RetrogeneDB ID: | retro_cjac_2736 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:75669316..75669760(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LIN37 | ||
| Ensembl ID: | ENSCJAG00000010100 | ||
| Aliases: | None | ||
| Description: | lin-37 homolog (C. elegans) [Source:HGNC Symbol;Acc:33234] |
Retrocopy-Parental alignment summary:
>retro_cjac_2736
ATGTTCCCCCTGAAGGCGAAAGTAGAGAAATCAGAGCTGGAGATGGCCAAAGCCCGGAACCAACTGGACGCCATCCTGCA
GTGTCTGCTGGAGAAGAGTCACATGGACAGGGAGCGTCTGGATGAGGAAGCTGGGAAAATTCCCTCAGACACCCACAATA
AGGACTGCTCCATTGCAGCCACTGGCAAAAGGCCTTCTGCCCGCTTCCCCTAGCAGCGGAGGAAGAAGAGGAGGGAAATG
GATGACGGGCTGGCTGAGGGAGGGCCGCAGCGATCAAACACATATGTGATCAAGCTGTTCGACCTGAGCGTGGACTTGGC
CCAGTTCAGTGAGAACACGCCACTCTACCTGATATGCCGTGCCTGGATGTGAAACAGCCCCTCTGTGCGCGAGCGTGAGT
GCTCTCCCAGCTCACTCCTGCCCTCGCTGCCTGAGGATGAGGAC
ORF - retro_cjac_2736 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.35 % |
| Parental protein coverage: | 60.83 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MFPVKVKVEKSELEMAKARNQLDAVLQCLLEKSHMDRERLDEEAGKTPSDTHNKDCSIASTGKR--VDWP |
| MFP.K.KVEKSELEMAKARNQLDA.LQCLLEKSHMDRERLDEEAGK.PSDTHNKDCSIA.TGKR.....P | |
| Retrocopy | MFPLKAKVEKSELEMAKARNQLDAILQCLLEKSHMDRERLDEEAGKIPSDTHNKDCSIAATGKRPSARFP |
| Parental | ERVGKELRGYARMLTHSHPHLPDTYVIKLFDRSVDLAQFSENTPLYPICRAWMRNSPSVRERECSPSSPL |
| ....K..R.....L....P....TYVIKLFD.SVDLAQFSENTPLY.ICRAWM.NSPSVRERECSPSS.L | |
| Retrocopy | *QRRKKRREMDDGLAEGGPQRSNTYVIKLFDLSVDLAQFSENTPLYLICRAWM*NSPSVRERECSPSSLL |
| Parental | PPLPEDEE |
| P.LPEDE. | |
| Retrocopy | PSLPEDED |
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 .13 RPM | 2 .13 RPM |
| SRP051959_heart | 0 .42 RPM | 3 .19 RPM |
| SRP051959_kidney | 0 .31 RPM | 2 .84 RPM |
| SRP051959_liver | 0 .26 RPM | 1 .99 RPM |
| SRP051959_lung | 0 .37 RPM | 2 .81 RPM |
| SRP051959_lymph_node | 0 .43 RPM | 3 .90 RPM |
| SRP051959_skeletal_muscle | 0 .74 RPM | 5 .15 RPM |
| SRP051959_spleen | 0 .29 RPM | 2 .75 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2736 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2736 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2736 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010100 | 1 retrocopy |
retro_cjac_2736 ,
|
| Echinops telfairi | ENSETEG00000004801 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000036845 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000003834 | 1 retrocopy |