RetrogeneDB ID: | retro_cjac_2757 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:118501773..118502316(+) | ||
| Located in intron of: | ENSCJAG00000005224 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | OGFRL1 | ||
| Ensembl ID: | ENSCJAG00000003635 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2757
GACCCGGGGCCGGGCCACTTCAGTGAGGGCCCGGAGCAGGAGCCCGAGCAGCCCCTGAAGCGAGCTGGCGGGCGGCCCAG
CGCCAGACCCGCACCGGAGAGGATGCGGAGGCGGCGGGCGCCGAGCAGGGTGATGATTCCACTGAAGCAATGGCCAAACC
AAAGAGAAGTTTTTATGCTGCGAGGGATTTGTACAAGTACCGACACCAGTACCCAAACTTCAAAGATATCCGATATCAAA
ATGACTTAAGCAATCTTCGTTTTTATAAGAATAAAATTCCATTCAAGCCAGATGGTGTTTACATTAAAGAAGTTCTAAAT
AAATGGAAAGGAGATTATGAAAAACTGGAGCACAACCGCACTTAACATTCAATGGCTTTTCCCCCTGAGAGAACAGGGCT
TGAACTTTTACCCTAAAGAACTACCTACATATGAAATTGAGGAATTCAAAAAAACAAAAGAAGCAATTAGAAGATTCCTC
CTGGCTTATAAAATGATGCTAGAATTTTTTGGAGTAAAACTGACTGATAAAATTGGAAATGTT
ORF - retro_cjac_2757 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.3 % |
| Parental protein coverage: | 51.68 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DPGPGGGSEGPGQEPEQPAQPPERAGGRPSASPAPD-EDAEAAGAEQGDDSTEATTAKPKRSFYAARDLY |
| DPGPG..SEGP.QEPE...QP..RAGGRPSA.PAP..EDAEAAGAEQGDDSTEA..AKPKRSFYAARDLY | |
| Retrocopy | DPGPGHFSEGPEQEPE---QPLKRAGGRPSARPAPE<EDAEAAGAEQGDDSTEAM-AKPKRSFYAARDLY |
| Parental | KYRHQYPNFKDIRYQNDLSNLRFYKNKIPFKPDGVYIEEVLNKWKGDYEKLEHNHT-YIQWLFPLREQGL |
| KYRHQYPNFKDIRYQNDLSNLRFYKNKIPFKPDGVYI.EVLNKWKGDYEKLEHN.T..IQWLFPLREQGL | |
| Retrocopy | KYRHQYPNFKDIRYQNDLSNLRFYKNKIPFKPDGVYIKEVLNKWKGDYEKLEHNRT>NIQWLFPLREQGL |
| Parental | NFYAKELTTYEIEEFKKTKEAIRRFLLAYKMMLEFFGIKLTDKIGNV |
| NFY.KEL.TYEIEEFKKTKEAIRRFLLAYKMMLEFFG.KLTDKIGNV | |
| Retrocopy | NFYPKELPTYEIEEFKKTKEAIRRFLLAYKMMLEFFGVKLTDKIGNV |
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 .18 RPM | 16 .37 RPM |
| SRP051959_heart | 0 .25 RPM | 8 .56 RPM |
| SRP051959_kidney | 0 .20 RPM | 15 .22 RPM |
| SRP051959_liver | 0 .17 RPM | 8 .62 RPM |
| SRP051959_lung | 0 .28 RPM | 24 .56 RPM |
| SRP051959_lymph_node | 0 .21 RPM | 7 .65 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 4 .48 RPM |
| SRP051959_spleen | 0 .17 RPM | 20 .17 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2757 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2757 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2757 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000002600 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000003635 | 1 retrocopy |
retro_cjac_2757 ,
|
| Myotis lucifugus | ENSMLUG00000007329 | 1 retrocopy |