RetrogeneDB ID: | retro_cjac_4169 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:57312989..57313544(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAD51L1 | ||
| Ensembl ID: | ENSCJAG00000015123 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4169
GCTTACGGGATAAAAGCACAGAGGTCTGCTGATTTCTCACCAGCATTCTTTTCTACTACCCTTTCTGCTTTGGATGAAGC
CCTGCATGCAGGTGTGGCTTGTGGATCCCTCACAGAGATTACAGGTCCACCAGGTTGTGGAAAAACTCAGTTTTGTATAA
TGATGAGCATTTTAGCTACATTATCCACCAATATGGGAGGATTAGAAGGAGCTGTGGTGTACATTGACACAGAGTCAGCA
TTTAGTGCTGAAAGACTGGTTGAGATAGCAGAATCCCATTTTCCCAGATATTTTAACACTGAAGAAAAATTAGTTTTGGC
AAGTAGTAAAGTTCATCTTTATCAGGAGCTCACCTATGATGAAGTTTTACAAAGGATTGAATCTTTGGAAGAAGAAATTA
TCTCAAAAGGAATTAAACTTGTGATTATTGACTCTCTTGCTTCTGTGGTCAATAAAGAGTTTGATACACAACTTCCAGGC
AATCTCAAAGAAAGAAACAAATTCTTGGCAAGAGAAGCATCTTCCTTGAAGTATTTGGCTGAGGAGTTTTCAGTA
ORF - retro_cjac_4169 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.97 % |
| Parental protein coverage: | 67.27 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AYGIKTQRSADFSPAFLSTTLSALDEALHGGVACGSLTEITGPPGCGKTQFCIMMSILATLPTNMGGLEG |
| AYGIK.QRSADFSPAF.STTLSALDEALH.GVACGSLTEITGPPGCGKTQFCIMMSILATL.TNMGGLEG | |
| Retrocopy | AYGIKAQRSADFSPAFFSTTLSALDEALHAGVACGSLTEITGPPGCGKTQFCIMMSILATLSTNMGGLEG |
| Parental | AVVYIDTESAFSAERLVEIAESRFPRYFNTEEKLLLTSSKVHLYRELTCDEVLQRIESLEEEIISKGVKL |
| AVVYIDTESAFSAERLVEIAES.FPRYFNTEEKL.L.SSKVHLY.ELT.DEVLQRIESLEEEIISKG.KL | |
| Retrocopy | AVVYIDTESAFSAERLVEIAESHFPRYFNTEEKLVLASSKVHLYQELTYDEVLQRIESLEEEIISKGIKL |
| Parental | VIIDSVASVVRKEFDTQLPGNLKERNKFLAREASSLKYLAEEFSI |
| VIIDS.ASVV.KEFDTQLPGNLKERNKFLAREASSLKYLAEEFS. | |
| Retrocopy | VIIDSLASVVNKEFDTQLPGNLKERNKFLAREASSLKYLAEEFSV |
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 | 4 .42 RPM |
| SRP051959_heart | 0 .05 RPM | 2 .95 RPM |
| SRP051959_kidney | 0 .02 RPM | 4 .97 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .32 RPM |
| SRP051959_lung | 0 .02 RPM | 5 .01 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 8 .24 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 2 .12 RPM |
| SRP051959_spleen | 0 .02 RPM | 6 .13 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4169 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4169 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4169 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015123 | 1 retrocopy |
retro_cjac_4169 ,
|