RetrogeneDB ID: | retro_rnor_2538 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 7:108495406..108497594(-) | ||
| 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_2538
AGGCTGTCCAGTCGTGCTCGGAAGAGGGCGGCCAAGAGGAGGTCAGGGTCTGTTGAAGTCCCTAAGCCAAATAAGTCTCC
TGGGATCAAAACATTGCCTGGAGAGTTACCCAAAGGCAGTCCAGGTTCGAGGTAAGAAGCGTCCAGCACCAATTCAAAAC
AGTGATGGGGATGAGGAGGAAGACTCTGAGGAAGAAGATGTGGTGACCCAGGGGGAACTTTGGGGCTCTGAAGACAGTAG
TGAATATATGGTGGACGACTATGGAGCAGACTCGGAGGATGAGGAGGAAAAGTTGTTGCCTATTGAAAGAGCTGCTCTGA
AGCAGAAGGCCCGGGACCCCGCAGATGGGACCCAGTGGAGTGAGGAGGACACTGATGAAGATGAAGGTGTTACCCCTGAG
TCCCACCCCAGAAAGGATGACAAAGCAGAGGGGGATTTGCAGATCAATGTGGAAGAGGAGGAAGCCTTCGTGCTGCCTCC
TGCTGGACAGATGGACCAGGATGCCCAGACTCCAGACCTGCAGCGAGTTCACAAGCGCATCCAGGATATAGTAGGAGTGC
TTTGGGATTTTGGGGCTCAGCGAGAGGAAGGCCGGTCTCGAACTGAGTATCTGAGTCAGCTTCAGAAGGATCTGGCCACC
TACTATTCTTATGGAGACTTCCTGTTGAGCAAGCTCATGGAGCTCTTCCCGCTGTCTGAGTTGATAGAGTTCTTAGAAGC
TAATGAGGTGCCCCGGCCAATCACCCTTCGGACCAACACCTTGAAAACCCGTCGCCGAGACCTTGCTCAGGCTCTGATCA
ATCGTGGGGTTAATCTGGATCCATTGGGAAAGTGGTCGAAGTCTGGACTTGTGGTATATGATTCTTCAGTGCCTATTGGT
GCTACTCCCGAGTACCTAGCTGGACACTATATGCTGCAGGGAGCTTCGAGCATGCTGCCTGTCATGGCCCTGGCACCTCA
GGAGCATGAGCGGATCTTGGACATGTGTTGTGCTCCCGGAGGGAAGACCAGCTACATAGCTCAGCTGATGAAGAACACGG
GTGTGATCCTTGCCAATGACGCCAATGCAGAGCAGCTCAAGAGTGTCGTGGGCAACCTGCACCGCTTGGGAGTCACCAAC
ACCATCGTCAGCCACTATGATGGGCGCCAGTTCCCCAAGGTGGTGGGCGGCTTTGATCGGGTGCTTCTGGACGCTCCTTG
CAGTGGCACAGGAGTCATCTCCAAAGACCCTGCTGTGAAGACGAACAAGGATGAGAAGGACATCCAGCGCTGTGCCCACC
TTCAGAAGGAATTGCTGCTCAGTGCTATAGACTCAGTCAACGCTGCCTCCAAGACCGGAGGCTACCTGGTCTACTGCACT
TGCTCCATTACGGTGGAAGAGAACGAGTGGGTGGTGGACTATGCCTTGAAGAAGAGGAATGTGCGGCTGGTGCCCACCGG
CCTGGACTTCGGGCAGGAAGGTTTCACCCGCTTCTGAGAAAGGCGCTTTCACTCCACTCTGCGGGCCACCCGACGCTTCT
ACCCTCACACTCACAATATGGATGGTTTCTTTATAGCCAAGTTCAAGAAATTTTCCAATTCTATCCCCCAGCCCCACTCA
GGAAACTCGGCAGCAGGTACTCCTACAGAACCTGACCTGAAGGGTCAGGTCACCCCAAAGTCTGAGAACAGTAGTCAGCC
CACCAAGAAAGCCCACGGGGCTGCAAAGGCAAAGCAAAAGTTAGTAGGGCAGCAACATTCCAAGAAGCCCTTCCAGAAGA
TGAATGGCATCTCCAAAGGGCCAGGCTTGCCCACTGAACCTTCTGTCCCAAATGTCCAAGTGTCTGCTAGGCCCCAGGAA
AGCAGTCTGTCTGATGTGAAACGGAAGAGGGCTGGAAAGCTGAAGCAGCGGGGACCGAAGCAGAGTGCCCCTCCCCCCAA
GATCGGGGACCTGGGGACACCTGCTATGCAGACTCCCTCTGAAATCAGTGCCACCCCAAGGCCTAAGTCCCCTGGGAAAG
CCAAAAAGAGAGAGGAAGTAAAGCAGGAGTTACCAGAGCAGCCTGCCAAGGGAACTGCTTCCCTGAAAGAAGACGCTGCC
CCCAAGAGACCCTCTGCCCCCACCACGGCTCACCACAGTTCCACCAGGCCCCCACCGGCAAAGAGGAGGAAATCTATGAC
CAAGGGCAGCAGCCAGCCACTGTTGTCT
ORF - retro_rnor_2538 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.36 % |
| Parental protein coverage: | 94.56 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RLSSRARKRAAKRRSGSVEVPKPNKSPGIKTLPGEL-PKGAVQVRGKKRPAPIQNSDGDEEEDSEEEDVV |
| RLSSRARKRAAKRRSGSVEVPKPNKSPGIKTLPGEL.PK.AVQVRGKKRPAPIQNSDGDEEEDSEEEDVV | |
| Retrocopy | RLSSRARKRAAKRRSGSVEVPKPNKSPGIKTLPGEL>PK-AVQVRGKKRPAPIQNSDGDEEEDSEEEDVV |
| Parental | TQGELWGSEDSSEDMVDDYGADSEDEEEKLLPIERAALKQKARDPADGTQWSEEDTDEDEGVTPESHPRK |
| TQGELWGSEDSSE.MVDDYGADSEDEEEKLLPIERAALKQKARDPADGTQWSEEDTDEDEGVTPESHPRK | |
| Retrocopy | TQGELWGSEDSSEYMVDDYGADSEDEEEKLLPIERAALKQKARDPADGTQWSEEDTDEDEGVTPESHPRK |
| Parental | DDKAEGDLQINVEEEEAFVLPPAGQTDQDAQTPDLQRVHKRIQDIVGVLRDFGAQREEGRSRTEYLSQLQ |
| DDKAEGDLQINVEEEEAFVLPPAGQ.DQDAQTPDLQRVHKRIQDIVGVL.DFGAQREEGRSRTEYLSQLQ | |
| Retrocopy | DDKAEGDLQINVEEEEAFVLPPAGQMDQDAQTPDLQRVHKRIQDIVGVLWDFGAQREEGRSRTEYLSQLQ |
| Parental | KDLATYYSYGDFLLSKLMELFPLSELIEFLEANEVPRPITLRTNTLKTRRRDLAQALINRGVNLDPLGKW |
| KDLATYYSYGDFLLSKLMELFPLSELIEFLEANEVPRPITLRTNTLKTRRRDLAQALINRGVNLDPLGKW | |
| Retrocopy | KDLATYYSYGDFLLSKLMELFPLSELIEFLEANEVPRPITLRTNTLKTRRRDLAQALINRGVNLDPLGKW |
| Parental | SKSGLVVYDSSVPIGATPEYLAGHYMLQGASSMLPVMALAPQEHERILDMCCAPGGKTSYIAQLMKNTGV |
| SKSGLVVYDSSVPIGATPEYLAGHYMLQGASSMLPVMALAPQEHERILDMCCAPGGKTSYIAQLMKNTGV | |
| Retrocopy | SKSGLVVYDSSVPIGATPEYLAGHYMLQGASSMLPVMALAPQEHERILDMCCAPGGKTSYIAQLMKNTGV |
| Parental | ILANDANAERLKSVVGNLHRLGVTNTIVSHYDGRQFPKVVGGFDRVLLDAPCSGTGVISKDPAVKTNKDE |
| ILANDANAE.LKSVVGNLHRLGVTNTIVSHYDGRQFPKVVGGFDRVLLDAPCSGTGVISKDPAVKTNKDE | |
| Retrocopy | ILANDANAEQLKSVVGNLHRLGVTNTIVSHYDGRQFPKVVGGFDRVLLDAPCSGTGVISKDPAVKTNKDE |
| Parental | KDIQRCAHLQKELLLSAIDSVNAASKTGGYLVYCTCSITVEENEWVVDYALKKRNVRLVPTGLDFGQEGF |
| KDIQRCAHLQKELLLSAIDSVNAASKTGGYLVYCTCSITVEENEWVVDYALKKRNVRLVPTGLDFGQEGF | |
| Retrocopy | KDIQRCAHLQKELLLSAIDSVNAASKTGGYLVYCTCSITVEENEWVVDYALKKRNVRLVPTGLDFGQEGF |
| Parental | TRFRERRFHPTLRATRRFYPHTHNMDGFFIAKFKKFSNSIPQPHSGNSAAGTPTEPDLKGQVTPKSENSS |
| TRF.ERRFH.TLRATRRFYPHTHNMDGFFIAKFKKFSNSIPQPHSGNSAAGTPTEPDLKGQVTPKSENSS | |
| Retrocopy | TRF*ERRFHSTLRATRRFYPHTHNMDGFFIAKFKKFSNSIPQPHSGNSAAGTPTEPDLKGQVTPKSENSS |
| Parental | QPTKKAHGAAKAKQQLVGQQHSKKPFQKMNGISKGPGLPTEPSVPNVQVSARPQESSLSDVKRKRAGKLK |
| QPTKKAHGAAKAKQ.LVGQQHSKKPFQKMNGISKGPGLPTEPSVPNVQVSARPQESSLSDVKRKRAGKLK | |
| Retrocopy | QPTKKAHGAAKAKQKLVGQQHSKKPFQKMNGISKGPGLPTEPSVPNVQVSARPQESSLSDVKRKRAGKLK |
| Parental | QRGPKQSAPPPKVGDLGTPAMQTPSEISATPRPKSPGKAKKREEVKQELPEQPAKGTASLKEDAAPKRLS |
| QRGPKQSAPPPK.GDLGTPAMQTPSEISATPRPKSPGKAKKREEVKQELPEQPAKGTASLKEDAAPKR.S | |
| Retrocopy | QRGPKQSAPPPKIGDLGTPAMQTPSEISATPRPKSPGKAKKREEVKQELPEQPAKGTASLKEDAAPKRPS |
| Parental | SPTTAHHSSTRPPPAKRRKSMTKGSSQPLLS |
| .PTTAHHSSTRPPPAKRRKSMTKGSSQPLLS | |
| Retrocopy | APTTAHHSSTRPPPAKRRKSMTKGSSQPLLS |
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 .50 RPM | 18 .19 RPM |
| SRP017611_kidney | 0 .07 RPM | 14 .58 RPM |
| SRP017611_liver | 0 .07 RPM | 14 .32 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2538 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2538 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2538 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,
|