RetrogeneDB ID: | retro_cjac_2721 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:47689705..47691015(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000035478 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ADSS | ||
| Ensembl ID: | ENSCJAG00000017069 | ||
| Aliases: | None | ||
| Description: | Adenylosuccinate synthetase [Source:UniProtKB/TrEMBL;Acc:F7IRU0] |
Retrocopy-Parental alignment summary:
>retro_cjac_2721
CCCAGGGCATGGCCCGGAGGAAACCAGGTGACGGTGGTGCTCGGTGCACAGTGGGGTGACAAAGGCAAAGGGAAGGTGGT
GGATCTGCTGGCGCAGGACGCCAACATCATGTGCCACTGCCAGGGAGGAAATAATCCTGGCCATACAGTTGTTGTGGATT
CTGTGGACTATGATTTTCATCTCTTACCCAGTGGAATAATTAATCCAAGTGTGGCTGCCTTCATTGGAAATGGTGTGGTA
ATTCATCTACCTGGATTGTTTGAAGAAGCAGAGAAAAATGTTCAAAAAGGAAAAGGACTAGAAGGCTGGGGAAAAAAGGC
TGATTATATCTGACAGAGCTCATACTGTATTTGATTTTCATCAAGCAGCTGATGGTATCCAGGAACAACAGAGACGAGCA
CAAGCAGGAAAAAATTTGGGTACAACAAAAACGGGGAATTGGGCCAGTTTATTCTTCCAAAGCTGCTCAGAGTGGACTTA
GGATGTCAGATCTTGTTTCTGACTTTGATGGCTTCTTGGAGAGGTTTAAAGTTTTAGCCAACCAATACAAATCTATATAC
CCCACTTTGGAAATAGACATCAAAGGTGATTTACAAAAACTCAAGGGTTATATGGAAAGGATTAGGCCAATGGTGAGAGA
TGAAGTTTATTTCCTATATGAGGCCCTACAGGGATCACCAAAGAAACTCTTGGTAGAAGGTTCAAATGCAGCACTAATAG
ATATTGATTTTTGAACTTACCCTTTTGTAATCTCTTCAAATTGTACTGTTGGAGGTGTTTGTACTGGTTTGGGTATACCC
CCTCAAAATGTAGGAGAAATTTATGGAGTTGTGAAAGCTTATACTACTAGAGTTTGTATTGGTGCCTTTCCTACAGAGCA
AGACAATGAAATTGGAAAATTATTACACACAAGGGGTAGAGAGTTTGGTGTAACTACTGGAAGGAAATGAAGATGTGGCT
GGTTGGACCTCGTTTTGCTCAAATATGCTTATATAATCAATGGATTTACTGTGTTGGCACTTACCAAGTTGGATATTTCA
CACATGTTTACGGAAATCAAAGTTGGAGTTGCTTGCAAGTTAGATGGTGAAATCATACCTCATATCCCAGCAAACCAAGA
AGTCTTAAATAAAGTTGAAGTTCAGTATAAGACTCTCCCAGGATGGAACACAGACATATCAAATGCAAGGATGTTTAAAG
AACTACCTGTTAATGCACAAAACTATGTTTGATTTATTAAAGATGAGCTTCAAATTCCAGTTAAATGGATTGGTGTTGGT
GAATCCAGAGAGTCTATGATTCAGCTCTTT
ORF - retro_cjac_2721 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.14 % |
| Parental protein coverage: | 97.13 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PAASPSGSPRVVTVVLGAQWGDEGKGKVVDLLAQDADIVCRCQGGNNAGHTVVVDSVEYDFHLLPSGIIN |
| P.A.P.G....VTVVLGAQWGD.GKGKVVDLLAQDA.I.C.CQGGNN.GHTVVVDSV.YDFHLLPSGIIN | |
| Retrocopy | PRAWPGGNQ--VTVVLGAQWGDKGKGKVVDLLAQDANIMCHCQGGNNPGHTVVVDSVDYDFHLLPSGIIN |
| Parental | PNVTAFIGNGVVIHLPGLFEEAEKNVQKGKGLEGW-EKRLIISDRAHIVFDFHQAADGIQEQQRQEQAGK |
| P.V.AFIGNGVVIHLPGLFEEAEKNVQKGKGLEGW.EKRLIISDRAH.VFDFHQAADGIQEQQR..QAGK | |
| Retrocopy | PSVAAFIGNGVVIHLPGLFEEAEKNVQKGKGLEGW>EKRLIISDRAHTVFDFHQAADGIQEQQRRAQAGK |
| Parental | NLGTT-KKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKSIYPTLEIDIEGELQKLKGYMER |
| NLGTT.K.GIGPVYSSKAA.SGLRM.DLVSDFDGF.ERFKVLANQYKSIYPTLEIDI.G.LQKLKGYMER | |
| Retrocopy | NLGTT>KRGIGPVYSSKAAQSGLRMSDLVSDFDGFLERFKVLANQYKSIYPTLEIDIKGDLQKLKGYMER |
| Parental | I-PMVRDGVYFLYE-LTGPPKKILFMVQFHTLKLSDKFLGTYPFVTSSNCTVGGVCTGLGMPPQNVGEVY |
| I.PMVRD.VYFLYE.L.G.PKK.L..V......L.D....TYPFV.SSNCTVGGVCTGLG.PPQNVGE.Y | |
| Retrocopy | IRPMVRDEVYFLYEALQGSPKKLL--VEGSNAALIDIDF*TYPFVISSNCTVGGVCTGLGIPPQNVGEIY |
| Parental | GVLKAYTTRVGIGAFPTEQENEIGELLQTRGREFGVTTGRKRRCGWLDLVLLKYAHMINGFTAIRLALTK |
| GV.KAYTTRV.IGAFPTEQ.NEIG.LL.TRGREFGVTTGRK.RCGWLDLVLLKYA..INGFT...LALTK | |
| Retrocopy | GVVKAYTTRVCIGAFPTEQDNEIGKLLHTRGREFGVTTGRK*RCGWLDLVLLKYAYIINGFTV--LALTK |
| Parental | LDILDMFTEIKVGVAYKLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNARTFKELPVNAQNYVRFI |
| LDI..MFTEIKVGVA.KLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNAR.FKELPVNAQNYV.FI | |
| Retrocopy | LDISHMFTEIKVGVACKLDGEIIPHIPANQEVLNKVEVQYKTLPGWNTDISNARMFKELPVNAQNYV*FI |
| Parental | EDELQIPVKWIGVGKSRESMIQLF |
| .DELQIPVKWIGVG.SRESMIQLF | |
| Retrocopy | KDELQIPVKWIGVGESRESMIQLF |
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 .04 RPM | 18 .99 RPM |
| SRP051959_heart | 0 .00 RPM | 14 .58 RPM |
| SRP051959_kidney | 0 .02 RPM | 24 .67 RPM |
| SRP051959_liver | 0 .06 RPM | 6 .28 RPM |
| SRP051959_lung | 0 .02 RPM | 17 .49 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 27 .51 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 9 .67 RPM |
| SRP051959_spleen | 0 .00 RPM | 16 .09 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2721 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2721 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2721 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017069 | 2 retrocopies |
retro_cjac_2721 , retro_cjac_452,
|
| Homo sapiens | ENSG00000035687 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000006559 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000013982 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000000057 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000002178 | 1 retrocopy |