RetrogeneDB ID: | retro_cjac_1186 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:14445797..14446331(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000031408 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MED30 | ||
| Ensembl ID: | ENSCJAG00000005824 | ||
| Aliases: | None | ||
| Description: | mediator complex subunit 30 [Source:HGNC Symbol;Acc:23032] |
Retrocopy-Parental alignment summary:
>retro_cjac_1186
ATGCCCACCCCTCCATGGGCCGCATCAGGAATGGCGCCCGGGCCCTTTGCCCGGCCCCAGGCTCAGCAGGCTGCCCGGGA
GGTGAACACGGCGTCGCTGTGCCGCATCGGGCAGGAGACGGTGACGGACATCGTGTGCCGCACCCTAGAGATCTTCCAGC
TCCTCAGGAATATGCAGCTGCCAAATGGTGTCACTTCCCACACTGGAACGTATCAAGACCGGTTAACGAAGCTACAGGAT
AATCTTCGCCAACTTTCAGTTCTCTTCAGGAAGCTGAGATTGGTATATGACAAGTGCAATGAAAACTGTGGAGGGATGGA
TCCCATTCCAGTAGAGCAACTTATTCCATATGTGAAAGAAGATGGCTCAAAGAATGATGATCGGGCTGGCCCACCTCGTT
TTGCTAGTGAGGAGAGGCGAGAAATTGCTGAAGTAAATAAGAAACTCAAACAGAAGAATCAACAGCTGAAGCAAATTATG
GATCAATTACAAAATCTCATCTGGGATATAAATGCCATGTTGGCAATGAGGAAC
ORF - retro_cjac_1186 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.89 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQDKLPNGVTYHT |
| M.TPP.AASGMAPGPFA.PQAQQAAREVNTASLCRIGQETV.DIV.RT.EIFQLLRNMQ..LPNGVT.HT | |
| Retrocopy | MPTPPWAASGMAPGPFARPQAQQAAREVNTASLCRIGQETVTDIVCRTLEIFQLLRNMQ--LPNGVTSHT |
| Parental | GTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEEDGSKNDDRAGPPRFASEE |
| GTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYV.EDGSKNDDRAGPPRFASEE | |
| Retrocopy | GTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVKEDGSKNDDRAGPPRFASEE |
| Parental | RREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN |
| RREIAEVNKKLKQKNQQLKQIMDQL.NLIWDINAMLAMRN | |
| Retrocopy | RREIAEVNKKLKQKNQQLKQIMDQLQNLIWDINAMLAMRN |
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 .09 RPM | 2 .29 RPM |
| SRP051959_heart | 0 .02 RPM | 3 .88 RPM |
| SRP051959_kidney | 0 .95 RPM | 2 .51 RPM |
| SRP051959_liver | 0 .76 RPM | 3 .14 RPM |
| SRP051959_lung | 0 .28 RPM | 4 .91 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .42 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 3 .49 RPM |
| SRP051959_spleen | 0 .04 RPM | 3 .97 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1186 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1186 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1186 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005824 | 1 retrocopy |
retro_cjac_1186 ,
|
| Sorex araneus | ENSSARG00000000870 | 2 retrocopies | |
| Tarsius syrichta | ENSTSYG00000009760 | 2 retrocopies |