGAAGCCAGCCTTGGCAT
CTGTGCGGACAGATGAGGCTTCTTACTATACCCGAGTGGTGGGGAAGCCGGTGCTCACTGCTGTATCGGGCGTCACTTGG
CCCTGGCAAAACGGCTCCCCACAGAGTCGTCCCAGAAAGGGGAGGTGGAGACCTCCGGGATTGGAGACTCAATACTGCAC
GTGAAGTGTGCGGCACAGACTCTGGAGAAAAGAGGTAAAGCCAAGCCCAAAGTAAATGTGAAGCCATCTGTGGTCAAGGT
TGTCTCAGCCCCCAAATTGGCTCCCAAGCGCAAGGCTGTGGAGGTGCACTCTGCTGTCATCGCAGCTGTGAAGCCGCTCA
GCTCCAGCAGTGTCCTGCAGGAAAGCCGCCAAGAAAGCAGCCGTGGCTGTTGTCCCACTCCTCTCTGAGGATAAATCCGT
CACTATGTCTGAGACAGAAAAACCGAAAGACAGTTCTGCGCTGTCT

ORF - retro_rnor_1673 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.94 %
Parental protein coverage: 90.39 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMPNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNETVCTLWQEGRCFRQVCRFRHMEIDKKRSEIPCYWEN
.PNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNETVCTLWQEG.CFRQVC.FRHMEIDKKRSEIPCYWEN
RetrocopyIPNQGEDCYFYFYSTCTKGDSCPFRHCEAALGNETVCTLWQEGHCFRQVCKFRHMEIDKKRSEIPCYWEN
ParentalQPMGCQKLNCAFHHNRSRYVDGLFLPPSKTVLPTVPESQEEEVKTSQLMVQQNKLSVQSNPCPQLRSVMK
QPMGCQKLNC.FHHNRSRYVDGLFL.PSKTVLPTVPESQEEEVKT.QL.VQQNKLSVQSNP.PQLRSVMK
RetrocopyQPMGCQKLNCTFHHNRSRYVDGLFLLPSKTVLPTVPESQEEEVKTGQLTVQQNKLSVQSNPSPQLRSVMK
ParentalVESSENVPSPTHPPVVINAADDDEDDDDQ-FSEEGDESKTPALQPTTDAHNGLRVASTRKPGASLKPGDS
VESSENVPSPT.PPVVINAADDDE..DD..FSEEGDESKTPALQPTTDAHNGL.VASTRKPGASLKPGDS
RetrocopyVESSENVPSPTYPPVVINAADDDE--DDN>FSEEGDESKTPALQPTTDAHNGLQVASTRKPGASLKPGDS
ParentalLNFGIKTLEEIKSKKMKEKSKKQGEGSSGMSSVLHQPQPNPGPEKENVRTVVRTVTLSSKQEEPLVRLSL
LNFGIKTLEEIKSKKMKEKSKKQGEGSSG.SSVLHQP.PNPGPE.ENVRTVVRTVTLSSKQEEPLVRLSL
RetrocopyLNFGIKTLEEIKSKKMKEKSKKQGEGSSGISSVLHQP*PNPGPE-ENVRTVVRTVTLSSKQEEPLVRLSL
ParentalTERLGKRKLPGGGDNDPPLKRSLAQRLGKK-VEAPETNIDKAPKKDEQERVNKTGEIHVKTLEEILLERA
TERLGKRKLPG.GD.DPPLKRSLAQRL....VEAPETNIDKAPKK...ERVNKTGEIHVKTLEEILLERA
RetrocopyTERLGKRKLPGDGDSDPPLKRSLAQRLXXX>VEAPETNIDKAPKK---ERVNKTGEIHVKTLEEILLERA
ParentalNQKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSEV
.QKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSEV
RetrocopySQKRGELQTKLKTEEPSGAEDSPSGTKSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLMLTEDSEV
ParentalKKTVSLPTVAVSKGQLEEEPAGRARPMQEVHIKTLEEIKLEKALRVQQSAERSGSSRPQAEAAPVAKRLL
KKTVSLPTVAVSKGQLEEEPA.RARPMQEVHIKTLEEIKLEKALRVQQSAERSGSSRPQAEAAPVAKRLL
RetrocopyKKTVSLPTVAVSKGQLEEEPADRARPMQEVHIKTLEEIKLEKALRVQQSAERSGSSRPQAEAAPVAKRLL
ParentalRITKRSGTREEKKLELEDNGGAPSQSSVTKMGVSETSDETISDPTKLPVNRCDIVKEKHTQRQQERGASQ
RITKRSG.REEKKLELED.GGAPSQSSVTKMG.SETSDETISDPTKLPVNRCDIVKEKHTQRQQERGASQ
RetrocopyRITKRSGAREEKKLELEDSGGAPSQSSVTKMGLSETSDETISDPTKLPVNRCDIVKEKHTQRQQERGASQ
ParentalKEKPALASVRTDEASYYTRVVGKPVLTAVSGVT-RHLAKRLPTESSQKGEVETSGIGDSILHVKCAAQTL
KEKPALASVRTDEASYYTRVVGKPVLTAVSGVT...LAKRLPTESSQKGEVETSGIGDSILHVKCAAQTL
RetrocopyKEKPALASVRTDEASYYTRVVGKPVLTAVSGVT<LALAKRLPTESSQKGEVETSGIGDSILHVKCAAQTL
ParentalEKRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES-PAKK-AAVKVRKILG
EKRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES.P..K.AAV.V...L.
RetrocopyEKRGKAKPKVNVKPSVVKVVSAPKLAPKRKAVEVHSAVIAAVKPLSSSSVLQES<PPRK<AAVAVVPLLS
ParentalYPRSPTMPKDSSALSSAQAS
...S.TM........S...S
RetrocopyEDKSVTMSETEKPKDSSALS

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 48 .89 RPM
SRP017611_kidney 0 .00 RPM 52 .69 RPM
SRP017611_liver 0 .00 RPM 47 .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_1673 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1673 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1673 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000586732 retrocopies
retro_hsap_3481, retro_hsap_508,
Monodelphis domestica ENSMODG000000011841 retrocopy
retro_mdom_1449,
Mus musculus ENSMUSG000000264642 retrocopies
retro_mmus_3323, retro_mmus_564,
Otolemur garnettii ENSOGAG000000002431 retrocopy
retro_ogar_3250,
Pan troglodytes ENSPTRG000000018765 retrocopies
retro_ptro_2980, retro_ptro_2981, retro_ptro_2991, retro_ptro_380, retro_ptro_382,
Rattus norvegicus ENSRNOG00000002993 3 retrocopies
retro_rnor_1570, retro_rnor_1673 , retro_rnor_602,


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