RetrogeneDB ID: | retro_mmus_2937 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:60132670..60133684(+) | ||
| Located in intron of: | ENSMUSG00000000948 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pdhx | ||
| Ensembl ID: | ENSMUSG00000010914 | ||
| Aliases: | Pdhx, AI481367, E3bp, Pdx1 | ||
| Description: | pyruvate dehydrogenase complex, component X [Source:MGI Symbol;Acc:MGI:1351627] |
Retrocopy-Parental alignment summary:
>retro_mmus_2937
CAACCCCCTCCACAGCCACAGATTCCTAGCCCTGACAGGAAGGAACACAAAGGGACACCACAGTTCTGCTTAAGTCCAGC
TGCCCCGCAACATTCTGGAAAAAACATTCATTGGACGCCAGCCAGGGCACAGCCCTCGTGGAATCCTCATTAAAGAAGGT
GCACTCAAGTTAGTCGAGCTGAAACAGTTGGGCAAGATTACTGAATTTAGACCAACCTCAGCTCCTCTGTCCTCTCTCTC
AGCATTTGTTCTTCCTCAGGCTACAGCTGGGCCATCTTACCCTTGGGCAACAATCCCACCAGTATCCATCGCTGGGCAAC
CTAATGCAGTGGGTACATTCACTGAAATTCCTGATAGAAATATTCTAAAAGTTATCACTAAGAGGTTAACTGAATCAAAA
GTACTGTGCCTCATGCCTATGCTACTGCTGACCATGAACTTGGAGCAGTTTTAAAGGTTAGATGCGATCTGGTCAAAAAT
GACATTAAAGTCTCAGTAAATGACTTTATCATCAGAGCAGTAGCTGTTACTGTTAAACAAATGCCTGGGTTTAATGTCAC
CTGGAATGGAGAAGGACCAAACAGCTGCCTTCTGTTGACATTTCAATTGCTGTGGCTACAGATAAAGGTTTAATTACACC
AATCATAAAAGATGCAGCCGCTAAGGGCATATAGAAGATCGCTGACTCTGTTAAGGTTCTGTTGAAGAAAGCAAGAGATG
GAAAATTGATGCCGGAGGAGTACCAAGGAGGATCTTTTAGTATTTCCAACTTGTGGATATTTGGCATCAATGAGTTCACT
GCAGTGATTAACCTGCCTCAGTCCTGAATCTTGGAAGTTGGGAAATTCCACCCAGTGCTGAAGCTCACTGAGGATGAAGG
GGGAACCCCAACTGCAGCAGCACCAGCTTATCACTGTCACAGTGTCAAGTGACAGCAGGGTGGTTGATGATGAGCTAGCT
ATCAGGTTTCTTGAAACTTTCAAAGCAAACCTAGAGGGTCACATGTGACTTGGC
ORF - retro_mmus_2937 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.48 % |
| Parental protein coverage: | 68.06 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | QPSPQPQIPCPARKEHKGTARFRLSPAA-RNILEKHSLDASQGTATGPRGIFTKEDALKLVELKQMGKIT |
| QP.PQPQIP.P.RKEHKGT..F.LSPAA.RNILEK.......G....PRGI..KE.ALKLVELKQ.GKIT | |
| Retrocopy | QPPPQPQIPSPDRKEHKGTPQFCLSPAA>RNILEKTFIGRQPGHS--PRGILIKEGALKLVELKQLGKIT |
| Parental | ESRPASAPPPSLSASVPPQATAGPSYPRPMTPPVSIPGQPNAAGTFTEIPASNIRRVIAKRLTESK-STV |
| E.RP.SAP..SLSA.V.PQATAGPSYP....PPVSI.GQPNA.GTFTEIP..NI..VI.KRLTESK.STV | |
| Retrocopy | EFRPTSAPLSSLSAFVLPQATAGPSYPWATIPPVSIAGQPNAVGTFTEIPDRNILKVITKRLTESK<STV |
| Parental | PHAYATADCDLGAVLKVRRDLVKDDIKVSVNDFIIRAAAVTLKQMPGVNVTWDGEGP-KQLPSVDISVAV |
| PHAYATAD..LGAVLKVR.DLVK.DIKVSVNDFIIRA.AVT.KQMPG.NVTW.GEGP.KQLPSVDIS.AV | |
| Retrocopy | PHAYATADHELGAVLKVRCDLVKNDIKVSVNDFIIRAVAVTVKQMPGFNVTWNGEGP<KQLPSVDISIAV |
| Parental | ATDKGLITPIIKDAAAKGIQEIADSVKVLSKKARDGKLMPEEYQGGSFSISNLGMFGIDEFAAVINPPQA |
| ATDKGLITPIIKDAAAKGI..IADSVKVL.KKARDGKLMPEEYQGGSFSISNL..FGI.EF.AVIN.PQ. | |
| Retrocopy | ATDKGLITPIIKDAAAKGI*KIADSVKVLLKKARDGKLMPEEYQGGSFSISNLWIFGINEFTAVINLPQS |
| Parental | CILAVGRFRPVLKLTEDE-EGNP-QLQQHQLITVTMSSDSRVVDDELATRFLETFKANLENPMRLG |
| .IL.VG.F.PVLKLTEDE..GNP.QLQQHQLITVT.SSDSRVVDDELA.RFLETFKANLE..M.LG | |
| Retrocopy | *ILEVGKFHPVLKLTEDE<RGNP<QLQQHQLITVTVSSDSRVVDDELAIRFLETFKANLEGHM*LG |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 30 .89 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 32 .96 RPM |
| SRP007412_heart | 0 .00 RPM | 102 .23 RPM |
| SRP007412_kidney | 0 .00 RPM | 46 .97 RPM |
| SRP007412_liver | 0 .00 RPM | 21 .55 RPM |
| SRP007412_testis | 0 .00 RPM | 50 .95 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2937 was not detected
No EST(s) were mapped for retro_mmus_2937 retrocopy.
No TSS is located nearby retro_mmus_2937 retrocopy 5' end.
retro_mmus_2937 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2937 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000003998 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000010888 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000010914 | 1 retrocopy |
retro_mmus_2937 ,
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