RetrogeneDB ID:

retro_rnor_2034

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:4:6497089..6497674(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000008946
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Chp
Ensembl ID:ENSRNOG00000004742
Aliases:Chp1, Chp, Wrch2
Description:Calcineurin B homologous protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P61023]


Retrocopy-Parental alignment summary:






>retro_rnor_2034
CTGGGGTCTCGGGCCTCCACGTTACTGCGGGACGAAGAGCTCGAGGAGATCAAGAAGGAGACTGGCTTTTCCCACAGTCA
GATCACACGCCTGTACAGCCGCTTCACCAGCCTGGACAAAGGGGAGAACGGAACTCTCAGCCGGGAAGATTTCCAGAGGA
TTCCAGAACTTGCCATCAACCCACTGGGGGACCGGATCATCAATGCCTTCTTCTCAGAGGGAGAGGATCAGGTAAACTTC
CGAGGATTCATGAGAACTTTGGCTCATTTCCGACCCATTGAGGATAACGAAAAGAGCAAAGATGTGAATGGACCGGAACC
CCTCAACAGCCGGAGCAACAAACTGCACTTTGCTTTCAGACTTTATGACTTGGATAAAGATGACAAGATCTCCCGCGATG
AGCTGTTACAGGTACTGCGAATGATGGTCGGAGTGAATATCTCAGATGAGCAGCTGGGCAGTATTGCAGACAGGACCATC
CAGGAGGCTGACCAAGATGGAGACAGTGCCATATCTTTTACAGAATTTGTTAAGGTTTTGGAGAAGGTGGATGTAGAACA
GAAGATGAGCATCCGATTTCTTCAC

ORF - retro_rnor_2034 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.49 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF
.GSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF
RetrocopyLGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF
ParentalFSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLR
FSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLR
RetrocopyFSEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLR
ParentalMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
MMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH
RetrocopyMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFLH

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 39 .04 RPM
SRP017611_kidney 0 .14 RPM 42 .78 RPM
SRP017611_liver 0 .00 RPM 28 .64 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2034 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2034 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2034 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000095251 retrocopy
Cavia porcellus ENSCPOG000000105772 retrocopies
Homo sapiens ENSG000001874462 retrocopies
Gorilla gorilla ENSGGOG000000073122 retrocopies
Macaca mulatta ENSMMUG000000170922 retrocopies
Mus musculus ENSMUSG000000140774 retrocopies
Nomascus leucogenys ENSNLEG000000034654 retrocopies
Procavia capensis ENSPCAG000000054191 retrocopy
Pongo abelii ENSPPYG000000063702 retrocopies
Pan troglodytes ENSPTRG000000069422 retrocopies
Rattus norvegicus ENSRNOG00000004742 2 retrocopies
retro_rnor_2034 , retro_rnor_2223,
Rattus norvegicus ENSRNOG000000432101 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000145031 retrocopy



Copyright © RetrogeneDB 2014-2017