RetrogeneDB ID: | retro_cjac_1459 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 16:28345225..28346364(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000033737 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000020641 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1459
ATGATTTCTTCAACGTCCAGATTTGGCATACACTATGGCCTCAAGACTCTACTTGAAGGAATTAGCAGAGCCACTATCAA
AAGCAACCCATCAAACATCAACCAGTTTGTAGTAGTTTATTTTGAAGAACTTACTATGTATAGAGAAGGGAATAGTTCTC
TGGATATAAAGGATCTGGTTAAACAGCTTCATCAGATTAAAGTACAGAAGTGGTCAGAGGATCAATATGAACGAAGAAAG
TAGAATGTTTAAAAGAACCAGGAAAAAAAAAATCTGTAGAATCTAAAGTACCTACACGGATGGAAAAATCTACAGACAGA
GGAGAACAATGTAACCGGAACAGGATATAGTGACAAAACCACCCAGTTTCCATCAACTTATGCTGAGCTAGGCGCTGAGC
AAACTGAAGCAGTTCATGATTCTCCTCCCAAAGCAGCTACCCCTAAGACTACTACCCTACCCTCCTCACCACCTCCAACA
GCTGTCTCACCAGAGTTTGCCTATAGCCCAGCTGACCCAGCTCAGTTTGCTGCTCGGATGTTAGCAATGGCAGCAAGCGA
ATCAGAACAGCCACCACCATATTCCAACCTGTGGACCCTTTATTGTCTAACTGATAAGAATCAACAAAGTCACTCACCAC
TCCCACCTGCACCTGGGCCTTTCCCCCGAGCAACCCTCTACATATCTAATCTTAAGGATCCGCAATTTCTGCAGCATCCA
CCAACAGTCACTCCTCCAATTTATGTGATCGACGACACAAAGATCAGTGCCCCATCTTTTATCTCAGTTGCCTCAAATGT
TCAGAAAGCACAGGAATGGGAACCTCTTCCGGGACATGCTGTTGTTTCGCAGTCAGATGTCCTGAAGAGATACGCTGCAG
TGCAAGTGCCTGTTGCTGTTCCTGCAGATGGGAAATTCCAGAAACATACTCTAAGTCCCCACAATGCTAATCCTCCAAGT
GGACAAGATGTCTCCAATCCAAAAAGCCCTGTTTTTCATTCTGTTGCTTTCCCAGTAGAAGATGTAGCTAAAAAAGTTCA
AGATCTGGTGACAAATGGGCTCCCTTTGGAAGTTACGGTATTGCTGGGGAGATAAGTGTGGCTACCGCTCACAAAGTTCG
CAAAGCAGAAACCGAAAAC
ORF - retro_cjac_1459 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.33 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MISSKPRFCIPYGLKTLLEGISIAIIKSNPSNIVQFAAVYFEELTMYRV-NTSLDIKDLVKQFHQIKVQK |
| MISS..RF.I.YGLKTLLEGIS.A.IKSNPSNI.QF..VYFEELTMYR..N.SLDIKDLVKQ.HQIKVQK | |
| Retrocopy | MISSTSRFGIHYGLKTLLEGISRATIKSNPSNINQFVVVYFEELTMYREGNSSLDIKDLVKQLHQIKVQK |
| Parental | WSE-GSIRPKKAECLKEP-EKSSVESKVPTHMEKSTDTEEDNVTGTGYSDKTTQFPSTYAELGAEQTEAV |
| WSE.GSI..KK.ECLKEP.EK.........H..K...TEE.NVTGTGYSDKTTQFPSTYAELGAEQTEAV | |
| Retrocopy | WSE<GSI*TKKVECLKEP>EKKNL*NLKYLHGWKNLQTEENNVTGTGYSDKTTQFPSTYAELGAEQTEAV |
| Parental | HDSSPKAATPKTTTPPFSPPPTAVSPEFAYVPADPAQFAAQMLAMAASEPEQLPPYSNMWTLYCLTD-NQ |
| HDS.PKAATPKTTT.P.SPPPTAVSPEFAY.PADPAQFAA.MLAMAASE.EQ.PPYSN.WTLYCLTD.NQ | |
| Retrocopy | HDSPPKAATPKTTTLPSSPPPTAVSPEFAYSPADPAQFAARMLAMAASESEQPPPYSNLWTLYCLTDKNQ |
| Parental | QSHSSPPPAPGPFPQATLYISNPKDPQFLQHPPTVTSPIYVMDDTKKISAPPFILVGSKFQKAQEWEPLP |
| QSHS..PPAPGPFP.ATLYISN.KDPQFLQHPPTVT.PIYV.DDT.KISAP.FI.V.S..QKAQEWEPLP | |
| Retrocopy | QSHSPLPPAPGPFPRATLYISNLKDPQFLQHPPTVTPPIYVIDDT-KISAPSFISVASNVQKAQEWEPLP |
| Parental | GHAVVSQSDVLKRYAAVQVPIAVPADGKFQKHTLSPHNANPPSGQDVPKPKSPVFLSVAFPVEDVAK-NN |
| GHAVVSQSDVLKRYAAVQVP.AVPADGKFQKHTLSPHNANPPSGQDV..PKSPVF.SVAFPVEDVAK... | |
| Retrocopy | GHAVVSQSDVLKRYAAVQVPVAVPADGKFQKHTLSPHNANPPSGQDVSNPKSPVFHSVAFPVEDVAK<KS |
| Parental | SGSGDKCAPFGSYGIAGEITVATAHKVRKAETEN |
| S.SGDK.APFGSYGIAGEI.VATAHKVRKAETEN | |
| Retrocopy | SRSGDKWAPFGSYGIAGEISVATAHKVRKAETEN |
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 | 3 .02 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .24 RPM |
| SRP051959_kidney | 0 .00 RPM | 5 .52 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .14 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .53 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .34 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 3 .76 RPM |
| SRP051959_spleen | 0 .00 RPM | 6 .81 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1459 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1459 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1459 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020641 | 1 retrocopy |
retro_cjac_1459 ,
|
| Cavia porcellus | ENSCPOG00000008281 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000014928 | 1 retrocopy |