RetrogeneDB ID: | retro_mmus_824 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:90859769..90861101(-) | ||
| Located in intron of: | ENSMUSG00000085940 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083764 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cct3 | ||
| Ensembl ID: | ENSMUSG00000001416 | ||
| Aliases: | Cct3, AL024092, Cctg, Tcp1-rs3, TriC-P5 | ||
| Description: | chaperonin containing Tcp1, subunit 3 (gamma) [Source:MGI Symbol;Acc:MGI:104708] |
Retrocopy-Parental alignment summary:
>retro_mmus_824
ATGCTGTCTGTGGCTGAGCATTTCTTAGAGCAGCAGATGCACCCAACAGTGGTAATCAGTGCTTATCGCATGACACTGGG
TGATATGATCAACACTCTGAAGAAAATCAGTACCCCTGTTGATGTCAATAACTATGAGATGATGTTAAACATCATCAATA
GCTCTATTACTACAAATGTCATCAACTGGTGATCCTCTTTGGCATGCAGCATTGCACTGGATACTGTTAAGACTGTGCAG
TTTGAAGAGAATGGCAGAAAAAAAATGACATCAAGAAGTATTCGAGGGTAGAAAAGATTCCTGGGGGCATCACTGAAGAC
TCATGCATCTTACACGGAGTTATAATTAACAAGGATGTGACCCATCCAGTAATGAGCTGCTATATTAAGAATCCTCAAAT
TGTGCTACTGAATTCTTCTCTGGAGTACAAGAAAGTAAGTCAGACTGACATTGAGATTACACGAAAGGAGGATTTCACCC
GAATCCTGCAAATGAAAGATGAGTGCATCCAGCAGTTGTGTGAGGATATTATCCAGCACAGGATATTATTCTGTGATGAC
CTTGTCATCACAGAAAAGGGCATCTCAGATTTAGCTCAGCACTACCTCATATGGGTCAATGTCACAGCCACTCATAGAGT
CTGGAAAACAGACAATAATCACTTTGCTAGAGCCTGTAGGGCACGGATAGTCGGCTGACCCAAGGAACTGAGAGAAGATG
ATGTTGGTACAGGGGCAGGCTTATTGGAAATCAAGACGATTGGAGATGAGTACTTTACATTCATCACTGACTGAAAAGGC
TCAAAGGCCTGCACCATTCTTCTTAGAGGAGCCAGCAAAGAGATACTCTCAGAAGTAGAACACAACCTCCAGGATGCCAC
GCAAGTGTGCCGCAATGTTCAACTGGATCCTCAACTGGTGCCTGGTTGTGGAGCCTCTGAGATAGCCGTGGCCCATGACT
TGACAGAAAAATCTAAGGCCATGACTGGTGTGGAACAATGGCCATATAGAGCTGTGGCTCAGGCGTTAGAGGCCATGCCT
CGGACCTGGATCCAGAATTGTGGGGCCAGTACCATTTGTCTGCTTACCTCCCTTCGGGCCAAGCACACACAGGAGAGTTG
CGAGACCTGGGGTGTGAATCGGTGAGACTGGTACCTTGGCGAACATGAAAGAGCAGGGTATTTGGGAGCCATTGGCTGTG
GAGCTACAAACATACAAAACAGCAGTGGAGACTGAAGTTCTGCATCTGTGGATTGATGACATCATCTGTGGCCACAAGAA
GAAGGGTGATGACCAGAACCGGCAAACCAGGGCCCCAGATGCTGACCAGGAG
ORF - retro_mmus_824 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.31 % |
| Parental protein coverage: | 86.98 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MLSVAEHFLEQQMHPTVVISAYRMALDDMISTLKKISTPVDVNNREMMLSIINSSITTKVISRWSSLACN |
| MLSVAEHFLEQQMHPTVVISAYRM.L.DMI.TLKKISTPVDVNN.EMML.IINSSITT.VI...SSLAC. | |
| Retrocopy | MLSVAEHFLEQQMHPTVVISAYRMTLGDMINTLKKISTPVDVNNYEMMLNIINSSITTNVINW*SSLACS |
| Parental | IALDAVKTVQFEENG-RKEIDIKKYARVEKIPGGIIEDSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDS |
| IALD.VKTVQFEENG.....DIKKY.RVEKIPGGI.EDSC.L.GV.INKDVTHP.M..YIKNP.IVLL.S | |
| Retrocopy | IALDTVKTVQFEENG<QXXXDIKKYSRVEKIPGGITEDSCILHGVIINKDVTHPVMSCYIKNPQIVLLNS |
| Parental | SLEYKKGESQTDIEITREEDFTRILQME----EEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANV |
| SLEYKK..SQTDIEITR.EDFTRILQM................I....D.VITEKGISDLAQHYL...NV | |
| Retrocopy | SLEYKK-VSQTDIEITRKEDFTRILQMKDECIQQLCEDIIQHRILFCDDLVITEKGISDLAQHYLIWVNV |
| Parental | TAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGA |
| TA..RV.KTDNN..ARAC.ARIV..P.ELREDDVGTGAGLLEIK.IGDEYFTFITD.K..KACTILLRGA | |
| Retrocopy | TATHRVWKTDNNHFARACRARIVG*PKELREDDVGTGAGLLEIKTIGDEYFTFITD*KGSKACTILLRGA |
| Parental | SKEILSEVERNLQDAMQVCRNVLLDPQLVPGGGASEMAVAHALTEKSKAMTGVEQWPYRAVAQALEVIPR |
| SKEILSEVE.NLQDA.QVCRNV.LDPQLVPG.GASE.AVAH.LTEKSKAMTGVEQWPYRAVAQALE..PR | |
| Retrocopy | SKEILSEVEHNLQDATQVCRNVQLDPQLVPGCGASEIAVAHDLTEKSKAMTGVEQWPYRAVAQALEAMPR |
| Parental | TLIQNCGASTIRLLTSLRAKHTQESCETWGVN-GETGTLVDMKELGIWEPLAVKLQTYKTAVETAVLLLR |
| T.IQNCGASTI.LLTSLRAKHTQESCETWGVN.GETGTL..MKE.GIWEPLAV.LQTYKTAVET.VL.L. | |
| Retrocopy | TWIQNCGASTICLLTSLRAKHTQESCETWGVN>GETGTLANMKEQGIWEPLAVELQTYKTAVETEVLHLW |
| Parental | IDDIVSGHKKKGDDQNRQTGAPDAGQE |
| IDDI..GHKKKGDDQNRQT.APDA.QE | |
| Retrocopy | IDDIICGHKKKGDDQNRQTRAPDADQE |
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 | 95 .67 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 110 .68 RPM |
| SRP007412_heart | 0 .00 RPM | 101 .98 RPM |
| SRP007412_kidney | 0 .00 RPM | 122 .12 RPM |
| SRP007412_liver | 0 .03 RPM | 93 .86 RPM |
| SRP007412_testis | 0 .09 RPM | 332 .48 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_824 was not detected
No EST(s) were mapped for retro_mmus_824 retrocopy.
No TSS is located nearby retro_mmus_824 retrocopy 5' end.
retro_mmus_824 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_824 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005776 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000009131 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000001416 | 2 retrocopies |
retro_mmus_2352, retro_mmus_824 ,
|
| Otolemur garnettii | ENSOGAG00000008967 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000019090 | 2 retrocopies | |
| Ictidomys tridecemlineatus | ENSSTOG00000001798 | 1 retrocopy |