RetrogeneDB ID: | retro_cjac_2442 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:54981734..54983880(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FTSJD2 | ||
| Ensembl ID: | ENSCJAG00000005567 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2442
CCCCCATCAACAAACAAAAAAAGAGTTGCAGAGCTTGCCCTGAGCCTCAGCTCCACGTCCAATGACGAACCTCCTTCCTC
TGTCAATCATGGAGCAAAAGCATCTGCTACAAGCCTTAGTGGGTCTGACAGTGATTCCGAGGGGAAACAACGCAGCTCTG
ACTCTTTTGATGATGCAGTCAAAGCAGACTCCCTTGTGGAGGGAACTTCTTCTCGCTACTCCATGTATAATAGTGTCTCC
CAGAAGCTTATGGCCAAGATGGGCTTCAGGGAAGGTGAAGGAATGGGCAAATACGACCAGGGTTGGAAGGACATCGTTGA
GACTTCCAATCAGAAAGGTCAACGAGACTTGGGTCTGACACTCCAGGGCTTTGACCAGATGCTGAACATGGACTGGTGAG
ATGATCCAGAACCCCGTGCCTGTGAGCAGGTGTCATGGTTCCCTGAATGTACCACTGAAATTCCTGACACTAAGGAAATG
AATGATTGGATGGTTGTAGAAAAGAGAAAGATGATTATTGAAGATGAAACAGAGTTTTGTGGGGAAGAGCTCTTCATAGT
GTTGCAGTGTAAGAGCATGTTGGATGTCCTGGATGGGGAAGAGATGCGGCAAGCTCAGACTCGGGCCAATCCCTACGAGA
TGATCCGAGGAGTCTTCTTTCTAAACAGGGCAGCAATGAAGATGGCTAACATGGATTTTGTGTTTGATTGCATGTTCACA
AATCTGAGGGACTCTTATGGGAAGCCACTGGTGAAGGACTGGGAAGCTGAGCTTCTGTACTTTGCTGATGTCTGCGCAGG
CCCAGGAGGCTTCTGAGAGTATGTGCTGTGGTGGAAGAAGTGGCATGCAAAGGGCTTTGGAATGACTTGGAAGGGCCCTA
ATGACTTCAAGCTGGAGGACTTCTACTCTGCCTCCAGTGAACTCTCTGAACCCTACTATGGTGAAGGTGGGATTGATGGA
GATGGAGATATCACCCGCCCAGAGAAAACATCTCTGCTTTTCAGAATTTTGTCCTGGATAACACAGATCGCAAGGGTGTC
CACTTTCTGATGGCCGATGGGGGTTTCTTAGTGGAGGGACAGGAGAACCTACAGGAGATCCTCAGCAAGCAGCTCCTGCT
GTGTCAGTTCCTCATGGCGCTGTCCATTGTCCGGACAGGAGGCCACTTCATCTGTAAAACCTTTGACCTTTTCACACCAT
TCAGTGTGGGGCTTGTCTACCTGCTGTACTGCTGCTTTGAACGAGTTTGTCTCTTCAAGCCTATTACCAGCCGTCCTGCC
AACTCAGAGAGGTACATGGTGTGCAAGGGCCTGAAGGTGGGCATAGATGACATTCAGGATTACCTCTTCGCAGTAAATAT
TAAACTCAATCAGCTGCAGAACACTGATTCTGACGTCAACTTGGTGGTCCCGCTGGAGGTGATCAAGGGAGACCATGAAT
TTACTGACTGCATGATATGGACCAAGGAGAGCCACTGTAGTCTACAAATTAAAGCTCTGGTGAAAAATTATGTCTTTGTT
CAAGACATGACACTAAGTGAGCCTCGGCAAGCAGAGATCCGGAAGGAGTGCCTCCGACTCTGGGGGATCCCAGACCAGGC
TCGTGCGGCTCCTTCCTCAGACCCCAAATCAAAGTTCTTTGAGCTGATCCAGGGTACTGAGATTGACATCTTCAGCTACA
AGCCCACACTGCTCACCTCTAAAACCCTGGAGAAGATCTGCCCTGTGTTTGACTACTGCTGCATGGTGTCTGGCAGTGAG
CAGAAGTTCCTCATTGGCCTAGGGAAATCCCAGATCTACACGTGGGATGGCTGCCAGTCAGACCACTGGGTCAAGCTAAA
CCTGAAGACAGAGCTGCCCTGGGACACTCTGCTGTCTGTGGAAATTGTACATGAGCTGAAAAGGGAGGGGAAGGCCCAGC
GGAAGATCAGTGCCATCTATATCCTTGATGTCCTTGTGCTGAATGGCACCGATCTCTGGGAGCAGCATTTTAACTGTGAA
TTCAGCTTGCTGAGAAATTTGTGAAAGCCGTTTCGAAGCCTAGTTGGCCTGACATGAATTGCATCAGGGTGAAGAAGGTG
TAAAGACTGGAAGAGATGGAGAAGATTTTTGTCAGGTTGGAGATGAAGATCATCAAGGGCTCCAGT
ORF - retro_cjac_2442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.72 % |
| Parental protein coverage: | 85.87 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PIKKQKKRVAELALSLSSTSDDEPPSSVNHGAKASATSLSGSDSETEGKQRSSDSFDDAFKADSLVEGTS |
| P....KKRVAELALSLSSTS.DEPPSSVNHGAKASATSLSGSDS..EGKQRSSDSFDDA.KADSLVEGTS | |
| Retrocopy | PPSTNKKRVAELALSLSSTSNDEPPSSVNHGAKASATSLSGSDSDSEGKQRSSDSFDDAVKADSLVEGTS |
| Parental | SRYSMYNSVSQKLMAKMGFREGEGLGKYSQGRKDIVEASNQKGRRGLGLTLRGFDQELNVDWRDEPEPSA |
| SRYSMYNSVSQKLMAKMGFREGEG.GKY.QG.KDIVE.SNQKG.R.LGLTL.GFDQ.LN.DW.D.PEP.A | |
| Retrocopy | SRYSMYNSVSQKLMAKMGFREGEGMGKYDQGWKDIVETSNQKGQRDLGLTLQGFDQMLNMDW*DDPEPRA |
| Parental | CEQVSWFPECTTEIPDTKEMSDWMVVGKRKMIIEDETEFCGEELLHSVLQCKSVFDVLDGEEMRRARTRA |
| CEQVSWFPECTTEIPDTKEM.DWMVV.KRKMIIEDETEFCGEEL...VLQCKS..DVLDGEEMR.A.TRA | |
| Retrocopy | CEQVSWFPECTTEIPDTKEMNDWMVVEKRKMIIEDETEFCGEELF-IVLQCKSMLDVLDGEEMRQAQTRA |
| Parental | NPYEMIRGVFFLNRAAMKMANMDFVFDRMFTNPRDSYGKPLVKDREAELLYFADVCAGPGGFSEYVLWRK |
| NPYEMIRGVFFLNRAAMKMANMDFVFD.MFTN.RDSYGKPLVKD.EAELLYFADVCAGPGGF.EYVLW.K | |
| Retrocopy | NPYEMIRGVFFLNRAAMKMANMDFVFDCMFTNLRDSYGKPLVKDWEAELLYFADVCAGPGGF*EYVLWWK |
| Parental | KWHAKGFGMTLKGPNDFKLEDFYSASSELFEPYYGEGGIDGDGDITRPENIS-AFR-NFVLDNTDRKGVH |
| KWHAKGFGMT.KGPNDFKLEDFYSASSEL.EPYYGEGGIDGDGDITRPE..S..FR.NFVLDNTDRKGVH | |
| Retrocopy | KWHAKGFGMTWKGPNDFKLEDFYSASSELSEPYYGEGGIDGDGDITRPEKTSLLFR<NFVLDNTDRKGVH |
| Parental | FLMADGGFSVEGQENLQEILSKQLLLCQFLMALSIVRTGGHFICKTFDLFTPFSVGLVYLLYCCFERVCL |
| FLMADGGF.VEGQENLQEILSKQLLLCQFLMALSIVRTGGHFICKTFDLFTPFSVGLVYLLYCCFERVCL | |
| Retrocopy | FLMADGGFLVEGQENLQEILSKQLLLCQFLMALSIVRTGGHFICKTFDLFTPFSVGLVYLLYCCFERVCL |
| Parental | FKPITSRPANSERYVVCKGLKVGIDDVRDYLFAVNIKLNQLRNTDSDVNLVVPLEVIKGDHEFTDYMIRS |
| FKPITSRPANSERY.VCKGLKVGIDD..DYLFAVNIKLNQL.NTDSDVNLVVPLEVIKGDHEFTD.MI.. | |
| Retrocopy | FKPITSRPANSERYMVCKGLKVGIDDIQDYLFAVNIKLNQLQNTDSDVNLVVPLEVIKGDHEFTDCMIWT |
| Parental | NESHCSLQIKALAKIHAFVQDTTLSEPRQAEIRKECLRLWGIPDQARVAPSSSDPKSKFFELIQGTEIDI |
| .ESHCSLQIKAL.K...FVQD.TLSEPRQAEIRKECLRLWGIPDQAR.AP.SSDPKSKFFELIQGTEIDI | |
| Retrocopy | KESHCSLQIKALVKNYVFVQDMTLSEPRQAEIRKECLRLWGIPDQARAAP-SSDPKSKFFELIQGTEIDI |
| Parental | FSYKPTLLTSKTLEKIRPVFDYRCMVSGSEQKFLIGLGKSQIYTWDGRQSDRWVKLDLKTELPRDTLLSV |
| FSYKPTLLTSKTLEKI.PVFDY.CMVSGSEQKFLIGLGKSQIYTWDG.QSD.WVKL.LKTELP.DTLLSV | |
| Retrocopy | FSYKPTLLTSKTLEKICPVFDYCCMVSGSEQKFLIGLGKSQIYTWDGCQSDHWVKLNLKTELPWDTLLSV |
| Parental | EIVHELKGEGKAQRKISAIHILDVLVLNGTDVREQHFNQR-IQLAEKFVKAVSKPSRPDMNPIRVKEVYR |
| EIVHELK.EGKAQRKISAI.ILDVLVLNGTD..EQHFN...IQLAEKFVKAVSKPS.PDMN.IRVK.V.R | |
| Retrocopy | EIVHELKREGKAQRKISAIYILDVLVLNGTDLWEQHFNCE<IQLAEKFVKAVSKPSWPDMNCIRVKKV*R |
| Parental | LEEMEKIFVRLEMKIIKGSS |
| LEEMEKIFVRLEMKIIKGSS | |
| Retrocopy | LEEMEKIFVRLEMKIIKGSS |
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 .42 RPM | 21 .46 RPM |
| SRP051959_heart | 0 .96 RPM | 22 .78 RPM |
| SRP051959_kidney | 0 .58 RPM | 24 .16 RPM |
| SRP051959_liver | 0 .17 RPM | 17 .78 RPM |
| SRP051959_lung | 1 .09 RPM | 24 .74 RPM |
| SRP051959_lymph_node | 1 .42 RPM | 24 .09 RPM |
| SRP051959_skeletal_muscle | 0 .13 RPM | 25 .09 RPM |
| SRP051959_spleen | 0 .63 RPM | 24 .79 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2442 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2442 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2442 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 | ENSCJAG00000005567 | 1 retrocopy |
retro_cjac_2442 ,
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