RetrogeneDB ID: | retro_cjac_1309 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:95049991..95051486(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EFTUD2 | ||
| Ensembl ID: | ENSCJAG00000012349 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1309
CCTGAGGTGCCACACTACTAAGATGTACATAGCACAAATGATGGAGTTCAGTTTCATGCCTTTGGCCCGGGTGCTGAGTG
GCACCATTCATGCTGGGCAGCCTGTGAAGGTACTCGGGGAGAACTACACCCTGGAGGATGAGGAAGACTCCCAGATATGT
ACTGTGGGCCACATTTGGATCTCTGTGGCCAGGTACCACATTGAGGTGAGCCATGTTCCTCTGGCAACTGGGTTCTGATT
GAAGGTGTTGATCAACCAGTTGTGAAGACAGCAACCATAACTGAACCCTGAGGCAATGAGGAGGCTCAGATTTTCCAGCC
CTTGAAGTTCAATGCCACATCTGTTATCAAGATTGCTGTGGAGCCAGTCAACCCCTCAGAGCTGCCCAAGATGCTTGATG
GCCTGTGCAAGGTTAACAAGAGCTATCTATCCCTCACCACCAAGGTGGATTCTGGCGAGCATGTGATTCTGGGCACCGGG
GAGCTCTACCTAGACTGTGTGATGCATGATCTACAGAAGATGTACTTGGAGATAGACATCAAGGTGGCTGACCCAGTTGT
CACATTTTGTGAGATGGTGGTGGAAACATCCTCCCTCAAGTGCTTTGCTGAAACACCTAATAAGAACAAGATCACCATGA
TTGATGAGCCTCTTGAGAAGGGCCTGGCAGAGGACATAGAGAATGAGGTGGTCCAGATTACATGGAACAGAAAGAAGCTA
GGAGAGTTCTTCCAGACCAAGTATGATTGGGATCTGCTGGCTGCCCGTTCCACCTGGGCTTTTGGCCCTGATGCCACTGG
CCCCAACATTCTGGTGGATGATACTCTACCCTCCGAGGTTGACAAGGCTCTTCTTGGCTCAGTGAAGGGCAGAATCGTTC
AAGGTTTCCAGTGGGGAACCAGGGAGGGGCCCCACTGTGATGAGTTGATTCAGAACGTCAAATTTAAGATTCTGGATGCA
GTGGTTGCCCAGGAGCCCCTGCACTGCAGCGGGGGCCAGATCATCCCCACAGCCAGGAGAGTTGTCTACTCTGCCTTCCT
CATGGCCACTCGTTGTCTGATGGAGCCTTACTACTTTGTAGAGGTCCAGGCGCCTGCAGATTGCATCTCTGTGGTTTATA
CTGTCCTAGCCAGGCGCAGAGGGCACGTGACTCGGGATGCACCCATCCCAGATTCCCCTCTGTACACCATCAAAGCTTTT
ATCCCAGCCATCGACTCTTTTGGCTTTGAAACTGATCTCCGGACTCACACCCGGGGACAGGCCTTTTCTCTGTCTGTCTT
CCACCATTGGCAGATTGTCCCTGGTGATCCTCTGGACAAGAGCATTGTCATTCGCCCTTTGGAGCCACAGCCGGCTCCTC
ACCTGGCCCGGGAATTCATGATCAAAACTTGTCGTAGGAAGGGCCTCAGTGAAGATGTGAACATAAGCAAATTCTTCGAT
GATCCTATTGTTGCTGGAACTCGCCAAACAGGATGTTGTGCTCAATTACCCCATG
ORF - retro_cjac_1309 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.66 % |
| Parental protein coverage: | 51.44 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | PLMCHTTKMYSTDDGVQFHAFG-RVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGRLWISVARYHIEV |
| P...H.....ST.DGVQFHAFG.RVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVG..WISVARYHIEV | |
| Retrocopy | PEVPHY*DVHSTNDGVQFHAFG>RVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGHIWISVARYHIEV |
| Parental | NRVP-AGNWVLIEGVDQPIVKTATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSELPKMLDGLRKV |
| ..VP..GNWVLIEGVDQP.VKTATITEP.GNEEAQIF.PLKFN.TSVIKIAVEPVNPSELPKMLDGL.KV | |
| Retrocopy | SHVP<SGNWVLIEGVDQPVVKTATITEP*GNEEAQIFQPLKFNATSVIKIAVEPVNPSELPKMLDGLCKV |
| Parental | NKSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVVTFCETVVETSSLKCFAETPN |
| NKSY.SLTTKV..SGEHVILGTGELYLDCVMHDL.KMY.EIDIKVADPVVTFCE.VVETSSLKCFAETPN | |
| Retrocopy | NKSYLSLTTKVD-SGEHVILGTGELYLDCVMHDLQKMYLEIDIKVADPVVTFCEMVVETSSLKCFAETPN |
| Parental | KKNKITMIAEPLEKGLAEDIENEVVQITWNRKKLGEFFQTKYDWDLLAARSIWAFGPDATGPNILVDDTL |
| K.NKITMI.EPLEKGLAEDIENEVVQITWNRKKLGEFFQTKYDWDLLAARS.WAFGPDATGPNILVDDTL | |
| Retrocopy | K-NKITMIDEPLEKGLAEDIENEVVQITWNRKKLGEFFQTKYDWDLLAARSTWAFGPDATGPNILVDDTL |
| Parental | PSEVDKALLGSVKDSIVQGFQWGTREGPLCDELIRNVKFKILDAVVAQEPLHRGGGQIIPTARRVVYSAF |
| PSEVDKALLGSVK..IVQGFQWGTREGP.CDELI.NVKFKILDAVVAQEPLH..GGQIIPTARRVVYSAF | |
| Retrocopy | PSEVDKALLGSVKGRIVQGFQWGTREGPHCDELIQNVKFKILDAVVAQEPLHCSGGQIIPTARRVVYSAF |
| Parental | LMATPRLMEPYYFVEVQAPADCVSAVYTVLARRRGHVTQDAPIPGSPLYTIKAFIPAIDSFGFETDLRTH |
| LMAT..LMEPYYFVEVQAPADC.S.VYTVLARRRGHVT.DAPIP.SPLYTIKAFIPAIDSFGFETDLRTH | |
| Retrocopy | LMATRCLMEPYYFVEVQAPADCISVVYTVLARRRGHVTRDAPIPDSPLYTIKAFIPAIDSFGFETDLRTH |
| Parental | TQGQAFSLSVFHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDP-MLL |
| T.GQAFSLSVFHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKT.RRKGLSEDV.ISKFFDDP..LL | |
| Retrocopy | TRGQAFSLSVFHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTCRRKGLSEDVNISKFFDDP>LLL |
| Parental | ELAKQDVVLNYPM |
| ELAKQDVVLNYPM | |
| Retrocopy | ELAKQDVVLNYPM |
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 | 29 .86 RPM |
| SRP051959_heart | 0 .00 RPM | 33 .10 RPM |
| SRP051959_kidney | 0 .02 RPM | 34 .21 RPM |
| SRP051959_liver | 0 .00 RPM | 37 .41 RPM |
| SRP051959_lung | 0 .03 RPM | 35 .17 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 37 .05 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 41 .93 RPM |
| SRP051959_spleen | 0 .00 RPM | 34 .98 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1309 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1309 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1309 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 | ENSCJAG00000012349 | 1 retrocopy |
retro_cjac_1309 ,
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