RetrogeneDB ID: | retro_rnor_2753 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | AABR06111084.1:17..1157(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000046278 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Acadsb | ||
| Ensembl ID: | ENSRNOG00000020624 | ||
| Aliases: | None | ||
| Description: | Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P70584] |
Retrocopy-Parental alignment summary:
>retro_rnor_2753
ATGGCGGTCTCTGCCCTTAGCTGTGGCGTATGGGCGGGCTGCTGAGAAGACGCTTCCCAACCTGCTTGTCTCCTTGGAAG
ATTCCTCCTCGTGTCCTCAAATCCTCACAACCGGAAGCTCTAGTCAGTCTGACAAACAATGCAGTAGCCTTTGCACCTCT
GCAGACACTTACTGATGAGGAAATTATGATGAAGCAGACAGTCAAAAAATTTGCACAGGAGCACGTTGCTCCTCTGGTTT
CCTCTATGGATGAGAACTCAAAAATGGAGAAATCGGTGATCCAGGGATTGTTCCAGCAAGGGCTGATGGGCATTGAAGTT
GAAGCACAATATGGAGGGACAGAAGCTTCCTTTTTCTGCTCTGTCCTAGTGATAGAGGAACTAGCTAAGGTGGATGCTTC
GGTGGCTCTCCTGTGTGACATCCAGAACACAATAATTAACAACCTGTTTAGAAAACACGCTTCAGAAGAACAGAAGGCCA
CCTATTTGCCAAAGCTGGTTACAGAAAAATTAGGGAGCTTTTGCCCCTCTGAAGCTGGAGCCGGTAGCGACTCTTTCGCT
ATGAAAACAAGAGCTGATAAAAGTGGAAATTACTACGTCCTCAATGGGTCGAAGATGTGGATCAGCCATGCCGAGCATGC
AGAGCTCTTCCTGGTCTTCGCCAATGTGGACCCCAGCTCTGGCTACAGAGGCATCACCTGCTTCTTAGTAGACCGAGATA
CAGAAGGTTTCCAGATAGGGAAACGAGAAAATAAAATGGGCATCAGAGCTTCATCCACCTGTCAGTTAACATTTGAAAAT
GTTAAGGTTCCAGAGACTAATATTTTGGGGAAAATTGGGCATGGTTATAAGTATGCCATAGGAAGTCTTAATGAAAGGGT
AGAAATCGGAATTGCTGCACAGAAATGCTAGGGACTGGCCCCAAGGGATGTTTTGACTACCTATTCCATACATTAAAGAA
AGGATGCAGTTTTTGGCAAAACGAATATTTGATTTTCAGGGGCTCCAACACCCCTTTAATGAGGTGGCCACCCAGCTGGA
AGCCACACGGTTGGTAANATANAANGNTGNTAGGNTNGTAGAAGNNGTCAGGCCATTTATAAAAGAAGCATCTATGGCCA
AATATTATGCATCTGAGGTC
ORF - retro_rnor_2753 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.51 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVSAFQ-LWRAGGLLRRNFLTHSSSWKIPPRVLKSSQPEALLSVTNNALCFAPLQTFTDEDIMMQKAVK |
| MAVSA...LWR.GGLLRR.F.T..S.WKIPPRVLKSSQPEAL.S.TNNA..FAPLQT.TDE.IMM...VK | |
| Retrocopy | MAVSALS<LWRMGGLLRRRFPTCLSPWKIPPRVLKSSQPEALVSLTNNAVAFAPLQTLTDEEIMMKQTVK |
| Parental | KFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGMMGIEVEAKYGGTEASFLCSVLVIEELAKVDASVALLC |
| KFAQE..APLVS.MDENSKMEKSVIQGLFQQG.MGIEVEA.YGGTEASF.CSVLVIEELAKVDASVALLC | |
| Retrocopy | KFAQEHVAPLVSSMDENSKMEKSVIQGLFQQGLMGIEVEAQYGGTEASFFCSVLVIEELAKVDASVALLC |
| Parental | DIQNTVINKLFRKHGTEEQKATYLPKLVTEKLGSFCLSEAGAGSDSFALKTRADKSGNYYVINGSKMWIS |
| DIQNT.IN.LFRKH..EEQKATYLPKLVTEKLGSFC.SEAGAGSDSFA.KTRADKSGNYYV.NGSKMWIS | |
| Retrocopy | DIQNTIINNLFRKHASEEQKATYLPKLVTEKLGSFCPSEAGAGSDSFAMKTRADKSGNYYVLNGSKMWIS |
| Parental | NAEHAELFLVFANVDPPSGYRGITCFLVDRDTEGFQIGRRENKMGIRASSTCQLTFENVKVPETSVLGKI |
| .AEHAELFLVFANVDP.SGYRGITCFLVDRDTEGFQIG.RENKMGIRASSTCQLTFENVKVPET..LGKI | |
| Retrocopy | HAEHAELFLVFANVDPSSGYRGITCFLVDRDTEGFQIGKRENKMGIRASSTCQLTFENVKVPETNILGKI |
| Parental | GHGYKYAIGSLNEG-RIGIAAQML-GLA-QGCFDYTIPYIKERMQF-GKRIFDFQGLQHQVAHVATQLEA |
| GHGYKYAIGSLNE...IGIAAQ...GLA.QG.F...IPYIKERMQF..KRIFDFQGLQH....VATQLEA | |
| Retrocopy | GHGYKYAIGSLNERVEIGIAAQKC*GLA>QGMF*LPIPYIKERMQFLAKRIFDFQGLQHPFNEVATQLEA |
| Parental | ARLLTYNAARLVEAGRPFIKEASMAKYYASEV |
| .RL......R.VE..RPFIKEASMAKYYASEV | |
| Retrocopy | TRLVXXXXXRXVEXVRPFIKEASMAKYYASEV |
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 | 17 .90 RPM |
| SRP017611_kidney | 0 .91 RPM | 51 .43 RPM |
| SRP017611_liver | 0 .54 RPM | 48 .68 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2753 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2753 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2753 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000017638 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000020624 | 4 retrocopies |