RetrogeneDB ID: | retro_cjac_2712 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:38002615..38003346(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000004064 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CA5B | ||
| Ensembl ID: | ENSCJAG00000004353 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2712
AGAGGGAGTGTTTATGATCTGGGTTTCAAACTGCTCACAGTCTCTTAGGACCCAGCTACCTGCTGCCACATCTGGAATAA
CGGGTCCTCTTTCCTTATGAAATTTGAAAATTCTACAGATAAATCAGTGATCAAGGAAGGACCCCTGGAACACAACTACC
GATTGAAGCAGTTCCATTTTTGCTGGGAGGCCATCGATGCCTGGGGCTCTGAGCATACCATGGATATCAAAGGCTTCCCA
GAGCTGCACTTAGTGCATTGGAATGCATCGAATTAGGAAACTTTGAGGATGCAGCACTGGAAGAAAATGGTTTGGTTGTG
ATAGGAGTGTTTGTAAAGCTAGGCAAACATCATAAAGAGCTACAAAAATTAGTGGATACTTTGCTATCAATTAAGCACAA
GGACACCTTTGTGGAATTGGGGTCATTTGACCCTTCCTGCCTGATACCTACCTGCCTGGATTACTGGGCCTACTCAGGGT
CTCTGACTACCCCATCCCTCTCCGACTCTGTCACCTGGATCATTAAGAGGCAACAAGTAGAGGTTGATCATGATCATCTG
GAGCAATTTTGGACCCTGCTTTTCATTTCTGAGGGGCAGAAAGAGAAAAGAATTGTGGACAACTTCCACCCTCTTCAGCC
ACTGATGAATCGCACTGTCCATTCAACTTTCCGGCACGATGATGAGCTGAATGTACAAGTGAAACCCAAGCCGGCCACCA
GCCAAGCAACC
ORF - retro_cjac_2712 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.49 % |
| Parental protein coverage: | 77.29 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RDSVYDPGLKPLTISYDPATCLHIWNNGYSFLVEFEDSTDKSVIKGGPLEHNYRLKQFHFHWGAIDAWGS |
| R.SVYD.G.K.LT.S.DPATC.HIWNNG.SFL..FE.STDKSVIK.GPLEHNYRLKQFHF.W.AIDAWGS | |
| Retrocopy | RGSVYDLGFKLLTVS*DPATCCHIWNNGSSFLMKFENSTDKSVIKEGPLEHNYRLKQFHFCWEAIDAWGS |
| Parental | EHTVDSKCFPAELHLVHWNA-VKFENFEDAALEENGLAVIGVFLKLGKYHKELQKLVDTLPSIKHKDTLV |
| EHT.D.K.FP.ELHLVHWNA.....NFEDAALEENGL.VIGVF.KLGK.HKELQKLVDTL.SIKHKDT.V | |
| Retrocopy | EHTMDIKGFP-ELHLVHWNA<IELGNFEDAALEENGLVVIGVFVKLGKHHKELQKLVDTLLSIKHKDTFV |
| Parental | EFGSFDPSCLMPTCPDYWTYSGSLTTPPLSESVTWIIKKQPVEVDHDQLEQFRTLLFTSEGEKEKRMVDN |
| E.GSFDPSCL.PTC.DYW.YSGSLTTP.LS.SVTWIIK.Q.VEVDHD.LEQF.TLLF.SEG.KEKR.VDN | |
| Retrocopy | ELGSFDPSCLIPTCLDYWAYSGSLTTPSLSDSVTWIIKRQQVEVDHDHLEQFWTLLFISEGQKEKRIVDN |
| Parental | FRPLQPLMNRTVRSSFQHDYVLNVQAKPKPATSQAT |
| F.PLQPLMNRTV.S.F.HD..LNVQ.KPKPATSQAT | |
| Retrocopy | FHPLQPLMNRTVHSTFRHDDELNVQVKPKPATSQAT |
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 .97 RPM |
| SRP051959_heart | 0 .00 RPM | 14 .07 RPM |
| SRP051959_kidney | 0 .00 RPM | 11 .54 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .17 RPM |
| SRP051959_lung | 0 .00 RPM | 13 .03 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 12 .03 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .38 RPM |
| SRP051959_spleen | 0 .00 RPM | 10 .32 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2712 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2712 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2712 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000012150 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000004353 | 1 retrocopy |
retro_cjac_2712 ,
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