RetrogeneDB ID: | retro_cjac_3848 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285052.1:11102..12242(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RANBP9 | ||
| Ensembl ID: | ENSCJAG00000019797 | ||
| Aliases: | None | ||
| Description: | RAN binding protein 9 [Source:HGNC Symbol;Acc:13727] |
Retrocopy-Parental alignment summary:
>retro_cjac_3848
AAGGGAAGAGATGGTTACATGGGAATTGGTCTTTCTGCTCAAGGTGTGAACATGAATAGACTACCAGGTTGGGATAAGCA
TTCATATGGTTACCATGGGGATGATGGACATTCATTTTGTTCTTCTGGAACTGGACAACCTGATGGACCAGCTTTCACAA
CTGGTGATGTCATTGGCTGTTGTGTTAATCTTATCAACAATACCCGCTTTTACATCAAGAATGGACATAGTTTAGGTATT
GCTTTCACTGACCTACCGCCAAATTTGTATCCTACCATGGGGCTTCGGACACCAGGAGAAGTGGTTGATGCCAATTTTGG
TCAACATCCTTTCGTGTTTGATATAGAAGACTATATGTGAGAGTGGAGAACCAAAATCCAGGCACAGATAGACCGGTTTC
CTATCGGAGACCGAGAAGGAGAATGGCAGACCATGATACAAAAAATGGTTTCATCTTATTTAGTCCACCATGGGTACTGT
GCCACAGCAGAGGCCTTTGCCAGATCTACAGACCAGACCGGTCTAGAAGAATTGGCTTCCGTTAAGAATAGACAAAGAAT
TCAGAAATTGCTATTAGCAGGAAGAATGGGAGAAGCCATTGAAACAACACAACAGTTATACCCAAGTTTCCTTGAAAGAA
ATCCTAATCTCCTTTTCACATTAAAAGTACGTCCGTTTATAGAAATGGTGAATGGTACACATAGTGAAGTACGATGTTTG
GGAGGCCGAAGTCCAAAGACTCAAGACAGTTATCCTGTTAGTCCTCGACCTTTTAGTAGTCCAAGTATGATCCCCAGCCA
TGGAATGAATATCCACAATTTAGCATCAGGCAAAGGAAGGACTGCACATTTTTCTGGTTTTGAAAGTTGTAGTAATGGTG
TAATATCAAATAAAGCACATCAATCATATTGCCATAGTAATAAACACCAGTCATCCAATTTGAATGTACCAGAACTGAAC
AGTATAAATGCGTCAAAATCACAGCAAGTTAATAATTTCACCAGTAATGATGTAGACATGGAAACAGATCACTACTCCAA
CGGAGTTGGAGAAACTTCATCCAATGGTTTCCTAAATGGTAGCTCTAAACATGATCACGAAATGGAAGATTGTGACACCG
AAATGGAAGTTGATTCATCA
ORF - retro_cjac_3848 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.01 % |
| Parental protein coverage: | 69.78 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGCCVNLINNTCF |
| KGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQP.GP.FTTGDVIGCCVNLINNT.F | |
| Retrocopy | KGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPDGPAFTTGDVIGCCVNLINNTRF |
| Parental | YTKNGHSLGIAFTDLPPNLYPTVGLQTPGEVVDANFGQHPFVFDIEDYMREWRTKIQAQIDRFPIGDREG |
| Y.KNGHSLGIAFTDLPPNLYPT.GL.TPGEVVDANFGQHPFVFDIEDYM.EWRTKIQAQIDRFPIGDREG | |
| Retrocopy | YIKNGHSLGIAFTDLPPNLYPTMGLRTPGEVVDANFGQHPFVFDIEDYM*EWRTKIQAQIDRFPIGDREG |
| Parental | EWQTMIQKMVSSYLVHHGYCATAEAFARSTDQTVLEELASIKNRQRIQKLVLAGRMGEAIETTQQLYPSL |
| EWQTMIQKMVSSYLVHHGYCATAEAFARSTDQT.LEELAS.KNRQRIQKL.LAGRMGEAIETTQQLYPS. | |
| Retrocopy | EWQTMIQKMVSSYLVHHGYCATAEAFARSTDQTGLEELASVKNRQRIQKLLLAGRMGEAIETTQQLYPSF |
| Parental | LERNPNLLFTLKVRQFIEMVNGTDSEVRCLGGRSPKSQDSYPVSPRPFSSPSMSPSHGMNIHNLASGKGS |
| LERNPNLLFTLKVR.FIEMVNGT.SEVRCLGGRSPK.QDSYPVSPRPFSSPSM.PSHGMNIHNLASGKG. | |
| Retrocopy | LERNPNLLFTLKVRPFIEMVNGTHSEVRCLGGRSPKTQDSYPVSPRPFSSPSMIPSHGMNIHNLASGKGR |
| Parental | TAHFSGFESCSNGVISNKAHQSYCHSNKHQSSNLNVPELNSINMSRSQQVNNFTSNDVDMETDHYSNGVG |
| TAHFSGFESCSNGVISNKAHQSYCHSNKHQSSNLNVPELNSIN.S.SQQVNNFTSNDVDMETDHYSNGVG | |
| Retrocopy | TAHFSGFESCSNGVISNKAHQSYCHSNKHQSSNLNVPELNSINASKSQQVNNFTSNDVDMETDHYSNGVG |
| Parental | ETSSNGFLNGSSKHDHEMEDYCDTEMEVDSS |
| ETSSNGFLNGSSKHDHEMED.CDTEMEVDSS | |
| Retrocopy | ETSSNGFLNGSSKHDHEMED-CDTEMEVDSS |
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 .07 RPM | 20 .01 RPM |
| SRP051959_heart | 0 .00 RPM | 22 .64 RPM |
| SRP051959_kidney | 0 .00 RPM | 19 .75 RPM |
| SRP051959_liver | 0 .00 RPM | 12 .67 RPM |
| SRP051959_lung | 0 .03 RPM | 24 .40 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 28 .88 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 25 .90 RPM |
| SRP051959_spleen | 0 .00 RPM | 23 .74 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3848 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3848 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3848 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000006785 | 2 retrocopies | |
| Callithrix jacchus | ENSCJAG00000016055 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000019797 | 1 retrocopy |
retro_cjac_3848 ,
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