RetrogeneDB ID: | retro_cjac_1807 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:67022040..67022772(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRKAR2A | ||
| Ensembl ID: | ENSCJAG00000003255 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1807
GCCGACGCCAACGGGGACAGCGAGTAGGAGAAGGACAAGGACTTAGAAGTTCCAGTTCCTAGCACATTTAATAGACGAGT
ATCAGTCTGTGCTGAGACCTATAACCCTAATGAGGAAGAGGAAGAGGAATATACAGATCCAAGGGTGATTCATCCTAAAA
CTGATGAACAGGGATGCAGACTTCAGGAAACTTGCAAAGATATTCTCCCTTTCAAAAATCTTCATTAGGAACAGCTTTCT
CAAGTTCTCGATGCCATGTTTGAAAGGATAGTCAAAGCTGATGAGCATGTCATTGACCAAGGAGATGATGGAGACAACTT
TTATGTCATAGAACGGGGAACTGATAACATTTTAGTAACAAAAAATAATCAAGCCTGCCCTGTTGCTCAATATGACAACC
ATGGCAGTTTTGGAGAACTAGCTCTGATGCACAACACCCCCGGAACTGCTACCATTCCTGCTACCTCGGAAGGCTCCCTT
CGGGGACTGGACCGGGTGACTTTTAGAAGAATCATAGTGAAAAATAATGCAAAGAAGAGGAAGATGTTTGAAGTATTTAT
TGAGTCTGTGCCCCTCCTTAAATCATTGGAGTTGTCAGAATGAATGACGATTGTGGATATAATAGGAGAGAAGATCTATA
AGGATGGAGAACACATAATTACTCAGGGTGAAAAGGCTGATAGCTTTTACATCATAGAGTCTGGTGAAGTGAGCATTTTG
ATTAGAAGCAAA
ORF - retro_cjac_1807 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.7 % |
| Parental protein coverage: | 59.9 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ADANGDSESEEDEDLEVPVPSRFNRRVSVCAETYNPDEEEED--TDPRVIHPKTDEQRCRLQEACKDILL |
| ADANGDSE.E.D.DLEVPVPS.FNRRVSVCAETYNP.EEEE...TDPRVIHPKTDEQ.CRLQE.CKDIL. | |
| Retrocopy | ADANGDSE*EKDKDLEVPVPSTFNRRVSVCAETYNPNEEEEEEYTDPRVIHPKTDEQGCRLQETCKDILP |
| Parental | FKNLDQEQLSQVLDAMFERIVKADEHVIDQGDDGDNFYVIERGTYDILVTKNNQTRSVGQYDNRGSFGEL |
| FKNL..EQLSQVLDAMFERIVKADEHVIDQGDDGDNFYVIERGT..ILVTKNNQ...V.QYDN.GSFGEL | |
| Retrocopy | FKNLH*EQLSQVLDAMFERIVKADEHVIDQGDDGDNFYVIERGTDNILVTKNNQACPVAQYDNHGSFGEL |
| Parental | ALMYNTPRAATIVATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESFIESVPLLKSLELSERMKIVDVIGE |
| ALM.NTP..ATI.ATSEGSL.GLDRVTFRRIIVKNNAKKRKMFE.FIESVPLLKSLELSE.M.IVD.IGE | |
| Retrocopy | ALMHNTPGTATIPATSEGSLRGLDRVTFRRIIVKNNAKKRKMFEVFIESVPLLKSLELSE*MTIVDIIGE |
| Parental | KIYKDGERIITQGEKADSFYIIESGEVSILIRSK |
| KIYKDGE.IITQGEKADSFYIIESGEVSILIRSK | |
| Retrocopy | KIYKDGEHIITQGEKADSFYIIESGEVSILIRSK |
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 .22 RPM | 28 .18 RPM |
| SRP051959_heart | 0 .04 RPM | 32 .52 RPM |
| SRP051959_kidney | 0 .18 RPM | 21 .85 RPM |
| SRP051959_liver | 0 .22 RPM | 18 .19 RPM |
| SRP051959_lung | 0 .10 RPM | 21 .54 RPM |
| SRP051959_lymph_node | 0 .14 RPM | 18 .68 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 32 .60 RPM |
| SRP051959_spleen | 0 .02 RPM | 27 .54 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1807 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1807 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1807 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 | ENSCJAG00000003255 | 1 retrocopy |
retro_cjac_1807 ,
|
| Monodelphis domestica | ENSMODG00000013392 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000012426 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000006822 | 1 retrocopy |