RetrogeneDB ID:

retro_rnor_2431

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:7:18452484..18453291(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000009072
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Otub1
Ensembl ID:ENSRNOG00000021175
Aliases:None
Description:Ubiquitin thioesterase OTUB1 [Source:UniProtKB/Swiss-Prot;Acc:B2RYG6]


Retrocopy-Parental alignment summary:






>retro_rnor_2431
ATGGCGGCAGAGGAACCTCAGCAGCAGAAGCAGGAGCCGCTGGGCAGCGACTCCGAAGGTGTTAACTGTCTAGTCTATGA
TGAAGCCATTATGGCTCAGCAAGACCAGATTCAACAAGAGATTGCTGTGCAGAATCCTCTGGTGTCAGAGCGACTGGAAC
TCTCAGTTCTGTATAACGAGTATGCTGAGGATGACAACATCTACCAACAGAAGAACCTCCACAAAAAGTACTCCTACATA
CGGAAGACCAGGCCCGACAGGAACTGCTTCTATCCAGCGTTCGGCTTCTCCCACTTGGAGGCACTGCTCGATGACAGCAA
GGAACTGCAGCGGTTCAAAGCCATGTCTGCCAAGAGTAAAGAGGACCTGGTGTCCCAGGGCTTCACTGAATTCACAATTG
AGGACTTCCACAACACATTCATGGACCTTATCGAGCAGGTGGAGAAGCAGACCTCAGTAGCTGACCTGCTGGCCTCCTTC
AATGACCAGAGCACATCACACTACCTTGTGGTCTACCTGCGACTGCTCACCTCAGGCTACCTGCAGCGGAAGAGCAAGTT
CTTCGAGCATTTCATAGAGGGTGGCCAGACTGTTAAGGAGTTCTGCCAGCAGGAGGTGGAACCCATGTGCAAGGAGAGCG
ACCACATCCACATCATCGCCCTGGCCCAGGCCCTCAGTGTGTCCATCCAGGTGGAGTACATGGACCGCGGCGAGGGCGGC
ACCACCAACCCACACGTCTTCCCTGAGGGCTCTGAGCCCAAGGTCTACCTGCTCTACCGACCTGGACACTACGATATCCT
CTACAAA

ORF - retro_rnor_2431 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.57 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAEEPQQQKQEPLGSDSEGVNCLAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIYQQ
MAAEEPQQQKQEPLGSDSEGVNCL.YDEAIMAQQD.IQQEIAVQNPLVSERLELSVLY.EYAEDDNIYQQ
RetrocopyMAAEEPQQQKQEPLGSDSEGVNCLVYDEAIMAQQDQIQQEIAVQNPLVSERLELSVLYNEYAEDDNIYQQ
ParentalKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHN
K...LHKKYSYIRKTRPD.NCFY.AFGFSHLEALLDDSKELQRFKA.SAKSKEDLVSQGFTEFTIEDFHN
RetrocopyK--NLHKKYSYIRKTRPDRNCFYPAFGFSHLEALLDDSKELQRFKAMSAKSKEDLVSQGFTEFTIEDFHN
ParentalTFMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEP
TFMDLIEQVEKQTSVADLLASFNDQSTS.YLVVYLRLLTSGYLQR.SKFFEHFIEGG.TVKEFCQQEVEP
RetrocopyTFMDLIEQVEKQTSVADLLASFNDQSTSHYLVVYLRLLTSGYLQRKSKFFEHFIEGGQTVKEFCQQEVEP
ParentalMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHVFPEGSEPKVYLLYRPGHYDILYK
MCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHVFPEGSEPKVYLLYRPGHYDILYK
RetrocopyMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHVFPEGSEPKVYLLYRPGHYDILYK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 134 .59 RPM
SRP017611_kidney 0 .00 RPM 49 .06 RPM
SRP017611_liver 0 .00 RPM 21 .38 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2431 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2431 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2431 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000180841 retrocopy
Bos taurus ENSBTAG000000039671 retrocopy
Canis familiaris ENSCAFG000000147292 retrocopies
Equus caballus ENSECAG000000026211 retrocopy
Myotis lucifugus ENSMLUG000000122352 retrocopies
Mustela putorius furoENSMPUG000000133141 retrocopy
Pteropus vampyrus ENSPVAG000000170992 retrocopies
Rattus norvegicus ENSRNOG00000021175 1 retrocopy
retro_rnor_2431 ,
Sarcophilus harrisii ENSSHAG000000041561 retrocopy



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