RetrogeneDB ID: | retro_rnor_2238 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 5:101415034..101415871(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dkc1 | ||
| Ensembl ID: | ENSRNOG00000048151 | ||
| Aliases: | Dkc1, Nap57 | ||
| Description: | H/ACA ribonucleoprotein complex subunit 4 [Source:RefSeq peptide;Acc:NP_596910] |
Retrocopy-Parental alignment summary:
>retro_rnor_2238
GCTGGCACCTACATTCGGACACTATGTGTACACCGTGGCTTGTTACTTGGAGTTGGTGGTCAGATGCAGGAACTTTGGAG
GGTGCGTTCTGGAGTCATGAGTGAAAAGGACCACACGGTGATGATGCATGAAGTACTTGATGCTCAGTGGCTGTATGATA
ACCGTAAGGATGAGAGTTACTTGCAGCTTGTTTACCATTTGGAAAAGCTGTTGACATCACATAAACATCTGGCTATGAAA
GATGAATGCAGTGGATGCAATCTGCTAGGGGGCAGAGATCATGCTTCCTGGTGTTCTTCAATATGAGGATGACATTAAGG
TCAACCAGGAGATTGTGGTCATTACCACTAAGGGGGAAGTTATCTGCATGGCTATCACATTGATGACTACAGCAGTGATT
TCTACCTGTGACCATGGTATAATAGGCAAGATAAAGAGGGTGATCATGGTAAGAGACACTTATCCTTAAAAGTGGGGTTT
AGGTCCAAAGGCAAGTCAGAAGAGGATGATGACCAAGCAAGGCCTTCTGGACAAGCATGGCAAACCCACAAACAGTACCC
CTGCCACATAGAAAAAGGATTTCATTGCCTATGATTCTGGCAAGAAAGCACTGGTTGCTGAAGCAATAAAACTCCTCAGC
TAGCTGCTGAAGCAGTGAACCTCATAAAACGGAAGCTGGATAGTGAGAATGAAAGTGGTGAGACCTCTTCAACAGTACCC
AGTTGAAGAAGGAAAAGGAGAATTAGAAGAAGGATTAAAAAGTCCAAAATGCTGCTAGAAAGTGGTGGCGATGCTGGAGA
TGGGGACAGCCATACTACCAAAAAGAAAAGAAGCAGG
ORF - retro_rnor_2238 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.48 % |
| Parental protein coverage: | 55.01 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVVGERDHMVTMHDVLDAQYLYDHHRDESYLRRVVFPLEK |
| AGTYIRTLCVH.GLLLGVGGQMQEL.RVRSGV..E.DH.V.MH.VLDAQ.LYD...DESYL...V..LEK | |
| Retrocopy | AGTYIRTLCVHRGLLLGVGGQMQELWRVRSGVMSEKDHTVMMHEVLDAQWLYDNRKDESYLQ-LVYHLEK |
| Parental | LLTSHKRLVMKD-SAVNAICYGAKIMLPGLLRYEDGIEVNQEVVVITTKGEAVCVAIALMTTAVISTCDH |
| LLTSHK.L.MKD..AV.AIC.GA.IMLPG.L.YED.I.VNQE.VVITTKGE..C.AI.LMTTAVISTCDH | |
| Retrocopy | LLTSHKHLAMKD>NAVDAIC*GAEIMLPGVLQYEDDIKVNQEIVVITTKGEVICMAITLMTTAVISTCDH |
| Parental | GVVAKIKRVIMERDTYPRKWGLGPKASQKKQLIKQGLLDKHGRPTDGTPASWTRDYVDYSDSSKKATAAE |
| G...KIKRVIM.RDTYP.KWGLGPKASQK....KQGLLDKHG.PT..TPA....D...Y.DS.KKA..AE | |
| Retrocopy | GIIGKIKRVIMVRDTYP*KWGLGPKASQKRMMTKQGLLDKHGKPTNSTPAT*KKDFIAY-DSGKKALVAE |
| Parental | A-TPGPGVTADAASIVKRKRDSDSDADEATPTTTP-RVKKEKKKKKEKADGGEEAAEDGDGDATRKKKKK |
| A....P...A.A....KRK.DS.....E...T....R.K........K.....E...D.........KKK | |
| Retrocopy | A<NKTPQLAAEAVNLIKRKLDSENESGETSSTVPS*RRKRRIRRRIKKSKMLLESGGDAGDGDSHTTKKK |
| Parental | KAR |
| ..R | |
| Retrocopy | RSR |
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 | 41 .63 RPM |
| SRP017611_kidney | 0 .00 RPM | 31 .19 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .80 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2238 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2238 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2238 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000016095 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000000221 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000048151 | 1 retrocopy |
retro_rnor_2238 ,
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