RetrogeneDB ID: | retro_cjac_2072 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 22:30704958..30705459(+) | ||
| Located in intron of: | ENSCJAG00000013364 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | C19orf38 | ||
| Ensembl ID: | ENSCJAG00000006309 | ||
| Aliases: | None | ||
| Description: | chromosome 19 open reading frame 38 [Source:HGNC Symbol;Acc:34073] |
Retrocopy-Parental alignment summary:
>retro_cjac_2072
CCAGCAAACCAGTGCAGAGTGATGTTCAATCTGAGTGGCAGCAGCAGTGAGGTTCCAGGGGGACCTTTCCACCACCAGTA
TGGAGTGATAGGCGGGCACAACCAGCCCCAGCTGTCAGACCTCAGCAAGTCCTTGAACATCTCCTTCCCAGTGCCCACTT
GGATCTTGGTGCTGTCCCTGAGCCTAGCTGGTGCCCTCCTCCTCCTTGCTGGGCTGGTGGCTGTTGCCCTTGTAGTCAGA
AAAGTTAAACTCAAAAATTTACAGAAGAAAAGAGATGGAGAATCCTGCTGGGCCCAGATTAATTCTGACACCACAGACAT
GTCCTTTGATAACTCCCTGTTTACCATCTTGCTGAAAATGATGCCAGAAGAAGACCCAGCCAGCTTGGATGATCACTCAG
GCACCACTGCCACCCCTGGCAATTCCAGGACCTGGAAGATGCCCACTTCCATGTCCTCCTCGCCTGAGACCCTCGAGTTC
AGCACTTTCTGGCCCTGCCAG
CCAGCAAACCAGTGCAGAGTGATGTTCAATCTGAGTGGCAGCAGCAGTGAGGTTCCAGGGGGACCTTTCCACCACCAGTA
TGGAGTGATAGGCGGGCACAACCAGCCCCAGCTGTCAGACCTCAGCAAGTCCTTGAACATCTCCTTCCCAGTGCCCACTT
GGATCTTGGTGCTGTCCCTGAGCCTAGCTGGTGCCCTCCTCCTCCTTGCTGGGCTGGTGGCTGTTGCCCTTGTAGTCAGA
AAAGTTAAACTCAAAAATTTACAGAAGAAAAGAGATGGAGAATCCTGCTGGGCCCAGATTAATTCTGACACCACAGACAT
GTCCTTTGATAACTCCCTGTTTACCATCTTGCTGAAAATGATGCCAGAAGAAGACCCAGCCAGCTTGGATGATCACTCAG
GCACCACTGCCACCCCTGGCAATTCCAGGACCTGGAAGATGCCCACTTCCATGTCCTCCTCGCCTGAGACCCTCGAGTTC
AGCACTTTCTGGCCCTGCCAG
ORF - retro_cjac_2072 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.63 % |
| Parental protein coverage: | 72.49 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PMNQRGVTFNLSGGSSEAPGGPFHCQYGVIGEHNQPQLSDLSEPVNISYPVPTWILALSLSLAGALLLLT |
| P.NQ..V.FNLSG.SSE.PGGPFH.QYGVIG.HNQPQLSDLS...NIS.PVPTWIL.LSLSLAGALLLL. | |
| Retrocopy | PANQCRVMFNLSGSSSEVPGGPFHHQYGVIGGHNQPQLSDLSKSLNISFPVPTWILVLSLSLAGALLLLA |
| Parental | GLVAVALLVRKVKLKNLQKKRDGESCWAQINFDTTDMSFDNSLFTISPKMMP-EDPANLDDHAGTSATPG |
| GLVAVAL.VRKVKLKNLQKKRDGESCWAQIN.DTTDMSFDNSLFTI..KMMP.EDPA.LDDH.GT.ATPG | |
| Retrocopy | GLVAVALVVRKVKLKNLQKKRDGESCWAQINSDTTDMSFDNSLFTILLKMMPEEDPASLDDHSGTTATPG |
| Parental | NSRTRKRPTSTSSSPEPPEFSTFRACQ |
| NSRT.K.PTS.SSSPE..EFSTF..CQ | |
| Retrocopy | NSRTWKMPTSMSSSPETLEFSTFWPCQ |
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 .02 RPM | 0 .18 RPM |
| SRP051959_heart | 0 .05 RPM | 0 .04 RPM |
| SRP051959_kidney | 0 .11 RPM | 0 .53 RPM |
| SRP051959_liver | 0 .09 RPM | 1 .54 RPM |
| SRP051959_lung | 0 .02 RPM | 1 .79 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 0 .37 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 1 .55 RPM |
| SRP051959_spleen | 0 .02 RPM | 1 .49 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2072 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2072 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2072 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 | ENSCJAG00000006309 | 1 retrocopy |
retro_cjac_2072 ,
|