RetrogeneDB ID: | retro_cjac_3988 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286475.1:116736..117070(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BET1L | ||
| Ensembl ID: | ENSCJAG00000000895 | ||
| Aliases: | None | ||
| Description: | Bet1 golgi vesicular membrane trafficking protein-like [Source:HGNC Symbol;Acc:19348] |
Retrocopy-Parental alignment summary:
>retro_cjac_3988
ATGGTGGACTGGGCTCAGGCTCAGAGTCCTGGTGCTGTGGAAGAGATACTAGACCAGGAGAACAAGCCAATGACCGACAG
CCTGGCCTCCAAAGTCACCAGGCTCAAATCGCTTGCCCTGGACATTGATAGGGACTCAAGAGGATCAGAACCAGTGCCTG
GATGGCATGGACTTGGATTTCACAAGCATGACCAGCCTGCTTACAGGGAGTGTGAAGCGCTTTTCCACAATGGCAAGGTC
TGGGCAAGACAACTGGAAGCTTCTATGTGGCATGACCATGGGTCTAATTGTGGCCTTCTTCATCCTCTCCTACTTCTTGT
CAAGGGCAAGGACG
ORF - retro_cjac_3988 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.82 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MADWGRGQSPGAVEEILDRENKRMTDSLASKVTRLKSLALDIDRDA-EDQNRYLDGMDSDFTSMTGLLTG |
| M.DW...QSPGAVEEILD.ENK.MTDSLASKVTRLKSLALDIDRD..EDQN..LDGMD.DFTSMT.LLTG | |
| Retrocopy | MVDWAQAQSPGAVEEILDQENKPMTDSLASKVTRLKSLALDIDRDS>EDQNQCLDGMDLDFTSMTSLLTG |
| Parental | SVKRFSAMARSGRDNRKLLCGMAMGLIVVFFILSYFLSRART |
| SVKRFS.MARSG.DN.KLLCGM.MGLIV.FFILSYFLSRART | |
| Retrocopy | SVKRFSTMARSGQDNWKLLCGMTMGLIVAFFILSYFLSRART |
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 .00 RPM | 3 .11 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .10 RPM |
| SRP051959_kidney | 0 .00 RPM | 2 .93 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .75 RPM |
| SRP051959_lung | 0 .00 RPM | 2 .20 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .28 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .66 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .13 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3988 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3988 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3988 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000895 | 1 retrocopy |
retro_cjac_3988 ,
|
| Callithrix jacchus | ENSCJAG00000013720 | 3 retrocopies |