RetrogeneDB ID: | retro_cjac_2740 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:79560573..79562221(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000034296 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ME1 | ||
| Ensembl ID: | ENSCJAG00000009064 | ||
| Aliases: | None | ||
| Description: | Malic enzyme [Source:UniProtKB/TrEMBL;Acc:F6Y1T8] |
Retrocopy-Parental alignment summary:
>retro_cjac_2740
CTTGATTCTGACTTGGCCTTTACCCTGGAAGAGAGACAGCAATTGAACATTCATGGATTGTTGCCACCTTCCTTCATCAG
TCAGGAGATTCAGGTCCTTAGAGTACTAATAAATTTTGAGCGTCTGAAGTCTGACTTTGACAGGTATCTTCTCTTAATGG
ATCTCCAAGGTAGAAATGAAAAACTCTTTTATCGAGTGCTAACATCTGACATTGAGAAATTCATGCCTATTGTTTATACT
CCCACTGTGGGTCTGGCTTGCCAACGATATAGTTTAGTGTTTCGAAAGCCAAGAGGTCTCTTTATTAGTATCCATGATTG
TGGGCATATTGCTTCAGTTCTCAATGCATGGCCAGAAGATGTCATCAAGGCCATTGTGATGACCGATGGAGAGTGTATTC
TTGGCTTGGGAGATCTTGGCTGTAATGGAATGGGCATCCCTGTGGGTAAATTGGCTCTATATACAGCTTGTGGAGGGATG
AATCCTCAAGAATGTCTGCCTGTCATTCTGGATGTGGGAACTGAAAATGAGGAGTTACTTAAAGATCCACTCTACGTTGG
ACTACGGCAGAGAAGAGTAAGAGGTTCTGAATATGATGATTTTTTTGGATGAATTCATGGAGGCAGTTTCTTCCAAGTAT
GGCATGAATTGCCTTACTCAGTTTGAAGATTTTGCCAACGTGAATGCACTTCGTCTCCCGAACAAGTATCGAAACCACTA
TTGCACATTCAATGATGATATTCAAGAAACAGCGTCTGTTGCAGTAGCAGGTCTCCTTGCAGCTCTTGGAATAACCAAGA
ACAAACTGTCTGATCAAACAATACTATTCCAAGGAGCTGGAGAGGCTGCCTTAGGGATTGCACACCTGATTGTGATGGCA
ATGGAAAAAGAAGGTTTACCAAAAGAGAAACCCATCAAAAAGATATGGTTGGTTGATTCAAAAGGATTAATAGTTAAGGG
ACGTGCTTCCTTAACACAAGAGAAAGAGAAATTTGCCCATGAACATGAAGAAATGAAGAATCTAGAAACCATTGTTCAAG
AAATAAAACCAACTGCCCTCATAGGAGTTGCTGCAATTGGTGGTGCATTCTCAGAACAAATTCTCAAAGATATGGCTGCC
TTCAATGAACGGCCTATTATTTTTGCTTTGAGTAATCCAACTAGCAAAGCAGAATGTTCTGCAGAGCAGTGCTATAAAAT
AACCAAGGGACGTGCAATTTTTGCCAGTGGCAGTCCTTTTGATCCAGTCAGTCTACCAAATGGACAGACCCTATATCCTG
GGCAAGGCAACAATTCCTATGTGTTCCCTGGAGTTGCTCTTGGTGTTGTGGCGTGTGGATTGAAGCACATCACAGATAAT
GTTTTCCTCACTACTGCTGAGGTTATAGCTCAGCAAGTGTCAGATAAACACTTGGAAGAGGGTTAGCTTTATCCTCCTTT
GAATACCATTAGAGATATTTCTCTGAAAATTGCAGAAAAGATTGTGAAAGATGCATACCAAGAAAAGACAGCCACAGTTT
ATCCTGAACTGCAAAACAAAGAAGCATTTATCCGCTCCCAGATGTATAGTACTGATTATGACCAGATTCTACCTGATTGT
TATTCTTGGCCTGAAGAGGTCCAGAAAATACAGACCAAAGTTGACCAG
ORF - retro_cjac_2740 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.64 % |
| Parental protein coverage: | 95.98 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LNKDLAFTLEERQQLNIHGLLPPSFISQEIQVLRVLKNFERLKSDFDRYLLLMDLQDRNEKLFYRVLTSD |
| L..DLAFTLEERQQLNIHGLLPPSFISQEIQVLRVL.NFERLKSDFDRYLLLMDLQ.RNEKLFYRVLTSD | |
| Retrocopy | LDSDLAFTLEERQQLNIHGLLPPSFISQEIQVLRVLINFERLKSDFDRYLLLMDLQGRNEKLFYRVLTSD |
| Parental | IEKFMPIVYTPTVGLACQQYSLVFRKPRGLFISIHDRGHIASVLNAWPEDVIKAIVVTDGERILGLGDLG |
| IEKFMPIVYTPTVGLACQ.YSLVFRKPRGLFISIHD.GHIASVLNAWPEDVIKAIV.TDGE.ILGLGDLG | |
| Retrocopy | IEKFMPIVYTPTVGLACQRYSLVFRKPRGLFISIHDCGHIASVLNAWPEDVIKAIVMTDGECILGLGDLG |
| Parental | CNGMGIPVGKLALYTACGGMNPQECLPVILDVGTENEELLKDPLYIGLRQRRVRGSEYDDF-LDEFMEAV |
| CNGMGIPVGKLALYTACGGMNPQECLPVILDVGTENEELLKDPLY.GLRQRRVRGSEYDDF.LDEFMEAV | |
| Retrocopy | CNGMGIPVGKLALYTACGGMNPQECLPVILDVGTENEELLKDPLYVGLRQRRVRGSEYDDF>LDEFMEAV |
| Parental | SSKYGMNCLIQFEDFANMNAFRLLNKYRNHYCTFNDDIQGTASVAVAGLLAALRITKNKLSDQTILFQGA |
| SSKYGMNCL.QFEDFAN.NA.RL.NKYRNHYCTFNDDIQ.TASVAVAGLLAAL.ITKNKLSDQTILFQGA | |
| Retrocopy | SSKYGMNCLTQFEDFANVNALRLPNKYRNHYCTFNDDIQETASVAVAGLLAALGITKNKLSDQTILFQGA |
| Parental | GEAALGIAHLIVMAMEKEGLPKEKAIKKIWLVDSKGLIVKGRASLTQEKEKFAHEHEEMKNLETIVQEIK |
| GEAALGIAHLIVMAMEKEGLPKEK.IKKIWLVDSKGLIVKGRASLTQEKEKFAHEHEEMKNLETIVQEIK | |
| Retrocopy | GEAALGIAHLIVMAMEKEGLPKEKPIKKIWLVDSKGLIVKGRASLTQEKEKFAHEHEEMKNLETIVQEIK |
| Parental | PTALIGVAAIGGAFSEQILKDMAAFNERPIIFALSNPTSKAECSAEQCYKITKGRAIFASGSPFDPVTLP |
| PTALIGVAAIGGAFSEQILKDMAAFNERPIIFALSNPTSKAECSAEQCYKITKGRAIFASGSPFDPV.LP | |
| Retrocopy | PTALIGVAAIGGAFSEQILKDMAAFNERPIIFALSNPTSKAECSAEQCYKITKGRAIFASGSPFDPVSLP |
| Parental | NGQTLYPGQGNNSYVFPGVALGVVACGLKHITDKVFLTTAEVIAQQVSDKHLEEGRLYPPLNTIRDVSLK |
| NGQTLYPGQGNNSYVFPGVALGVVACGLKHITD.VFLTTAEVIAQQVSDKHLEEG.LYPPLNTIRD.SLK | |
| Retrocopy | NGQTLYPGQGNNSYVFPGVALGVVACGLKHITDNVFLTTAEVIAQQVSDKHLEEG*LYPPLNTIRDISLK |
| Parental | IAEKIVKDAYQEKTATVYPEPQNKEAFILSQMYSTDYDQILPDCYSWPEEVQKIQTKADQ |
| IAEKIVKDAYQEKTATVYPE.QNKEAFI.SQMYSTDYDQILPDCYSWPEEVQKIQTK.DQ | |
| Retrocopy | IAEKIVKDAYQEKTATVYPELQNKEAFIRSQMYSTDYDQILPDCYSWPEEVQKIQTKVDQ |
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 .31 RPM |
| SRP051959_heart | 0 .02 RPM | 18 .14 RPM |
| SRP051959_kidney | 0 .02 RPM | 5 .17 RPM |
| SRP051959_liver | 0 .00 RPM | 15 .40 RPM |
| SRP051959_lung | 0 .03 RPM | 3 .30 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .30 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 12 .71 RPM |
| SRP051959_spleen | 0 .02 RPM | 2 .96 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2740 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2740 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2740 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001929 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000009064 | 1 retrocopy |
retro_cjac_2740 ,
|
| Mus musculus | ENSMUSG00000032418 | 1 retrocopy |