RetrogeneDB ID:

retro_rnor_1439

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:19:3783762..3785011(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Fus
Ensembl ID:ENSRNOG00000023360
Aliases:None
Description:RNA-binding protein FUS [Source:RefSeq peptide;Acc:NP_001012137]


Retrocopy-Parental alignment summary:






>retro_rnor_1439
GGCTATGGGACTCAGTCATCTCCCCAGGGATATGGTTCCACTGGTGGATGGCAGCAGCCCAAGTTCCCAGTGTTCTTATG
GGCACCAGTCCTCCTATCCTGGCTATGGCCAAAAATCAGCTCCTAGCAGCACCTCTGGAAATTATGGTGGCAGTTCTCAG
AGCAGCAGCTATGGGCAGCCCCAGAGCAGAGGCAACAGTCTGGCTATAGTGAACAGCAACAAAGCTCCTAGAACCCACCT
CAGGGTTATGGACAACAGAACCTATACAACAGCAGCAGTGGAGGTGGTAGAGTGGGTGGTGGAGGCAACTAGGGCCAAGA
TCAGTCCTCTATGAGTGGTGGTGGTGGCTGTGGTGGTTACAGCAATCAGGATCAGAGTGATGGCAGTGGTGGTGGCTACA
GGAGTGGCTATGAACCCAACGGCCATGAAGGTGGCAGAGGAGGCAGAGGCAGCATGGGCAGAAGTGACCATGGTGGCTTT
AATAAATTTGGTGGTCCTTGGGATCAAGGATCTCGTCATGATTCTGAACAGGACACTTCAGACAACAATACCATCTTCAT
GCAAGGCCGAGGTGAGAATGTTACAATTGAACCTTTGTCTAATTACTTTAAGCAGATTGGAATTATTAAGACAAACAAGA
AAACTGGACAGCCTATGATTAATTTGTATACAGACAGGGAAACTGGGAATTTGAAGGGTGAGGCAACAGTCTCATTTGTT
AACCTACCTCCTGCTAAAGCTGTAATCGACTAGTTCGATGGTAAATGATTCTCTGTGAATCCTATTAAAGTTTCACTTGC
TACTCACCAAGCTGACATCAATTGGTGTGGTGGAAATGGTTGTGAAGGCTGAGGTTGAGGAGGACACATGGGCCATGGAA
ACTATGGAGGTGGCGGTGGCCAGGGAGGATTCCCCAGTGGGGGAGGTGGAGTTGGAGGACAGTGATGTGCTGGGGACTGG
ATGTGTCCTAATTCTAAATGTGAGAACATGAACTTCCTTTGGAGAAATGAAAGCAAATAGTGTAAGGCACCTAAGCTAGA
TTGTCCAGGAGGGGGACCAGGAGCCTCTCATATGTGGGCAAACTATGGAGATGATCCACAAGACAGAGGAGGATATGATC
AGGGTGTCTAATGGGCAAAAGAGGGGACCTTGGGGTTTTCAAAGGGGGCCTGGTGGTGCAGACAGAAGTGGATTTGTCCC
TGGCAAGATGGACTCCATGGCTGAGCCCAGACAGGATCACCATGACAGG

ORF - retro_rnor_1439 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.86 %
Parental protein coverage: 80.5 %
Number of stop codons detected: 8
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalGYGQQPAPSSTSGSYG-GSSQSS--SYGQPQS-GGYGQQSGYGGQQQSYG--QQQSSYNPPQGYG-QQNQ
GYG.Q..P.......G.GSS.SS..SYG...S..GYGQ.S........YG...Q.SSY..PQ..G.QQ..
RetrocopyGYGTQSSPQGYGSTGG>GSSPSSQCSYGHQSSYPGYGQKSAPSSTSGNYGGSSQSSSYGQPQSRG<QQSG
ParentalYNSSSGGGGGGGGGNYGQDQ--SSMSGGG--GGGGYGNQDQSGGGGGGYGGGQQDRGGRGRGGGGGYNRS
Y............G.YGQ.....S.SGGG..GGGG...QDQS...GGG..GG.........G.GGGY...
RetrocopyYSEQQQSS*NPPQG-YGQQNLYNSSSGGGRVGGGGN*GQDQSSMSGGGGCGGYSNQD-QSDGSGGGYR--
ParentalSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSRHDSEQDNSDNNTIFVQGLGENVTIESVADYF
..GYEP.G..GGRGGRG.MG.SD.GGFNKFGGP.DQGSRHDSEQD.SDNNTIF.QG.GENVTIE....YF
Retrocopy-SGYEPNGHEGGRGGRGSMGRSDHGGFNKFGGPWDQGSRHDSEQDTSDNNTIFMQGRGENVTIEPLSNYF
ParentalKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF
KQIGIIKTNKKTGQPMINLYTDRETG.LKGEATVSF...P.AKA.ID.FDGK.FS.NPIKVS.AT..AD.
RetrocopyKQIGIIKTNKKTGQPMINLYTDRETGNLKGEATVSFVNLPPAKAVID*FDGK*FSVNPIKVSLATHQADI
ParentalNRGGGNGRGGRGRGGPMGRGGYGGGGSGGGGRGGFPSGGGGGGGQQRAGDWKCPNPTCENMNFSWRSECN
N..GGNG..G.G.GG.MG.G.YGGGG....G.GGFPSGGGG.GGQ..AGDW.CPN..CENMNF.WR.E..
RetrocopyNWCGGNGCEG*G*GGHMGHGNYGGGG----GQGGFPSGGGGVGGQ*CAGDWMCPNSKCENMNFLWRNESK
ParentalQCKAPKPDGPGGGPGGSHMGGNYGDDRRGRGGYDR-GGYRGRGGDRG-GFRGGRGGGDRGGFGPGKMDSR
.CKAPK.D.PGGGPG.SHM..NYGDD...RGGYD..G...G..GD.G.GF..G.GG.DR.GF.PGKMDS.
Retrocopy*CKAPKLDCPGGGPGASHMWANYGDDPQDRGGYDQ<GCLMGKRGDLG<GFQRGPGGADRSGFVPGKMDSM
ParentalGEHRQDRRER
.E.RQD...R
RetrocopyAEPRQDHHDR

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 118 .63 RPM
SRP017611_kidney 0 .00 RPM 70 .90 RPM
SRP017611_liver 0 .00 RPM 51 .17 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1439 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1439 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1439 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Macropus eugenii ENSMEUG000000009681 retrocopy
Myotis lucifugus ENSMLUG000000048063 retrocopies
Macaca mulatta ENSMMUG000000196371 retrocopy
Mus musculus ENSMUSG000000307952 retrocopies
Rattus norvegicus ENSRNOG00000023360 4 retrocopies



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