RetrogeneDB ID:

retro_rnor_2856

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:X:117900009..117900729(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000043411
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_2856
ATGAAGGAATATATTGTTGTCCTTATTTTGAACAATAGCCCTAGCACGTGCAAAGCTGTCTTTTTGGGCGATGATGCTCC
CTAGGCCATTTTCCCCTTCAACCTGGGCCGTCCTGAGTCCCAACACATGATGGTGGGTATGGGTCAGAAGGACTCCTATG
TCAACAAGAGGGTTCAAAGAAAGAGAGGCACTCTGACTCTAAAATACCCCCACTGAACACGGCATTGCCACCTACTGGGA
CAATACGGAGAAGATCTTGCACTATAACTTCTACAACGAGCTTCGTTTGGCTCCAGAAGAGCACACTGTGCTGCTCACCA
AGGCTTCCCTGAACCTTAGGCCAACCGTAAAAAGATGACTCAGATCATGTTTGAGACCTTTAACACCCTAGCCATGTACG
TAACCATCAATTCAATGCTGTCCCTGTATGCCTCTGGTCCCACCAGTGACATTGTGATGTACTCTGGAGACAGGGTCACT
TACATTGTGCCCATCTATGAGGGCTATGCTGTCCCTGATGTCATCCTCCATTTGGACTTGACTGACTGGGACCCAACAGA
CTACCTCATGAAGATCCTGACCCAGAGTAGCTTCACACCCACAGTTGAGAGGGAAATCATGTGTAACATCAAAGAGAAGC
TGTACTGTGTTGACATAGACTCCAAGCAAGAGATGGACACTAACGCATCCTCTTCCTTCCTGAAGAAGAGCTATGAGCTG

ORF - retro_rnor_2856 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.57 %
Parental protein coverage: 64.53 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
M...I..L...N....CKA.F.GDDAP.A.FP...GRP..Q..MVGMGQKDSYV....Q.KRG.LTLKYP
RetrocopyMKEYIVVLILNNSPSTCKAVFLGDDAP*AIFPFNLGRPESQHMMVGMGQKDSYVNKRVQRKRGTLTLKYP
Parental-IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLN-PKANREKMTQIMFETFNTPAMYVAIQA
..EHGI.T.WD..EKI.H..FYNELR.APEEH.VLLT.A.LN.P.ANR.KMTQIMFETFNT.AMYV.I..
Retrocopy>TEHGIATYWDNTEKILHYNFYNELRLAPEEHTVLLTKASLN<P*ANRKKMTQIMFETFNTLAMYVTINS
ParentalVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREI
.LSLYASG.T..IVM.SGD.VT..VPIYEGYA.P..IL.LDL...D.TDYLMKILT....SFT.T.EREI
RetrocopyMLSLYASGPTSDIVMYSGDRVTYIVPIYEGYAVPDVILHLDLTDWDPTDYLMKILTQS--SFTPTVEREI
ParentalVRDIKEKLCYVALDFEQEMATAASSSSLEKSYEL
...IKEKL..V..D..QEM.T.ASSS.L.KSYEL
RetrocopyMCNIKEKLYCVDIDSKQEMDTNASSSFLKKSYEL

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 .00 RPM 855 .93 RPM
SRP017611_kidney 0 .00 RPM 1102 .49 RPM
SRP017611_liver 0 .00 RPM 363 .62 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2856 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2856 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2856 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
Cavia porcellus ENSCPOG000000134671 retrocopy
Homo sapiens ENSG000000756246 retrocopies
Gallus gallus ENSGALG000000096211 retrocopy
Gorilla gorilla ENSGGOG0000000113318 retrocopies
Loxodonta africana ENSLAFG000000091671 retrocopy
Meleagris gallopavo ENSMGAG000000039602 retrocopies
Macaca mulatta ENSMMUG000000111531 retrocopy
Mustela putorius furoENSMPUG000000166122 retrocopies
Mus musculus ENSMUSG000000295807 retrocopies
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
Otolemur garnettii ENSOGAG000000083481 retrocopy
Petromyzon marinus ENSPMAG000000041611 retrocopy
Pongo abelii ENSPPYG0000001733623 retrocopies
Rattus norvegicus ENSRNOG00000034254 10 retrocopies
Rattus norvegicus ENSRNOG000000367011 retrocopy
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
Sus scrofa ENSSSCG000000075851 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
Xenopus tropicalis ENSXETG000000251161 retrocopy



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