RetrogeneDB ID: | retro_cjac_811 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:99448311..99448803(-) | ||
| Located in intron of: | ENSCJAG00000020436 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GSTM1 | ||
| Ensembl ID: | ENSCJAG00000003123 | ||
| Aliases: | None | ||
| Description: | glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632] |
Retrocopy-Parental alignment summary:
>retro_cjac_811
ATGCCTATGATACTGGGATACTGGGACATCCGCGCGCTAGCCCACGCCATCTGCCTGCTCCTGGAATACACACACAGACT
CAAACTACGAGGAAAAGATGTACACAATGGGGGACGCTCCTGACTATGACAGAAGCCAGTGGCTGAATGAAAAGTTCAAG
CTTGGCCTGGACTTTTCCAATCTGCCCTACTTGATTGATGGGGCTCACAAGATCACTCAGAGCCATGCCATCCTGCGCTA
TATTGCCCGCAAGCACAACCTGTGTGGGGAGACAGAAAAGGAGAAGATTTGAGAAGACATTTTGGAGAACCAGCTTATGG
ACAACCACATGCAGCTGGCCAGACTCTGCTACGATCCAGATTTTGAGAGACTAAAGCCAGAATACCTGGAGGGACTTCCT
GAAATGCTGAAGCTCTACTCACAGTTTCTGGGGAAGCGGCCATGGTTTCTTGGGGACAGATCACCTTTGTGGATTTCATC
GCTTATGAAATC
ORF - retro_cjac_811 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.12 % |
| Parental protein coverage: | 74.77 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MPMTLGYWDIRGLAHAIRLLLEYT-DSSYEEKK-YTMGDAPDYDRSQWLKEKFKLGLDFPNLPYLIDGAH |
| MPM.LGYWDIR.LAHAI.LLLEYT...S..E.K.YTMGDAPDYDRSQWL.EKFKLGLDF.NLPYLIDGAH | |
| Retrocopy | MPMILGYWDIRALAHAICLLLEYT>TDSNYEEKMYTMGDAPDYDRSQWLNEKFKLGLDFSNLPYLIDGAH |
| Parental | KITQSNAILRYIARKHSLCGETEEEKIRVDILENQTMDTRMQLAMLCYNPEFEKLKPKYLEELPEKLKLY |
| KITQS.AILRYIARKH.LCGETE.EKI..DILENQ.MD..MQLA.LCY.P.FE.LKP.YLE.LPE.LKLY | |
| Retrocopy | KITQSHAILRYIARKHNLCGETEKEKI*EDILENQLMDNHMQLARLCYDPDFERLKPEYLEGLPEMLKLY |
| Parental | SQFLGKRPWFAGDK-ITFVDFLAYDV |
| SQFLGKRPWF.GD..ITFVDF.AY.. | |
| Retrocopy | SQFLGKRPWFLGDR<ITFVDFIAYEI |
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 .53 RPM | 24 .03 RPM |
| SRP051959_heart | 0 .19 RPM | 18 .65 RPM |
| SRP051959_kidney | 0 .33 RPM | 30 .02 RPM |
| SRP051959_liver | 0 .41 RPM | 15 .47 RPM |
| SRP051959_lung | 0 .29 RPM | 19 .57 RPM |
| SRP051959_lymph_node | 0 .39 RPM | 13 .36 RPM |
| SRP051959_skeletal_muscle | 0 .39 RPM | 8 .84 RPM |
| SRP051959_spleen | 0 .29 RPM | 22 .65 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_811 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_811 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_811 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 7 parental genes, and 17 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000879 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000003123 | 7 retrocopies |
retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004, retro_cjac_3084, retro_cjac_811 ,
|
| Callithrix jacchus | ENSCJAG00000003168 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000005148 | 2 retrocopies | |
| Nomascus leucogenys | ENSNLEG00000003194 | 2 retrocopies | |
| Pongo abelii | ENSPPYG00000001064 | 2 retrocopies | |
| Pan troglodytes | ENSPTRG00000001061 | 2 retrocopies |