RetrogeneDB ID: | retro_cjac_3896 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286126.1:7487..8584(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAD23A | ||
| Ensembl ID: | ENSCJAG00000004494 | ||
| Aliases: | None | ||
| Description: | RAD23 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:9812] |
Retrocopy-Parental alignment summary:
>retro_cjac_3896
GGCCCCGCCATGGCTGTCACCATCACGCTCAAAACACTGCAGCAGCAGACCTTCAAGATCCTCATGGAGACCGACGAGAC
AGTGAGGGTACTAAAGGAGAAGATAGAAGCTGAGAAAGGTCGTGATGCTTTCCCCATGGCTGGACAGAAACTTATTTATG
CCAGCAAGATCTTGAGCGATGATGTCCGCATCAGGGGCTATCATATTGATGAGAAGAATTTTGTAATCATCATGGTGACC
AAGACCAAAGCTGGCCAGGGTACCTCAGCACCCCCAGAGGCCTCACCTACAGCTGCCCCAGAGTCCTCTACATCCTTCCC
GCCTGCCCCTACCTCAGGCATGTCCCACCCCCCACCTGCCGCCAGACAGGACAAGAGCCCGTGGGATGAATCCACCCCCA
CGACGTCCCCAGAGTCCGTGTCAGGCTCTGTTCCCTCTTCAGGTAGCAGCGGGCGAGAGGAAGATGCAGCCTCCACGCTA
GTGACGGGCTCTGAGTATGAGACGGTGATCACAGAGATCATGTCCATGGGCTATGAGCGGGAGCGGGTCCTGGCTGCCCT
GAGAGCCAGCTAAAACAACCCCCACTGAGCAGTGGAGTATATGCTCACGGGAATTCCTGGGAGCCCCGAGCCGGAACACG
ATTCTGTCCAGGAGAGCCAGGTATCTGAGCAGCTGGCCACGGAAGCAGCAGGAGAGAAACCCCTGGAGTTCCTGCGGGAC
CAGCCCCAGTTCTAGAACATGCGGCAGGTGATTCAGCAGAACCCTGCACTGCTGCCCGCTCTGCACCAACAGCTGGGCCA
GGAGAATCCTCAGCTTTTGCAGCAAATTAGCTGGCACCAGGAGCAGTTCATCCAGATGCTGAACGAACCCCCTGGAGAGC
TGGCAGACATCTCAGATGTGGAGGCAGAGGTGGGTGCCATAGGAGAGGAGGCCCGCCTATGAACTACATCCAGATGATGC
TGCAGGAGAAAGAAGCTATAGAGAGGTTGAAGGCCCTGGGGTTTCCAGAGAGCCTGGTTATCCAGGCCTATTTCGCGTGT
GAAAAAAACGAAAACTTGGCTGCCAACTTCCTCTTGAGTCAGAACTTTGATAATGAG
ORF - retro_cjac_3896 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.83 % |
| Parental protein coverage: | 96.57 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GPAMAVTITLKTLQQQTFKIRMEPKVEVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRID |
| GPAMAVTITLKTLQQQTFKI.ME....V.VLKEKIEAEKGRDAFP.AGQKLIYA.KILSDDV.IR.Y.ID | |
| Retrocopy | GPAMAVTITLKTLQQQTFKILMETDETVRVLKEKIEAEKGRDAFPMAGQKLIYASKILSDDVRIRGYHID |
| Parental | EKNFVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFLPAPTSGMSHPPPAAREDKSPSEESAPTTSPESV |
| EKNFV..MVTKTKAGQG................TSF.PAPTSGMSHPPPAAR.DKSP..ES.PTTSPESV | |
| Retrocopy | EKNFVIIMVTKTKAGQGXXXXXXXXXXXXXXXXTSFPPAPTSGMSHPPPAARQDKSPWDESTPTTSPESV |
| Parental | SGSVPSSGSSGREEDAASTLVTGSEYETMLTEIMSMGYERERVVAALRASYNNPHRAVEYLLTGIPGSPE |
| SGSVPSSGSSGREEDAASTLVTGSEYET..TEIMSMGYERERV.AALRAS.NNPH.AVEY.LTGIPGSPE | |
| Retrocopy | SGSVPSSGSSGREEDAASTLVTGSEYETVITEIMSMGYERERVLAALRAS*NNPH*AVEYMLTGIPGSPE |
| Parental | PEHGSVQESQVSEQPATEAAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQ |
| PEH.SVQESQVSEQ.ATEAAGE.PLEFLRDQPQF.NMRQVIQQNPALLPAL.QQLGQENPQLLQQIS.HQ | |
| Retrocopy | PEHDSVQESQVSEQLATEAAGEKPLEFLRDQPQF*NMRQVIQQNPALLPALHQQLGQENPQLLQQISWHQ |
| Parental | EQFIQMLNEPPGELADISDVEAEVGAIGEEA-PQMNYIQVTPQEKEAIERLKALGFPESLVIQAYFACEK |
| EQFIQMLNEPPGELADISDVEAEVGAIGEEA.P.MNYIQ...QEKEAIERLKALGFPESLVIQAYFACEK | |
| Retrocopy | EQFIQMLNEPPGELADISDVEAEVGAIGEEA<PPMNYIQMMLQEKEAIERLKALGFPESLVIQAYFACEK |
| Parental | NENLAANFLLSQNFDDE |
| NENLAANFLLSQNFD.E | |
| Retrocopy | NENLAANFLLSQNFDNE |
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 | 9 .65 RPM |
| SRP051959_heart | 0 .00 RPM | 19 .43 RPM |
| SRP051959_kidney | 0 .04 RPM | 16 .77 RPM |
| SRP051959_liver | 0 .00 RPM | 12 .56 RPM |
| SRP051959_lung | 0 .00 RPM | 16 .28 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 14 .29 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 72 .48 RPM |
| SRP051959_spleen | 0 .00 RPM | 14 .85 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3896 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3896 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3896 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004494 | 1 retrocopy |
retro_cjac_3896 ,
|
| Callithrix jacchus | ENSCJAG00000016908 | 2 retrocopies |