RetrogeneDB ID: | retro_cjac_3317 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:76935487..76937194(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TLE1 | ||
| Ensembl ID: | ENSCJAG00000003424 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3317
ACAGAGAGCCGGGCACAAGTAATTCCCTCCTGGTCCCAGACAGATAAATGTAGAAATGAGCCAGAATTTTCCAATGACAT
CAAGAAAAGGAAGGTGGATGATAAGGACTCCAGCCATTATGACAGTGATGGTGACAAAAGAGACAACTAAGTTGTAGATG
TGTCTAATGAGGACCCACCTTCCCCATGAGCAAGCCCTGCCCACTCTCCCAGGGAAAATGGAATCGACAAGAACCGCCTG
CTAAAGAAGGATGCTTCTAGCAGGCCGGCTTCCACAGCCTCCTCATGAAGTTCCACGTCTTTGAAATCCAAAGAAATGAC
TTTGCATGAAAAAGCCAGCAGGCCTGTTCTGAAATCTAGCACACCAATGCCTCGGAGTGACATGCCAATGCCAGGCACCA
GCGCCACTTCAGGCCTCCGTCCAGGCCTCAGCAAGCCTTCAGCCATAGACCCCCTCATTAACCAAGCAGCAGCTGGCTTT
AGAACACCCCTGGCAGTGCCCAGCCCATACCCTGCTTCTTTTGGGATGGTCCCCCATGCTGGCTTGAACAGCGAGCTGAC
CAGCCCAGGTGCCGCCTCTGCCAGTTTACACAACATGTCACCCTAGATGAGTGCTGCAGCTGTCATGGCTGCCGTGGTGG
CCTATGGGCGCTCCCCCATGGTGGGGTTTGATCCTCCCCCTCACATGAGAGTATTTACCATTCCTCCAAAACTGGCAGGA
ATCCCCAGGGGAAAACCTGCATATTCCTTCCATGTTACTGCAGACGGTCAGTTGCAGCCTGTCCCTTTCCCCCCCAACGC
CTTCATCAGACCTGGAATCCCCCGGCACGCTCACCAGATCAACACCCTCAACCACAGGGACTTGGTGTGCACTGTGACCA
TCAGCAACCACACGACATAGGTGTACATGGGCGGGAAGGACTGCGTCAAGGTCTGGGACATCAGCCGCCCTGGCAATAAG
AGTCCTGTCTCCCAGCTCAACTGTCTGAATAGAGATAATGATATCTGTTCCTGTAAATTGCTACCTGATGGCTGCACTCT
TATAGTGGGAGGAGAAGCCAGTACTTTGTCCATTTGGGACCTGGCAGCTCTGACCCTGTGCATCAAGGCAGAGCTGACAT
CCTTGGCCCCTGCCTGCCACGCCCTGGCCATCAGCCCTGATTCCGAGGTCTGCTTCTCATGCTGCAGTGACAGCAGCATT
GCTGTGTGGGATCTGCACAACCAGATACTAGTGAGGCAATTCCAGAGCCACACAGATGGAGCCAGCTTTTCTAATGATGG
CACCAAGCTCTGGATGGGCGGTTTGGACAACACGGTCAGGTCCTGGGACCTGCGCAAGGGGCAGCAGCTGCAGCAGCACG
ACTTCACCTCCCAGATCTTCTCCCTGGGGTACTGCGTCACCAGGGAGTGGCTGGTGGTGGGTATGAAAAGCAGCAACGTG
TAGATGCTGCACATGAACAAGCCTGACAAGTACCAGCTGCACCTGCATGAGAGCTGCATGTTGTCCCTGAAATTTGCTTT
CTGCGGTAAATGGTTTGTGAGTACTGGAAAAGATAATCTCCTCAATGCTTGGCGGACCCCATATGGAGTCAGTATATTCC
AGTCCAAAGAGTACTCATCAGTGCCTAGCTGTGACATCTCTGTGGATGACAAGTACATAGTCACTGGCTCAGGGGACAAG
AAGGCTACGGTCTATGAAGTTATCTAC
ORF - retro_cjac_3317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.99 % |
| Parental protein coverage: | 74.42 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TSNSLLVPDSLRGTDKRRNGPEFSNDIKKRKVDDKDSSHYDSDGDKSDDNLVVDVSNEDPSSPRASPAHS |
| T.....V..S...TDK.RN.PEFSNDIKKRKVDDKDSSHYDSDGDK.D.N.VVDVSNEDP.SP.ASPAHS | |
| Retrocopy | TESRAQVIPSWSQTDKCRNEPEFSNDIKKRKVDDKDSSHYDSDGDKRD-N*VVDVSNEDPPSP*ASPAHS |
| Parental | PRENGIDKNRLLKKDASSSPASTASSGSSTSLKSKEMSLHEKASTPVLKSSTPTPRSDMPTPGTSATPGL |
| PRENGIDKNRLLKKDASS.PASTASS.SSTSLKSKEM.LHEKAS.PVLKSSTP.PRSDMP.PGTSAT.GL | |
| Retrocopy | PRENGIDKNRLLKKDASSRPASTASS*SSTSLKSKEMTLHEKASRPVLKSSTPMPRSDMPMPGTSATSGL |
| Parental | RPGLGKPPAIDPLVNQAAAGLRTPLAVPGPYPAPFGMVPHAGMNGELTSPGAAYASLHNMSPQMSAAAAA |
| RPGL.KP.AIDPL.NQAAAG.RTPLAVP.PYPA.FGMVPHAG.N.ELTSPGAA.ASLHNMSP.MSAAA.. | |
| Retrocopy | RPGLSKPSAIDPLINQAAAGFRTPLAVPSPYPASFGMVPHAGLNSELTSPGAASASLHNMSP*MSAAAVM |
| Parental | AAVVAYGRSPMVGFDPPPHMRVPTIPPNLAGIPGGKPAYSFHVTADGQMQPVPFPPDALIGPGIPRHARQ |
| AAVVAYGRSPMVGFDPPPHMRV.TIPP.LAGIP.GKPAYSFHVTADGQ.QPVPFPP.A.I.PGIPRHA.Q | |
| Retrocopy | AAVVAYGRSPMVGFDPPPHMRVFTIPPKLAGIPRGKPAYSFHVTADGQLQPVPFPPNAFIRPGIPRHAHQ |
| Parental | INTLNHGEVVCAVTISNPTRHVYTGGKGCVKVWDISHPGNKSPVSQLDCLNRDNYIRSCKLLPDGCTLIV |
| INTLNH...VC.VTISN.T..VY.GGK.CVKVWDIS.PGNKSPVSQL.CLNRDN.I.SCKLLPDGCTLIV | |
| Retrocopy | INTLNHRDLVCTVTISNHTT*VYMGGKDCVKVWDISRPGNKSPVSQLNCLNRDNDICSCKLLPDGCTLIV |
| Parental | GGEASTLSIWDLAAPTPRIKAELTSSAPACYALAISPDSKVCFSCCSDGNIAVWDLHNQTLVRQFQGHTD |
| GGEASTLSIWDLAA.T..IKAELTS.APAC.ALAISPDS.VCFSCCSD..IAVWDLHNQ.LVRQFQ.HTD | |
| Retrocopy | GGEASTLSIWDLAALTLCIKAELTSLAPACHALAISPDSEVCFSCCSDSSIAVWDLHNQILVRQFQSHTD |
| Parental | GASCIDISNDGTKLWTGGLDNTVRSWDLREGRQLQQHDFTSQIFSLGYCPTGEWLAVGMESSNVEVLHVN |
| GAS....SNDGTKLW.GGLDNTVRSWDLR.G.QLQQHDFTSQIFSLGYC.T.EWL.VGM.SSNV..LH.N | |
| Retrocopy | GAS---FSNDGTKLWMGGLDNTVRSWDLRKGQQLQQHDFTSQIFSLGYCVTREWLVVGMKSSNV*MLHMN |
| Parental | KPDKYQLHLHESCVLSLKFAYCGKWFVSTGKDNLLNAWRTPYGASIFQSKESSSVLSCDISVDDKYIVTG |
| KPDKYQLHLHESC.LSLKFA.CGKWFVSTGKDNLLNAWRTPYG.SIFQSKE.SSV.SCDISVDDKYIVTG | |
| Retrocopy | KPDKYQLHLHESCMLSLKFAFCGKWFVSTGKDNLLNAWRTPYGVSIFQSKEYSSVPSCDISVDDKYIVTG |
| Parental | SGDKKATVYEVIY |
| SGDKKATVYEVIY | |
| Retrocopy | SGDKKATVYEVIY |
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 .02 RPM | 14 .13 RPM |
| SRP051959_heart | 0 .18 RPM | 5 .38 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .74 RPM |
| SRP051959_liver | 0 .02 RPM | 12 .67 RPM |
| SRP051959_lung | 0 .15 RPM | 15 .71 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 20 .07 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 5 .35 RPM |
| SRP051959_spleen | 0 .04 RPM | 6 .01 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3317 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3317 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3317 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 | ENSCJAG00000003424 | 1 retrocopy |
retro_cjac_3317 ,
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