RetrogeneDB ID: | retro_cjac_3012 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:106778564..106779777(-) | ||
| Located in intron of: | ENSCJAG00000022946 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RANBP3 | ||
| Ensembl ID: | ENSCJAG00000016791 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3012
GAGCCCAGGGAAAAGCAGCGGAGCGTGCTTCCTATGGCAGTGATCAGGCCCCGCAGCCAAAGGCGCTGTCCCAGATGGTC
CCCAGCAGTGGCACCAATGGGGTCAGCCTCCCAGCCGACCGCACGGAGGCCGTGCCAGCAGCATCCCCTGACAACCCTGC
AGGGAAGAGTCCTTCCCAAGCTGCCGACGAGGTGTGTGCACTTGAGGAGAAGGAGCCCCAGAAAAATGAGTCCAGCGATG
CCTCTGAAGAGGAAGCCTGTGAGAAAAAAGACCCCACCACACAACAAGCGTTTGTACTTGGGCAGAACTTGAGGGACGGA
GTTAAGCTGATCAATGAGAGTGTGGACAAAGCCGACATGGAGAGTGCTGGACACCCCAGCGCAGACACACCGGCCGGACA
AACTATTTCCTTCAGCGTATCAGTTCCAGTTTAGAGAACTCAACCAATAGTGCCGATGCCTCCAGCAACAAACTCGTATT
TGGCCAGAATTTGAGTGAGCGAGTTTTGAGCTTTCCAAAATTAAATGAGGTCAGTTCAGATGCCAGTAGGGAAAATGCAG
CTGCCAACGCGGGGTCCACGTCCTCATCCCAAGAGGCCACCCCCGAGAAGGAGTCCCTGGCCAAGTCGGCAGCCGCCTAC
ACCAAGGCAAAGGAGCGGAAGTGCTTGTTGGAAAAAAGTGGAAGTCATCACGGGGAGGAGGCGGAGAGCAACGTGTTACA
GATGTAGTGCAAGCTCTTTGTCTTTGACAAGGCCTCACAGTCCTGGGTGGAGAGAGGCCGGGGGCTGCTCAGACTCAATG
ACATGGCGTCCACTGACGATGGCACGCTACAGTCCCGACTAGTAATGCGGACCCAGGGGAGCCTGCGACTGATCCTCAAC
ACCAAGCTGTGGGCCCAGATGCAGATCGACAAGGCCAGCGAGAAGAGCATCCGCATCATGGCCATGGACACCGAGGACCA
GGGCGGGAAGGTCTTCCTGATCTCGGCCAGCTCCAAGGACACAGGTCAGCTGTATGCAGCCCTGCAGCACCACATCCTGG
CCTTAGGCAGCCGCGGGGAGTGGGAGCAGGTGGCCAAGATGCCCGCCCCGGAGCCTGGAGCAGCCCCATCCAACGAGGAG
GATGACAGTGACGACGACGATGTCCTGGCTCCTTCAGGGGCAACTGCAGCCGGTGCTAATGACGAAGGGGACGGGCAGAC
GACTGGGAGCACA
ORF - retro_cjac_3012 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.57 % |
| Parental protein coverage: | 71.43 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | KPKEQQRSVLRPAVL-QAPQPKALSQTVPSSGTNGVSIPADCTEAVPAASPDNPARRSPSEAADEVCALE |
| .P.E.QRSVL..AV..QAPQPKALSQ.VPSSGTNGVS.PAD.TEAVPAASPDNPA..SPS.AADEVCALE | |
| Retrocopy | EPREKQRSVLPMAVI<QAPQPKALSQMVPSSGTNGVSLPADRTEAVPAASPDNPAGKSPSQAADEVCALE |
| Parental | EKEPQKNESGNASEEEACEKKDPATQQAFVFGQNLRDRVKLINESADEADMENAGHPSADTPAA-TNYFL |
| EKEPQKNES..ASEEEACEKKDP.TQQAFV.GQNLRD.V.................PSADTPA..TNYFL | |
| Retrocopy | EKEPQKNESSDASEEEACEKKDPTTQQAFVLGQNLRDGVXXXXXXXXXXXXXXXXXPSADTPAG<TNYFL |
| Parental | QYISSSLENSTNSADASSNKFVFGQNMSERVLSFPKLNEVSSDASRENAAAESGSESSSQEATPEKESLA |
| Q.ISSSLENSTNSADASSNK.VFGQN.SERVLSFPKLNEVSSDASRENAAA..GS.SSSQEATPEKESLA | |
| Retrocopy | QRISSSLENSTNSADASSNKLVFGQNLSERVLSFPKLNEVSSDASRENAAANAGSTSSSQEATPEKESLA |
| Parental | ESAAAYTKATARKCLLEK-VEVITG-EEAESNVLQMQCKLFVFDKASQSWVERGRGLLRLNDMASTDDGT |
| .SAAAYTKA..RKCLLEK.VEVITG.EEAESNVLQM.CKLFVFDKASQSWVERGRGLLRLNDMASTDDGT | |
| Retrocopy | KSAAAYTKAKERKCLLEK>VEVITG<EEAESNVLQM*CKLFVFDKASQSWVERGRGLLRLNDMASTDDGT |
| Parental | LQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRITAMDTEDQGVKVFLISASSKDTGQLYAALHHRI |
| LQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRI.AMDTEDQG.KVFLISASSKDTGQLYAAL.H.I | |
| Retrocopy | LQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRIMAMDTEDQGGKVFLISASSKDTGQLYAALQHHI |
| Parental | LALRSRVEQEQEAKMPAPEPGAAPSNEEDDSDDDDVLAPSGATSAGAGDEGDGQTTGST |
| LAL.SR.E.EQ.AKMPAPEPGAAPSNEEDDSDDDDVLAPSGAT.AGA.DEGDGQTTGST | |
| Retrocopy | LALGSRGEWEQVAKMPAPEPGAAPSNEEDDSDDDDVLAPSGATAAGANDEGDGQTTGST |
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 | 7 .52 RPM |
| SRP051959_heart | 0 .02 RPM | 10 .72 RPM |
| SRP051959_kidney | 0 .00 RPM | 10 .87 RPM |
| SRP051959_liver | 0 .02 RPM | 5 .24 RPM |
| SRP051959_lung | 0 .00 RPM | 13 .88 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 13 .24 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 9 .06 RPM |
| SRP051959_spleen | 0 .00 RPM | 11 .34 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3012 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3012 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3012 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 | ENSCJAG00000016791 | 1 retrocopy |
retro_cjac_3012 ,
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