RetrogeneDB ID: | retro_cjac_1139 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 13:38810066..38810663(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CBR1 | ||
| Ensembl ID: | ENSCJAG00000038083 | ||
| Aliases: | None | ||
| Description: | carbonyl reductase 1 [Source:HGNC Symbol;Acc:1548] |
Retrocopy-Parental alignment summary:
>retro_cjac_1139
GAGTACGGAGGCCTGGACATGCTGGTCAACAACGCGGGCATCGCCTTCAAGGTTGCTGATCCCATACCCTTTCATATTCA
AGCTGAAGTGACGATGAAGACAAACTTCTTTGGTACTTGAGATGTCTGCACAGAGTTACTCCCTCTAATAAAACCCCAAG
GGAGAGTGGTGAATGTATCTAGCACCGTGAGTCTCAGGGCCCTAAAAAGCTGCAGCCCTGAGCTGAAGCAGAAGTTCCTC
AGTGAGACCGTCATCACTGAGGAGGAGCTGGTGGGGCTCATGAATAAGTTCGTGGAGGATACAAAGAAGGGAGTGCACCA
GAAGGCGGGCTGGCCCAACACCGCATACGGGGTGATGAAGGTCGGCGTCACCATGCTGTCCAGGATCCACGCCAGGAAAC
TGAGCGAGCAGAGGAAAGTGCACAAGATCCTCCTGAATGTCTGCTGCCCAGGGTGGGTGAGAACGGACATGGCGTGACCC
AATGCCACCAAGAGCCCGGAAGAAGGAGCAGAGACCCCTGTGTACTTGGCCCTTTTGACCCCGGATGCGGAGGGGCCCCA
TGGACAGTTTGTTTCAGAGAAGAAAGTTGAACAGTGG
ORF - retro_cjac_1139 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.46 % |
| Parental protein coverage: | 71.48 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVCTELLPLIKPHGRVVNVSSTVSLRALKS |
| EYGGLD.LVNNAGIAFKVADP.PFHIQAEVTMKTNFFGT.DVCTELLPLIKP.GRVVNVSSTVSLRALKS | |
| Retrocopy | EYGGLDMLVNNAGIAFKVADPIPFHIQAEVTMKTNFFGT*DVCTELLPLIKPQGRVVNVSSTVSLRALKS |
| Parental | CSPELQQKFRSET-ITEEELVGLMNKFVEDTKKGVHQKAGWPNTAYGVSKIGVTVLSRIQARKLNEQRKG |
| CSPEL.QKF.SET.ITEEELVGLMNKFVEDTKKGVHQKAGWPNTAYGV.K.GVT.LSRI.ARKL.EQRK. | |
| Retrocopy | CSPELKQKFLSETVITEEELVGLMNKFVEDTKKGVHQKAGWPNTAYGVMKVGVTMLSRIHARKLSEQRKV |
| Parental | DKILLNACCPGWVRTDMAGPNATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKKVEQW |
| .KILLN.CCPGWVRTDMA.PNATKSPEEGAETPVYLALL.PDAEGPHGQFVSEKKVEQW | |
| Retrocopy | HKILLNVCCPGWVRTDMA*PNATKSPEEGAETPVYLALLTPDAEGPHGQFVSEKKVEQW |
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 .49 RPM | 34 .46 RPM |
| SRP051959_heart | 1 .32 RPM | 4 .49 RPM |
| SRP051959_kidney | 0 .62 RPM | 20 .41 RPM |
| SRP051959_liver | 0 .45 RPM | 125 .20 RPM |
| SRP051959_lung | 1 .25 RPM | 6 .04 RPM |
| SRP051959_lymph_node | 1 .42 RPM | 3 .20 RPM |
| SRP051959_skeletal_muscle | 0 .61 RPM | 6 .27 RPM |
| SRP051959_spleen | 1 .43 RPM | 6 .64 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1139 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1139 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1139 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000038083 | 1 retrocopy |
retro_cjac_1139 ,
|
| Monodelphis domestica | ENSMODG00000021047 | 1 retrocopy |