RetrogeneDB ID: | retro_cjac_560 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:81373868..81374642(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000004593 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARRDC3 | ||
| Ensembl ID: | ENSCJAG00000010525 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_560
GTGATGGGAAAGGTGAAAAGTTTGACAATAAGTTTTGACTGTGTTAATGACAGTAATGTCCCTGTGTATTCTAGTGAAGA
TATCATCTCAAGAAGGGTAAATTTAGAAGTTACTGGCAAAATCAGAGTAAAATCTCTTAAAATTCATGCAAGAGGATGTT
TAGAAGTATGCTTGGCTGAATCTAGAAACACTGGCACCAATACTGCCTGTACACAGAATTACATTGCAGAAGTAGAATAT
TTCAACCATAAAGATATCTTAATTGGGCATGAAAGAGACAATAATAATTCCAAAGAAGGCTTCAAGGCTATTCATTCAGG
AAGGCATGCATATGCATTCAGCCGTAAGCGTCCACAGATACCACTTGCTACTTCATTTAAAGGCAGCCATGGTGTGTGCA
CTGTTGTGTGAAAGCTGAATCTCACAGGCCTTGGCTACTAACAGTAACATCAAAGAAAAAATTTACAGTCTTTGAATATA
TAAATATGAACACTCCTTCATCACTGTCACCCAAGCAGGCACAGAAGAAAAGACACTAGGTTGCTGGTTTTCTACCTCAG
GCTCAATATCCTTAAGTGCCAAAATTGAAAGGAAGGGCTATTACATGGGTGAATCAACTCAGATATTTGCTAAGACTGAG
AACTGCTCTTCCCAAATGCTGGTGCCAGAGTCAGACATTACCAAACACACTTTCGTGCCAAAGGGGAAATGAAGGAAGTA
AAACAGTGCATGGCTAACTTGCATGAGGAATCCTTGTCATTTGGAAAGAGAGAT
ORF - retro_cjac_560 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.0 % |
| Parental protein coverage: | 62.8 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VLGKVKSLTISFDCLNDSNVPVYSSGDTVSGRVNLEVTGEIRVKSLKIHARGHAKVRWTESRNAGSNTAY |
| V.GKVKSLTISFDC.NDSNVPVYSS.D..S.RVNLEVTG.IRVKSLKIHARG...V...ESRN.G.NTA. | |
| Retrocopy | VMGKVKSLTISFDCVNDSNVPVYSSEDIISRRVNLEVTGKIRVKSLKIHARGCLEVCLAESRNTGTNTAC |
| Parental | TQNYTEEVEYFNHKDILIGHERDDDNSEEGFHTIHSGRHEYAFSFELPQTPLATSFEGRHG-SVRYWVKA |
| TQNY..EVEYFNHKDILIGHERD..NS.EGF..IHSGRH.YAFS...PQ.PLATSF.G.HG..V...VKA | |
| Retrocopy | TQNYIAEVEYFNHKDILIGHERDNNNSKEGFKAIHSGRHAYAFSRKRPQIPLATSFKGSHG<CVHCCVKA |
| Parental | ELHRPWLLPVKLKKEFTVFEHIDINTPSLLSP-QAGTKEKTLCCWFCTSGPISLSAKIERKGYTPGESIQ |
| E.HRPWLL.V..KK.FTVFE.I..NTPS.LSP.QAGT.EKTL.CWF.TSG.ISLSAKIERKGY..GES.Q | |
| Retrocopy | ESHRPWLLTVTSKKKFTVFEYINMNTPSSLSP<QAGTEEKTLGCWFSTSGSISLSAKIERKGYYMGESTQ |
| Parental | IFAEIENCSSRMVVPKAAI-YQTQAFYAKGKMKEVKQLVANLRGESLSSGKTE |
| IFA..ENCSS.M.VP...I.YQT..F.AKG.MKEVKQ..ANL..ESLS.GK.. | |
| Retrocopy | IFAKTENCSSQMLVPESDI<YQTH-FRAKGEMKEVKQCMANLHEESLSFGKRD |
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 | 96 .52 RPM |
| SRP051959_heart | 0 .00 RPM | 36 .45 RPM |
| SRP051959_kidney | 0 .00 RPM | 282 .74 RPM |
| SRP051959_liver | 0 .00 RPM | 58 .53 RPM |
| SRP051959_lung | 0 .00 RPM | 240 .34 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 91 .69 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 80 .91 RPM |
| SRP051959_spleen | 0 .00 RPM | 164 .27 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_560 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_560 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_560 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010525 | 1 retrocopy |
retro_cjac_560 ,
|
| Callithrix jacchus | ENSCJAG00000036002 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000013887 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000015628 | 1 retrocopy |