RetrogeneDB ID: | retro_cjac_467 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:136737788..136738034(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SYF2 | ||
| Ensembl ID: | ENSCJAG00000018559 | ||
| Aliases: | None | ||
| Description: | SYF2 homolog, RNA splicing factor (S. cerevisiae) [Source:HGNC Symbol;Acc:19824] |
Retrocopy-Parental alignment summary:
>retro_cjac_467
AAATTACCTGCAAACTGGGAAGCTAATAAGCATCATTTCAAATGGGAATTGCAGGAAGAAGGAGGAAAAAAAAATGTTCA
GACAAAGACTATGAGAAAAGATACAGAAAGATGGGAGAGAAAAAAAAAAAGGAAAAACTTCAATCTGGGATTTTTACATT
ATGCTGCTTCCCAGTTGCACCAGTATCACTGGTTGACCAAGCAGATCAAACCTGACACAGAAATATATTAAAGACTAACA
GAAAAA
ORF - retro_cjac_467 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.38 % |
| Parental protein coverage: | 53.85 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KARLEWELQEEEKKKECAARGEDYEKVKLLEISAEDAERWERKKKRKNPDLGFSDYAAAQLRQYHRLTKQ |
| K....WE......K.E.....E...K.........D.ERWERKKKRKN..LGF..YAA.QL.QYH.LTKQ | |
| Retrocopy | KLPANWEANKHHFKWEL--QEEGGKKNVQTKTMRKDTERWERKKKRKNFNLGFLHYAASQLHQYHWLTKQ |
| Parental | IKPDMETYERLREK |
| IKPD.E.Y.RL.EK | |
| Retrocopy | IKPDTEIY*RLTEK |
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 .00 RPM | 4 .53 RPM |
| SRP051959_heart | 0 .00 RPM | 6 .47 RPM |
| SRP051959_kidney | 0 .00 RPM | 7 .94 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .14 RPM |
| SRP051959_lung | 0 .02 RPM | 7 .84 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 6 .94 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 7 .40 RPM |
| SRP051959_spleen | 0 .00 RPM | 7 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_467 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_467 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_467 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4152 |
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000010115 | 1 retrocopy | |
| Bos taurus | ENSBTAG00000001651 | 1 retrocopy | |
| Choloepus hoffmanni | ENSCHOG00000005273 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000018559 | 1 retrocopy |
retro_cjac_467 ,
|
| Homo sapiens | ENSG00000117614 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000013951 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000013050 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000007152 | 1 retrocopy |