RetrogeneDB ID: | retro_rnor_2003 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 4:192473238..192475001(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Nop2 | ||
| Ensembl ID: | ENSRNOG00000018453 | ||
| Aliases: | Nop2, Nol1 | ||
| Description: | putative ribosomal RNA methyltransferase NOP2 [Source:RefSeq peptide;Acc:NP_001178714] |
Retrocopy-Parental alignment summary:
>retro_rnor_2003
AGTCTTCTGGGATCAAAACCCAAAGGAGCAGTCCAGGTTCGAGGTAAGAAGCGCCCAGCACTAATTCAAAACAGTGATGG
GGACGAGGAGGAAGACTCTGAGGAAGAAGGTGTGGTGACCCAGGGGGAACTTTGGGGCTCTGAGGGCAGTAGTGAAGATA
TGGTGGATGACTATGGAACAGACTCGGAGGATGAGAAGGAAAAGTTGTTGCCTATTGAAAGAGCTGCTCTGAAGCCGAAG
GCCCGGGACCCCGCAGATGGGGCCCAGTGGAGTGAGGAGGACACTGATGACGATGAAGATGAAGGTGTTACCCCTGAGTC
CCACCCCAGAAAGGATGACAAAGCAGAGGGGGATTTTCAGATTAATGTAGAAGACGAGGAAGCCTTTGTGCTGCCTCCTG
CTAGAGAGATGGACCAGGATGCCCAGGCTCCAGACCTGCAGCGAGTTCACAAGTGCATCCAGGATATAGTAGGAGTGCTT
CAGGATTTTGGGGCTCAGTGAGAGGAAGGCCGGTCTCGAACTCAGTATCTGAGTCGGCTTCAGAAGGATCTGGCCACCTA
CTATTCTTATGGAGACTTCCTGTTGAGCAAGCTCATGGAGCTGTTTCCGCTGTCTGAGTTGATAGAGTTCTTAGAAGCTA
ATGAGGTGCCCTGGCCAATCACCCTTCGGACCAATACCTCCTTGAAAACCCATCGCTGAGACCTTGCTCAGGCTCTGATC
AATCGTGGGGTTAATCTGGATCCATTGGGAAAGTGGTCAAAGTCTGGGCTTGTGGTATATGATTCTTCCGTGCCTATTGG
TGCTACTCCCGAGTACCTAGCTGGACACTATATGCTGCAGGGAGCTTCGAGCATGCTGCCTGTCATGGCCCTGGCACCCC
AGGAGCATGAGTGGATCTTGGACATGTGTTGTGCTCCTGGAGGGAAGACCAGCTACATGGCTCAGCTGATGAAGAACACG
AGTGTGATCCTTGCCAATGATGCCAATGCAAAGCGGCTCAAGAGCATCGTGGGCAACCTGCACCGCTTGGGAGTCAACAA
CACCATCGTCAGCCACTATGATGGGCGCCAGTTCCCCAAGGTGGTGGGCAGCTTTGATCGAGTGCTTCTGGACGCTCCTT
GTAGTGGCACAGGAGTCATCTCCAAAGACCCTGCTGTGAAGACGAACAAGGATGAGAAGGACATCCAGCGCTGTGCCACC
TTCAGAAGGAATTGCTGCTCAGAGCTATAGACTCAGTCAACGCTGCCTCAAAGACCGGAGGCTACCTGGTCTACTGCACT
TGCTCCATTACGGTGGAAGAGAGCAAGTGGGTGGTGGACTATGCCTTGAAGAAGAGGAATATGCGGCTGGTGCCCCCCGG
CCTGGACTTCGGTCAGGAAGGTTTTACCCTCTTCCAAGAAAGGTGCTTTCACCCCACTCTGCGGGCCACCTGACGCTTCT
ACCCTCACATTCACAATATGGATGATTTCTTTATAGCTAAGTTCAAGAAATTTTCCAATTCTATTCCCCAGCCCCACTCA
GGAAACTCGGCAGCAGCTACTCCTACAGAACCTGACCTGAAGGTCACCTCAAAGTCTGAGAACAGTAGTCAGCCTACCAA
GAAAGCCCACGTGGCTGCAAAGGCAAAGCAGCAGTTAGTAGGGCAGCAACATACCAAGAAGCTTTTCCAGAAGATGAATG
GCATCTCCAAAGGGCCAGGCTTGCCCACTGAACCTTCTGTCCCAAATGTCCAAGTGTCTGCTAGGCCCGGAAAGCAGTCT
GTC
ORF - retro_rnor_2003 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.19 % |
| Parental protein coverage: | 76.04 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TLPGELPKGAVQVRGKKRPAPIQNSDGDEEEDSEEEDVVTQGELWGSEDSSEDMVDDYGADSEDEEEKLL |
| .L.G..PKGAVQVRGKKRPA.IQNSDGDEEEDSEEE.VVTQGELWGSE.SSEDMVDDYG.DSEDE.EKLL | |
| Retrocopy | SLLGSKPKGAVQVRGKKRPALIQNSDGDEEEDSEEEGVVTQGELWGSEGSSEDMVDDYGTDSEDEKEKLL |
| Parental | PIERAALKQKARDPADGTQWSEEDTD--EDEGVTPESHPRKDDKAEGDLQINVEEEEAFVLPPAGQTDQD |
| PIERAALK.KARDPADG.QWSEEDTD..EDEGVTPESHPRKDDKAEGD.QINVE.EEAFVLPPA...DQD | |
| Retrocopy | PIERAALKPKARDPADGAQWSEEDTDDDEDEGVTPESHPRKDDKAEGDFQINVEDEEAFVLPPAREMDQD |
| Parental | AQTPDLQRVHKRIQDIVGVLRDFGAQREEGRSRTEYLSQLQKDLATYYSYGDFLLSKLMELFPLSELIEF |
| AQ.PDLQRVHK.IQDIVGVL.DFGAQ.EEGRSRT.YLS.LQKDLATYYSYGDFLLSKLMELFPLSELIEF | |
| Retrocopy | AQAPDLQRVHKCIQDIVGVLQDFGAQ*EEGRSRTQYLSRLQKDLATYYSYGDFLLSKLMELFPLSELIEF |
| Parental | LEANEVPRPITLRTNT-LKTRRRDLAQALINRGVNLDPLGKWSKSGLVVYDSSVPIGATPEYLAGHYMLQ |
| LEANEVP.PITLRTNT.LKT.R.DLAQALINRGVNLDPLGKWSKSGLVVYDSSVPIGATPEYLAGHYMLQ | |
| Retrocopy | LEANEVPWPITLRTNTSLKTHR*DLAQALINRGVNLDPLGKWSKSGLVVYDSSVPIGATPEYLAGHYMLQ |
| Parental | GASSMLPVMALAPQEHERILDMCCAPGGKTSYIAQLMKNTGVILANDANAERLKSVVGNLHRLGVTNTIV |
| GASSMLPVMALAPQEHE.ILDMCCAPGGKTSY.AQLMKNT.VILANDANA.RLKS.VGNLHRLGV.NTIV | |
| Retrocopy | GASSMLPVMALAPQEHEWILDMCCAPGGKTSYMAQLMKNTSVILANDANAKRLKSIVGNLHRLGVNNTIV |
| Parental | SHYDGRQFPKVVGGFDRVLLDAPCSGTGVISKDPAVKTNKDEKDIQRCA-HLQKELLLSAIDSVNAASKT |
| SHYDGRQFPKVVG.FDRVLLDAPCSGTGVISKDPAVKTNKDEKDIQRCA.HLQKELLL.AIDSVNAASKT | |
| Retrocopy | SHYDGRQFPKVVGSFDRVLLDAPCSGTGVISKDPAVKTNKDEKDIQRCA<HLQKELLLRAIDSVNAASKT |
| Parental | GGYLVYCTCSITVEENEWVVDYALKKRNVRLVPTGLDFGQEGFTRFRERRFHPTLRATRRFYPHTHNMDG |
| GGYLVYCTCSITVEE..WVVDYALKKRN.RLVP.GLDFGQEGFT.F.ER.FHPTLRAT.RFYPH.HNMD. | |
| Retrocopy | GGYLVYCTCSITVEESKWVVDYALKKRNMRLVPPGLDFGQEGFTLFQERCFHPTLRAT*RFYPHIHNMDD |
| Parental | FFIAKFKKFSNSIPQPHSGNSAAGTPTEPDLKGQVTPKSENSSQPTKKAHGAAKAKQQLVGQQHSKKPFQ |
| FFIAKFKKFSNSIPQPHSGNSAA.TPTEPDLK..VT.KSENSSQPTKKAH.AAKAKQQLVGQQH.KK.FQ | |
| Retrocopy | FFIAKFKKFSNSIPQPHSGNSAAATPTEPDLK--VTSKSENSSQPTKKAHVAAKAKQQLVGQQHTKKLFQ |
| Parental | KMNGISKGPGLPTEPSVPNVQVSARPQESSL |
| KMNGISKGPGLPTEPSVPNVQVSARP...S. | |
| Retrocopy | KMNGISKGPGLPTEPSVPNVQVSARPGKQSV |
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 | 18 .19 RPM |
| SRP017611_kidney | 0 .00 RPM | 14 .58 RPM |
| SRP017611_liver | 0 .00 RPM | 14 .32 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2003 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2003 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2003 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000018453 | 3 retrocopies |
retro_rnor_2003 , retro_rnor_2538, retro_rnor_2775,
|