RetrogeneDB ID: | retro_cjac_3469 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01180985.1:11028..11763(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RANBP10 | ||
| Ensembl ID: | ENSCJAG00000016055 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3469
GAGAAGGAGCTGCAGCCGCGGCTGAAGCGCCTCGACCCGGCTGTGAACGAGCAGGAGACGCCGCTGCCCCGCTCCTGGAG
CAGGAAGGACAAGGTCGGCTACATCGGCCTCTCTCAGAACAACCTGCGGGTGCACTACAAAGGTCATGGCAAAACCCCAA
AAGATGCAGCATCAGTTCGAGCCACGCATCCAATACCAGCAGCCTGTGGGATTTATTATTTTGAAGTAAAAATTGTCAGT
AAGGGAAGAGATGGTTACATGGGAATTGGTCTTTCTGCTCAAGGTGTGAACATGAATAGACTACCAGGTTGGGATAAGCA
TTCATATGGTTACCATGGGGATGGTGGACATTCGTTTTGTTCTTCTGGAACTGGACAACCTGATGGACCAGCTTTCACAA
CTGGTGATGTCATTGGCTGTTGTGTTAATCTTATCAACAATACCCGCTTTTACATCAAGAATGGACATAGTTTAGGTATT
GCTTTCACTGACCTACCGCCAAATTTGTATCCTACCATGGGGCTTCGGACACCAGGAGAAGTGGTTGATGCCAATTTTGG
TCAACATCCTTTCGTGTTTGATATAGAAGACTATATGCGAGAGTGGTGAACCAAAATCCAGGCACAGATAGACCGGTTTC
CTATCGGAGACCGAGAAGGAGAATGGCAGACCATGATACAAAAAATGGTTTCATCTTATTTAGTCCACCATGGGTACTGT
GCCACAGCAGAGGCC
ORF - retro_cjac_3469 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.27 % |
| Parental protein coverage: | 78.78 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EQELSRRLQHLYPAVNQQETPLPRSWSPKDKYNYIGLSQGNLRVHYKGHGKNHKDAASVRATHPIPAACG |
| E.EL..RL..L.PAVN.QETPLPRSWS.KDK..YIGLSQ.NLRVHYKGHGK..KDAASVRATHPIPAACG | |
| Retrocopy | EKELQPRLKRLDPAVNEQETPLPRSWSRKDKVGYIGLSQNNLRVHYKGHGKTPKDAASVRATHPIPAACG |
| Parental | IYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGC |
| IYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGD.GHSFCSSGTGQP.GP.FTTGDVIGC | |
| Retrocopy | IYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDGGHSFCSSGTGQPDGPAFTTGDVIGC |
| Parental | CVNLINGTCFYTKNGHSLGIAFTDLPANLYPTVGLQTPGEIVDANFGQQPFLFDIEDYMREWRAKVQGTV |
| CVNLIN.T.FY.KNGHSLGIAFTDLP.NLYPT.GL.TPGE.VDANFGQ.PF.FDIEDYMREW..K.Q... | |
| Retrocopy | CVNLINNTRFYIKNGHSLGIAFTDLPPNLYPTMGLRTPGEVVDANFGQHPFVFDIEDYMREW*TKIQAQI |
| Parental | HCFPISARLGEWQAVLQNMVSSYLVHHGYCATATA |
| ..FPI..R.GEWQ...Q.MVSSYLVHHGYCATA.A | |
| Retrocopy | DRFPIGDREGEWQTMIQKMVSSYLVHHGYCATAEA |
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 .58 RPM | 6 .72 RPM |
| SRP051959_heart | 0 .86 RPM | 11 .40 RPM |
| SRP051959_kidney | 0 .40 RPM | 8 .54 RPM |
| SRP051959_liver | 0 .45 RPM | 12 .04 RPM |
| SRP051959_lung | 0 .76 RPM | 9 .96 RPM |
| SRP051959_lymph_node | 0 .78 RPM | 6 .99 RPM |
| SRP051959_skeletal_muscle | 1 .44 RPM | 15 .68 RPM |
| SRP051959_spleen | 0 .53 RPM | 11 .26 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3469 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3469 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3469 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 | ENSCJAG00000016055 | 1 retrocopy |
retro_cjac_3469 ,
|
| Callithrix jacchus | ENSCJAG00000019797 | 1 retrocopy |