RetrogeneDB ID: | retro_cjac_987 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:71794934..71795741(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RMDN3 | ||
| Ensembl ID: | ENSCJAG00000020807 | ||
| Aliases: | None | ||
| Description: | regulator of microtubule dynamics 3 [Source:HGNC Symbol;Acc:25550] |
Retrocopy-Parental alignment summary:
>retro_cjac_987
GTGATGCTGCTGTGGGCTGTCCCTGGTGGGGCTGGAGATGCCGCAGTGCTGCCCAGCCTTCCACGGGAAGGTCAGGAGAA
GGTGCTGGACCGCCGGGACTTTGTGCTGACCAGCCTTGTGGCGCTGCGACAGGAGGTGGAGGAGTTAAGGAGCAGCCTGC
TAGGGCTTGCAGGGGAGATAGTTGGGGAGTTCCAATCCCACATGGAAGAGAACCAGAGAGTGGCTAGGCGGGGAAGGTCT
CCTTTTGTCCGGGAGAGGGGTGACTCCACTGGCTCCAGCTCTGTCTATTTCACGGCTTCCTCCGGAGCTACCTTTACAGA
TGCCGAGAGCGAAGGGGATTATATAACAGCCAATGCAGAGTCTCACAATGAATGGGACTCTGACAAAGAGAGTGAGGATG
GGGAAGATGAAGCAAGTTGTGAGACTGTGAAGATGGGGAGAAAGGATTCTCTGGATCTGGAGGTGGAGGAAGCTTCAGGT
ATGGTGCCCAGTGCCCTGGAGACTGGAACTTCCTCAGGCTTGGAGGACATGCTGCCCCTCCTGCAGCAGGCAGATGAGAT
GCACCAGGGTGATGAGCAGGGCAAGCGGGAGGGCTTCCAGCTGCTGCTCAACAACAAGCTGGCGTATGGAAGCTGGCAGG
ACTTTCTCTGGCGCCTGGCCCGGGCCTACAGTGACATGTGTGAGCTCACTGAGGAGGTGAGCAAGAAGAAGTCATAGGCC
TTAGCTGGAAAAGAAGAAGCAGAGGCTGCTCTAGAGAAGGGGGAGGAGAGTACTGACTGTCACCTGTGGTATGCAGTGCT
TTGTGGT
ORF - retro_cjac_987 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.19 % |
| Parental protein coverage: | 57.11 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VMLLRAVPGGAGDAAVLPSLPREGQEKVLDRLDFVLTSLVALRQEVEELRSSLRGLAGEIVGEVRSHMEE |
| VMLL.AVPGGAGDAAVLPSLPREGQEKVLDR.DFVLTSLVALRQEVEELRSSL.GLAGEIVGE..SHMEE | |
| Retrocopy | VMLLWAVPGGAGDAAVLPSLPREGQEKVLDRRDFVLTSLVALRQEVEELRSSLLGLAGEIVGEFQSHMEE |
| Parental | NQRVARRRRFPFVRERSDSTGSSSVYFTASSGATFTDAESEGGLQTANAESDNERDSDKESEDGEDEASC |
| NQRVARR.R.PFVRER.DSTGSSSVYFTASSGATFTDAESEG...TANAES.NE.DSDKESEDGEDEASC | |
| Retrocopy | NQRVARRGRSPFVRERGDSTGSSSVYFTASSGATFTDAESEGDYITANAESHNEWDSDKESEDGEDEASC |
| Parental | ETVKMGRKDSLDLEVEAASGLVPSALETGASSGLEDMLPLLQQADEMHQGDEQGKREGFQLLLNNKLAYG |
| ETVKMGRKDSLDLEVE.ASG.VPSALETG.SSGLEDMLPLLQQADEMHQGDEQGKREGFQLLLNNKLAYG | |
| Retrocopy | ETVKMGRKDSLDLEVEEASGMVPSALETGTSSGLEDMLPLLQQADEMHQGDEQGKREGFQLLLNNKLAYG |
| Parental | SQQDFLWRLARAYSDMCELTEEVSEKKSYALAGKEEAEAALEKGEESADCHMWYAVLCG |
| S.QDFLWRLARAYSDMCELTEEVS.KKS.ALAGKEEAEAALEKGEES.DCH.WYAVLCG | |
| Retrocopy | SWQDFLWRLARAYSDMCELTEEVSKKKS*ALAGKEEAEAALEKGEESTDCHLWYAVLCG |
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 |
|---|---|---|
| SRP051959_colon | 0 .04 RPM | 27 .25 RPM |
| SRP051959_heart | 0 .02 RPM | 17 .86 RPM |
| SRP051959_kidney | 0 .07 RPM | 47 .43 RPM |
| SRP051959_liver | 0 .06 RPM | 25 .80 RPM |
| SRP051959_lung | 0 .05 RPM | 26 .78 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 13 .08 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 22 .10 RPM |
| SRP051959_spleen | 0 .06 RPM | 15 .53 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_987 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_987 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_987 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020807 | 1 retrocopy |
retro_cjac_987 ,
|
| Oryctolagus cuniculus | ENSOCUG00000016912 | 1 retrocopy |