RetrogeneDB ID: | retro_rnor_1839 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 3:152675998..152677176(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000036943 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Galk1 | ||
| Ensembl ID: | ENSRNOG00000006359 | ||
| Aliases: | Galk1, Galk, Glk | ||
| Description: | galactokinase [Source:RefSeq peptide;Acc:NP_001008283] |
Retrocopy-Parental alignment summary:
>retro_rnor_1839
ATGGCTGTTTGGAGTTTGCCCTGGGTTGTAGAGCTGCTGGCCAAGGACTTGGCGGGCCTTCATGGATGAGTTAGGAGCCA
AACATGAGCTGACAGTGTTGGCACCTGGCCATGACAACTACATCGGGAGCACAGGGAATACAACCAGGTCCTGGTGCTGC
CCATGGCTGTGGAGCTTGTGACCTCGCTAGTGGGCAGCCCGTGTGCAGATGGGCTTCTTTCTCTCCTCACAGTTTCCAAA
GATGCAGATGAGTCCCAGTGACTGCTATCCCCACAGCCCTCAGCAGAGTGGTCCTTGGAGCCAGGAAACCCACAGTGGGA
CAATTATGTCAAGGGAATGATTCAATATTACCCAGCTTTTACCCCCTCTCTGGCTTCAGTGCAGTGGCGGTCAGCTCAGT
GCTCCAAGGGGTTGGACTTTCCAGCTCAGCTTCCCTAGAAGTGACCAGGTACACCTTCCCCCAGCAGCTCTGCCCAGACT
CAGGGGCAATAGCTGCCAGGGTTCAGGTGTGACAACGGGCTGAGCACAGTTTTGCAGGGGCATCCTGTGGCTTCATGGAC
CAACTCATCAATGAACTGCTGTGGCAGAAAGGCTATGTGCTACTCATTGACTGCAGGTCCCAGAAACAAGTCTGGCACTA
CTGTCAGACCCCAAATTGGTTGTGCTCAACACAAACTTCAATGTCCTCCAAACCCCTGGGCTCCAGAAAGTACCAGATTC
ATTGGTGTAAATGTGAAGAAGTGGTCCAGGCCCTGGGCAAGGAGAGGCTTCCATACATGTGGATGGAGGAGCTTGAGGCA
GGAAGGGAGCTGATGTGCAAGGAGAGCTGGCAGGCCTGGCACATGGTAGGCAAGATCTGGAGAACAGCCCAGGCAGCAGC
TGCTCTGAGCCGAGGAGACTACACGGCCTTTGGGTGTATCATGGTGGAGAATCACTATTCACTCAGGGATGTCTATGGGT
TGAGCTGTCCCGAGCTGGACCAATTGGTTGAGGCTGCGGTCTCGGTGCCTGGGATTTATGGCTGTTGCATGACAGGCGTT
GGCTTTGGTGGCTGCACTGTCACATTGCTGGAGGCCTCTGCTGCCCTCCTTGTCATGCATCACATACAGGAGCAGGACAG
TGGGACAGCCACCTTCTACCTCTCTCATGCTGCCGATGGAGCCCAGTTCCTGAGCTTG
ORF - retro_rnor_1839 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.18 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAWRPPRVEELLAE-ARRAFMEEFGAEPELAVSAPGRVNLIG-EHTDYNQGLVLPMALELVTVMVGSPR |
| MA.W..P.V.ELLA....RAFM.E.GA..EL.V.APG..N.IG.EH..YNQ.LVLPMA.ELVT..VGSP. | |
| Retrocopy | MAVWSLPWVVELLAK>TWRAFMDELGAKHELTVLAPGHDNYIG<EHREYNQVLVLPMAVELVTSLVGSPC |
| Parental | TDGLVSLLTTSKDADEPQRLQFPLPSAQWSLEPGIPQWANYVKGVIQYYPA-SP-LCGFSAVVVSSVPLG |
| .DGL.SLLT.SKDADE.Q.L..P.PSA.WSLEPG.PQW.NYVKG.IQYYPA..P.L.GFSAV.VSSV..G | |
| Retrocopy | ADGLLSLLTVSKDADESQ*LLSPQPSAEWSLEPGNPQWDNYVKGMIQYYPAFTP<LSGFSAVAVSSVLQG |
| Parental | GGLSSSASLEVATYAFLQQLCPDSGSIAARAQVCQRAEHSFAGVPCGIMDQLI-ALLGQKGYALLIDCRS |
| .GLSSSASLEV..Y.F.QQLCPDSG.IAAR.QV.QRAEHSFAG..CG.MDQLI..LL.QKGY.LLIDCRS | |
| Retrocopy | VGLSSSASLEVTRYTFPQQLCPDSGAIAARVQV*QRAEHSFAGASCGFMDQLINELLWQKGYVLLIDCRS |
| Parental | L-ETSLVPLSDPKLTVLITNSNVRHS-LASSEYPIRRRQCEEVAQALGKESLREVRMEELEAGRELMSKE |
| ..ETSL..LSDPKL.VL.TN.NV....L.S..Y.I....CEEV.QALGKE.L....MEELEAGRELM.KE | |
| Retrocopy | Q<ETSLALLSDPKLVVLNTNFNVLQT>LGSRKYQIHWCKCEEVVQALGKERLPYMWMEELEAGRELMCKE |
| Parental | GFRRARHVVSEIRRTAQGAAALSRGDYKAFGRLMVESHYSLRDDYEVSCPELDLLVEAALSVPGVYGSRM |
| ....A.H.V..I.RTAQ.AAALSRGDY.AFG..MVE.HYSLRD.Y..SCPELD.LVEAA.SVPG.YG..M | |
| Retrocopy | SW-QAWHMVGKIWRTAQAAAALSRGDYTAFGCIMVENHYSLRDVYGLSCPELDQLVEAAVSVPGIYGCCM |
| Parental | TGGGFGGCTVTLLEASVAPLVMHHIQEQYSGTATFYLTQAADGAQVLSL |
| TG.GFGGCTVTLLEAS.A.LVMHHIQEQ.SGTATFYL..AADGAQ.LSL | |
| Retrocopy | TGVGFGGCTVTLLEASAALLVMHHIQEQDSGTATFYLSHAADGAQFLSL |
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 .29 RPM | 13 .80 RPM |
| SRP017611_kidney | 0 .63 RPM | 22 .68 RPM |
| SRP017611_liver | 1 .34 RPM | 43 .30 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1839 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1839 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1839 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000013012 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000006359 | 1 retrocopy |
retro_rnor_1839 ,
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