RetrogeneDB ID: | retro_cjac_1985 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 20:4538523..4539792(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AP1M1 | ||
| Ensembl ID: | ENSCJAG00000014070 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1985
ATGTCCACCTCAGCTGTCTTCATTCTCGATGTCAAGGGCAAGCCCCTGATCAGCCACAACTGCAAGGGCAATGTGCCCAT
GAGCAAGATTGATTACTTCATGCCTCTGCTGGTGCAGCAGGATGAGGAGGGCTCCCTCACCCTAAGGCTGAGCTATGGCA
AGGTCCACTTCCTATGGATCAAACACAGCAACCTCTACCTGGTGGCCACCACATTGAAGAATGCCAATGCCTCACTGGTG
TGCTCTTTCCTGTATAAGACAATAGAGGAATTCTGTGAATACTTCAAGGAGCTGTAGGAGAGCATCAGGGACAACTTTGT
CATCGTCTATGAGTTGCTGGACAAGCTCATGGACTTTGGCTTCCCGCAGACCACCGACATCAAGATCCTGCAGGAGTACA
TCACTCAGCAGAGCAACAAGCTGGAGATGGGTTAATCATGGGTACCACCCACTGTCACCAATGCTGTGTCCTGGCACTCT
GAGGCTATCAAGTATAAGAAGAACGAGGTCTTCATCGATGTCATAGAGTCTGTCAACCTGCTGGTCAATGCCAATGACAG
TGTCCTGCTGAGCGAGATCATTGGTACCATCAACCTCAAAGTGCTTCTGTCAGGAATGCCTGAGCTGCGGCTGGGCCTCA
ATGACCATGTGCTCTTTGAGCTCACTGGCTACAGCAAGAACAAATTGTTAGAGCTAGAGGATATGAAATTCCACCAGTGT
GTGCAGCTCTCATGCTTTGACAACAACCGCACCATCTCTTTCATCCTGCCTGATGATGACTTTGAGCTCATGTCCTACCG
CCTCAGCACCCAGGTGAAGCCACTGATCTGGATTGAGTTTGTCATTGGGAAGTTCTCCCACAGCCATGTGGAGATCTTAG
TCAAGACCAAGGGGCAGTTTAAGAAACAGTCAGTGGCCAATGGTGTGGAGATATCTGTGCCTGTGCCTGTGCCCAGTGAT
GCCGACTCCCCCAGATTCAAGACCAGTGTGGGCAGTGCTAACTATGTGCCAGAGAAAAACATTGTGATTTAGAGTATTAA
GTCTTTCCTGGGGAGCAAGGAGTGCTTGATGCGAGCCCACTTTGGCCTCCCCAGCATGGAGAAGGAGGAGGTGGAGGGCC
GGCCCCCTATCCGGGTCAAGTTTGAGATCCTCTACTTCACCATCTCTGGGATCCAGGTCCGATACATGAAGATCATTGAG
AAAAGTGGTCACCAGGCCCTGCCCTGGGTTCACTACATCACCCAGAGTGGCAATTACCAACTTCATACC
ORF - retro_cjac_1985 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.92 % |
| Parental protein coverage: | 99.76 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVAT |
| MS.SAV..LD.KGK.LI..N..G.V.MS....FMP.L....EEG.L...L..G.V.F.WIKH.NLYLVAT | |
| Retrocopy | MSTSAVFILDVKGKPLISHNCKGNVPMSKIDYFMPLLVQQDEEGSLTLRLSYGKVHFLWIKHSNLYLVAT |
| Parental | SKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYITQEGH |
| ..KNA..SLV.SFLYK....F.EYFKEL.E.SIRDNFVI.YELLD.LMDFG.PQTTD.KILQEYITQ... | |
| Retrocopy | TLKNANASLVCSFLYKTIEEFCEYFKEL*E-SIRDNFVIVYELLDKLMDFGFPQTTDIKILQEYITQQSN |
| Parental | KLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIESVNLLVSANGNAC-SEIVGSIKMRVFLSGMPEL |
| KLE.G....P.TVTNAVSW.SE.IKY.KNEVF.DVIESVNLLV.AN.....SEI.G.I...V.LSGMPEL | |
| Retrocopy | KLEMG*SWVPPTVTNAVSWHSEAIKYKKNEVFIDVIESVNLLVNANDSVLLSEIIGTINLKVLLSGMPEL |
| Parental | RLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIE |
| RLGLND.VLF..TG..K.K..ELED.KFHQCV.LS.F.N.RTISFI.PD..FELMSYRL.T.VKPLIWIE | |
| Retrocopy | RLGLNDHVLFELTGYSKNKLLELEDMKFHQCVQLSCFDNNRTISFILPDDDFELMSYRLSTQVKPLIWIE |
| Parental | SVIEKHSHSRIEYMIKAKSQFKRRSTANNVEIH--IPVPNDADSPKFKTTVGSVKWVPENSEIVWSIKSF |
| .VI.K.SHS..E...K.K.QFK..S.AN.VEI....PVP.DADSP.FKT.VGS...VPE......SIKSF | |
| Retrocopy | FVIGKFSHSHVEILVKTKGQFKKQSVANGVEISVPVPVPSDADSPRFKTSVGSANYVPEKNIVI*SIKSF |
| Parental | PGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDY |
| .G.KE.LMRAHFGLPS.E.E..EG.PPI.VKFEI.YFT.SGIQVRY.KIIEKSG.QALPWV.YITQ.G.Y | |
| Retrocopy | LGSKECLMRAHFGLPSMEKEEVEGRPPIRVKFEILYFTISGIQVRYMKIIEKSGHQALPWVHYITQSGNY |
| Parental | QLRT |
| QL.T | |
| Retrocopy | QLHT |
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 | 6 .66 RPM |
| SRP051959_heart | 0 .00 RPM | 10 .80 RPM |
| SRP051959_kidney | 0 .00 RPM | 13 .67 RPM |
| SRP051959_liver | 0 .00 RPM | 14 .95 RPM |
| SRP051959_lung | 0 .00 RPM | 10 .87 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 13 .95 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 12 .58 RPM |
| SRP051959_spleen | 0 .00 RPM | 12 .98 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1985 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1985 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1985 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012998 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000014070 | 3 retrocopies |
retro_cjac_1985 , retro_cjac_2135, retro_cjac_3873,
|