RetrogeneDB ID: | retro_cjac_2966 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:19422462..19423304(-) | ||
| Located in intron of: | ENSCJAG00000008044 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000008077 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BPHL | ||
| Ensembl ID: | ENSCJAG00000017700 | ||
| Aliases: | None | ||
| Description: | biphenyl hydrolase-like (serine hydrolase) [Source:HGNC Symbol;Acc:1094] |
Retrocopy-Parental alignment summary:
>retro_cjac_2966
CTGCAGCTGCGGCTGCTGCTCTGGGCACTGACGCCCAGTATCCTCGTCCCACAGGCCTGACCCGCGGCAGCGTTCAGCAC
CTTGGTAACCTCTGCCAAAGTGGCTGTGAATGGCATCCATCTGTATTACCAGCAGGCTGGAGAGGGAGATCACGCAGTCC
TGCTACTTCCTGGGATGTTGGGAAGTGGAGAGACTGATTCCGGACCTCAGCTCACGAACCTCAATAAGAAGCTCTTTAAA
GTGGTCGCCTGGGATCCTGGAGGCTATGGGCATTCCAAGCCTTCACATCGCGATTTCCCAGTAGACTTTTTTGAAAGAGA
CGCAAAAGATGCTGTTGATTTGATGAAGGCGCTGAAGTTTAAGAAGGTTTCTCTGCCGGGGTGGAGTGATGGGGGCATAA
CCGCACTCACTGCTGCTGCAAAATACCCATCTTACATCCACAAGATGGTGATTTGGGGCCCCAATGCCTACGTCACTGAT
GAAGACAGCATGTCTTACGAGGGCATCGAGATTTTTCTAAATGGCGTGAGAGAACAAAAAAGCCTCTAGAAGCCCCCTAT
GGGCATGACTACTTTGCCAGAACCTGTGAAAAGTGGGTGGATGGCATAAGCCTGTTTAAACATCTTCCAGATGGTAACAT
CTGCCAGCACCTGCTGCCCCAGGTCCAGCGCCCCACCTTGATTGTGCATGGCGAGAAGTATCTTCTGGTCCTAAGGTTTC
ATGCCGACTTCATTCATTGGCACGTGAAAGGCTCACGGCTGCATTTGATGCCAGAAAGCAAACACAACCTGCATTTGCGT
TTTGCAGATGAATTTAACAAGTTAGCAGAAGACTTCCTACAA
ORF - retro_cjac_2966 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.82 % |
| Parental protein coverage: | 95.25 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LRLRMLLTALKPGVLVSQAGPAAAFGTSITSAKVAVNGVHLHYQQTGEGDHAVLLLPGMLGSGETDFGPQ |
| L.LR.LL.AL.P..LV.QA.PAAAF.T..TSAKVAVNG.HL.YQQ.GEGDHAVLLLPGMLGSGETD.GPQ | |
| Retrocopy | LQLRLLLWALTPSILVPQA*PAAAFSTLVTSAKVAVNGIHLYYQQAGEGDHAVLLLPGMLGSGETDSGPQ |
| Parental | LKNLNKKLFTVVALDPRGYGHSKPPDRDFPVDFFERDAKDAVDLMKALKFKKVSLLGWSDGGITALIAAA |
| L.NLNKKLF.VVA.DP.GYGHSKP..RDFPVDFFERDAKDAVDLMKALKFKKVSL.GWSDGGITAL.AAA | |
| Retrocopy | LTNLNKKLFKVVAWDPGGYGHSKPSHRDFPVDFFERDAKDAVDLMKALKFKKVSLPGWSDGGITALTAAA |
| Parental | KYPSYIRKMVIWGANAYVTDEDSVIYEGI-RDVSKWSERTKKPLEALYGYDYFARTCEKWVDGISQFKHL |
| KYPSYI.KMVIWG.NAYVTDEDS..YEGI.RD.SKW.ERTKKPLEA.YG.DYFARTCEKWVDGIS.FKHL | |
| Retrocopy | KYPSYIHKMVIWGPNAYVTDEDSMSYEGI<RDFSKWRERTKKPLEAPYGHDYFARTCEKWVDGISLFKHL |
| Parental | PDGNICRHLLPQVQCPTLIVHGEKDPLVPRFHADFIHEHVKGSRLHLMPEGKHNLHLRFADEFNKLAEDF |
| PDGNIC.HLLPQVQ.PTLIVHGEK..LV.RFHADFIH.HVKGSRLHLMPE.KHNLHLRFADEFNKLAEDF | |
| Retrocopy | PDGNICQHLLPQVQRPTLIVHGEKYLLVLRFHADFIHWHVKGSRLHLMPESKHNLHLRFADEFNKLAEDF |
| Parental | LQ |
| LQ | |
| Retrocopy | LQ |
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 .44 RPM | 4 .53 RPM |
| SRP051959_heart | 0 .56 RPM | 5 .77 RPM |
| SRP051959_kidney | 0 .58 RPM | 7 .52 RPM |
| SRP051959_liver | 0 .50 RPM | 5 .31 RPM |
| SRP051959_lung | 0 .57 RPM | 4 .91 RPM |
| SRP051959_lymph_node | 0 .37 RPM | 5 .07 RPM |
| SRP051959_skeletal_muscle | 0 .83 RPM | 2 .58 RPM |
| SRP051959_spleen | 0 .40 RPM | 3 .87 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2966 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2966 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2966 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017700 | 1 retrocopy |
retro_cjac_2966 ,
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