RetrogeneDB ID: | retro_cjac_586 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:90556574..90557883(-) | ||
| Located in intron of: | ENSCJAG00000003268 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LSG1 | ||
| Ensembl ID: | ENSCJAG00000013962 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_586
AGCGCCTGGGCCACACACTTTGAAAAAGAAGACGTGAAGGTTATTTTCTGGTCAGCTCTGGCCAGAGGCATTCACCTGAA
CGCTGACTCTGAGGAAGAGGTAAACAGAGATGATAGACAAAGCAACACAATTGAGTTTGAAAACTCCAGTTTCGACAAGG
CTGAAATTTCACACAATGAGATCAAACATCTCCCAGCCAGGGACTCTCCTTCACTTAGTGAAAATCCCACTACTGATGAA
GAGGACAGTGAGTATGGGCACTGTCAGGAGGAAGAGGAAGATGACTGGCAGACACGTTCAGAAGAAGACAGTCCTGATGA
AGAGGACTGTGGCCAGGACTGGAAGGAAAGCTATATGACAGATTCTGAGGCTCCGGGCAGGAACACCCCACAGAAGAGAC
AGACACACAACTTTAGCCATCTGGTATCAAAGCAGGAGTTACTAGAGCTTTTTAAGGAGCTACATACCGGGAAGAAGGTG
AAAGATGGGCAACTTACAGTCGGACTGGTGGGCTACCCTAATGTTGGTAAGAGTTCAACAATCAACACCATCATGGGCAA
CAAGAAAGTATCTGTGTCTGCCACACCTGGTCACACGAAGCACTTTCAGACACTCTACGTGGAGCCTGGCCTCTGCCTAT
GTGACTGCCTAGGTTTGGTGATGCCATCTTTTGTGTCCACCAAGGCAGAAATGACTTGCAGCAGAATCCTCCCAATTGAT
CAGATGGGAGATCTCGTTCCACCTGTATCATTAGTTTGCCAGAATATTCTAAGACATGTTTTAGAAGTTACCTATGGGAT
GAATATCATAAAGCCTAGAGAGGATGATGATCCCCACCGACCTCCAACATCAGAAGAACTGTTAACAGCTTATGGATATA
TGCGAGGATTCATGACAGCGCATGGACAGTCAGACCAGCCTCGATCTGCGCACTATATCCTGAAGGACTATGTCAGTGGT
AAGCTGCTGTACTGCCATCCTCCCTCCTGGAAGAGATCCTGTAACTTTTCGGATCAACACCAGTGACTCCTAGAGAGCAA
AACGAATGGTGATGAAATAAAAATGCAGCCAGGCAGAAATAAAAAAAGCAAAGCAGATTAAAAATATAGTTGATAAAACT
TTTTTCCATCAAGAGAATGTGAGAGCTTTGACCAAAGGAGTCCAGGCTGTGATGGGTTACAAGCCCAGGAGCAGGGTATT
GACTGCGGCTACTGTGAGCTCTGAGAATGGGGCAGAGATGCCCTGGAAGAAACATGGCAACAGAAATAAAAAAGAAAAAA
GTCATAGACTCTATAAGCACCTGGAAATG
ORF - retro_cjac_586 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.66 % |
| Parental protein coverage: | 66.26 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SAWATHFEKEDVKVIFWSALAGGIHLNADSEEEVNRDDRQSNTTEFENSSFDEAEISHSETEHLPARDSP |
| SAWATHFEKEDVKVIFWSALA.GIHLNADSEEEVNRDDRQSNT.EFENSSFD.AEISH.E..HLPARDSP | |
| Retrocopy | SAWATHFEKEDVKVIFWSALARGIHLNADSEEEVNRDDRQSNTIEFENSSFDKAEISHNEIKHLPARDSP |
| Parental | SRSENPTTDEDDSEYEDCQEEEEDDWQTCSEEDSPDEEDCGQDWKESCMSDSEAPGRNTPQKRQIHNFSH |
| S.SENPTTDE.DSEY..CQEEEEDDWQT.SEEDSPDEEDCGQDWKES.M.DSEAPGRNTPQKRQ.HNFSH | |
| Retrocopy | SLSENPTTDEEDSEYGHCQEEEEDDWQTRSEEDSPDEEDCGQDWKESYMTDSEAPGRNTPQKRQTHNFSH |
| Parental | LVSKQELLELFKELHTGKKVKDGQLTVGLVGYPNVGKSSTINTIMGNKKVSVSATPGHTKHFQTLYVEPG |
| LVSKQELLELFKELHTGKKVKDGQLTVGLVGYPNVGKSSTINTIMGNKKVSVSATPGHTKHFQTLYVEPG | |
| Retrocopy | LVSKQELLELFKELHTGKKVKDGQLTVGLVGYPNVGKSSTINTIMGNKKVSVSATPGHTKHFQTLYVEPG |
| Parental | LCLCDCPGLVMPSFVSTKAEMTCSGILPIDQMRDHVPPVSLVCQNIPRHVLEVTYGINIIKPREDEDPHR |
| LCLCDC.GLVMPSFVSTKAEMTCS.ILPIDQM.D.VPPVSLVCQNI.RHVLEVTYG.NIIKPRED.DPHR | |
| Retrocopy | LCLCDCLGLVMPSFVSTKAEMTCSRILPIDQMGDLVPPVSLVCQNILRHVLEVTYGMNIIKPREDDDPHR |
| Parental | PATSEELLTAYGYMRGFMTAHGQPDQPRSARYILKDYVSGKLLYCHP-PPGRDPVTFQ-HQHQQLLESKT |
| P.TSEELLTAYGYMRGFMTAHGQ.DQPRSA.YILKDYVSGKLLYCHP.PPGRDPVTF...QHQ.LLESKT | |
| Retrocopy | PPTSEELLTAYGYMRGFMTAHGQSDQPRSAHYILKDYVSGKLLYCHP>PPGRDPVTFR<DQHQ*LLESKT |
| Parental | NGDEIKIQPGRN-KKAKQIENIVDETFFHQENVRALTKGVQAVMGYKPESRIVTAATASSENGAGKPWKK |
| NGDEIK.QPGRN.KKAKQI.NIVD.TFFHQENVRALTKGVQAVMGYKP.SR..TAAT.SSENGA..PWKK | |
| Retrocopy | NGDEIKMQPGRN>KKAKQIKNIVDKTFFHQENVRALTKGVQAVMGYKPRSRVLTAATVSSENGAEMPWKK |
| Parental | HGNRNKKEKSRRLYKHLDM |
| HGNRNKKEKS.RLYKHL.M | |
| Retrocopy | HGNRNKKEKSHRLYKHLEM |
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 | 2 .80 RPM | 15 .29 RPM |
| SRP051959_heart | 1 .89 RPM | 24 .63 RPM |
| SRP051959_kidney | 2 .35 RPM | 55 .51 RPM |
| SRP051959_liver | 0 .54 RPM | 24 .50 RPM |
| SRP051959_lung | 2 .21 RPM | 27 .70 RPM |
| SRP051959_lymph_node | 0 .87 RPM | 24 .73 RPM |
| SRP051959_skeletal_muscle | 1 .03 RPM | 24 .92 RPM |
| SRP051959_spleen | 2 .69 RPM | 26 .83 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_586 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_586 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_586 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 | ENSCJAG00000013962 | 1 retrocopy |
retro_cjac_586 ,
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