RetrogeneDB ID: | retro_cjac_2577 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:144386567..144386992(+) | ||
| Located in intron of: | ENSCJAG00000018570 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000010374 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2577
CAAACTTATATGGAAACAAATTCTGTAGAACGTGTTCAAGTAAAACAAGGAGACCAAAGAAAGGGTAAGCAAGATATAGT
AGAAAAGTTAAAAGAAAATCGGTCTTTGCAGACATAAGCAGCATCTTAAGAGAACTTATTTAAGAGAGAATAAAGTTGCT
TCAATAAGAAGTCGGAGGGAGCTGAGAAAGATCTGAAATCTGAACTCTTGAAAATGAAAACTTTCCACAAGACTAATCAA
ACTGACTTGGAAAGATATAAGCAGCTCTATCTACAAGAATTTAAAGTCAGAAAATCATTGGCAACTATACTAAACAAAAC
CAATGATAAAACAGCAGAGGTTAAGAGCAAACTTTTTGTAGAGAACAGCAGATCAGATCTTTACACCACTGTTACTACGA
GGCAGTCCTAGCGTCAGCTTGTGTG
ORF - retro_cjac_2577 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.29 % |
| Parental protein coverage: | 54.12 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RSHLERNMVERGQVKQYKQEIEERARQEIVEKLKEVNLFLQAQAASQENLEQLRENSFASMKSQMELRIN |
| ....E.N.VER.QVKQ..Q.......Q.IVEKLKE.N..LQ..AAS.ENL...RE.S....KS....... | |
| Retrocopy | QTYMETNSVERVQVKQGDQR---KGKQDIVEKLKE-NRSLQT*AAS*ENLFK-RE*SCFNKKSEGAEK-- |
| Parental | DLESELSKMKTFQEDVNKTELEKYKQLYLEELKVRKSLSNKLNKTNERLAEVNTKLLMEKQQTRSLFTTL |
| DL.SEL.KMKTF....N.T.LE.YKQLYL.E.KVRKSL...LNKTN...AEV..KL..E......L.TT. | |
| Retrocopy | DLKSELLKMKTFHK-TNQTDLERYKQLYLQEFKVRKSLATILNKTNDKTAEVKSKLFVENSRS-DLYTTV |
| Parental | TTR-PVLVSPCV |
| TTR..VL.S.CV | |
| Retrocopy | TTR<AVLASACV |
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 .29 RPM | 0 .11 RPM |
| SRP051959_heart | 0 .26 RPM | 0 .09 RPM |
| SRP051959_kidney | 0 .13 RPM | 0 .04 RPM |
| SRP051959_liver | 0 .02 RPM | 0 .11 RPM |
| SRP051959_lung | 0 .23 RPM | 0 .13 RPM |
| SRP051959_lymph_node | 0 .25 RPM | 0 .14 RPM |
| SRP051959_skeletal_muscle | 0 .11 RPM | 0 .07 RPM |
| SRP051959_spleen | 0 .25 RPM | 0 .11 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2577 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2577 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2577 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 | ENSCJAG00000010374 | 1 retrocopy |
retro_cjac_2577 ,
|
| Gorilla gorilla | ENSGGOG00000027866 | 1 retrocopy |