RetrogeneDB ID: | retro_cjac_3873 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL285540.1:11072..12323(-) | ||
| 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_3873
ATGTCTGCCTCAGCTGTCTTTATTCTCGACATCAAGGGCAAGTCTCTGATGAGCCACAACTACAAAGGCGATTAGCCCTT
GAGTAAGATGGAGCACTTCATGCCTCTGCTGGTACAGTGGGAGGATGAGGGTGCCCTGACTCTGCTTCTGAGCTATGGTG
AGGCCCACTTCCTATGGATCAAACAAAGCAGCCTCTACTTGGTGGCCACCACATTGAAGAATGCCAATGCCACCTTTTTT
TATAAGACAATACAGTTGTTCTGTGAATACTTCAAGGAACTAGAGGAGGAGAGCATCTGGGACAGCTTTGTCATCATCTA
CAAATTGCTGAATAAGCTGATGGACTTTGGCTTCCTGCAGAGCACCGACAGCAAGATCCTGCAAGAGTACATCAGTCAGC
AGAGCAACAAGCTGGAGACAGGCAAGAGGGTGCCACCCACTGTCACCAACGCTGTGTGGTGGCACTCTGAGGGTATCAAG
TATAAGAACGAGGTCTTCATCGATTTCATAGAGTTGTCAACCTGCTGGTCAATGCCAATGGCAACATCCTGCTGAGTGAG
ATTGTGGGTACCATCAAGCTCAAGGTGTTTCTGTTGGGAATGCCAGAGTCGTGGCTGAGCCTCAATCACTGCGTGCTCTT
CGAGCTCACTGGCCTTTCAGGGAGCAAGAACAAATCAATAAAGCTAAAGGATGTAAAATTCCACCAGCACATGTGGCTCT
CATGCTTTGGCAATGACCGCACCAACTCCTTCATCCCATCTGATGGTGACTTTAAGCTCATGTCCTACCTCCTCAGCACC
CAGGTGAAGCTACTGATCTGGATTGGGTCTATCATTGAGAAGTTCTCCCAGAGCCACGTGGAGATCATGGTCAAGGCCAA
GGGGCAGTTAAGAAACAGCCAGTGGCCACCAGTGTGGATATACCTGTGACCATGCCCAGCAATGCCAACTCCCCCAGATT
CAAGACCAGTGTGGGCAGCACCAAGTATGTGCCAGAGAAAAATGTCGTAATTTGGAGTATTAAGTCTTTCCTGGGGGCAA
GGAGTACTCGCTGCGAGCCCACTTTGGTCTCCCCAGCATGGAGAAGGAGGAGCTGGAGGGCTGGCCCCCAATCGGGGTCA
AGTTTGAGATCCCCTACTTCACCATCTCTGGGATCCAGGTCCGATACATTAAGATTATTGAGAAAAGTGGTTACCAGGCC
CTGCCCTGCGTTTGCTACATCACCCAGAGTGGGGATTACCAACTTTGTACC
ORF - retro_cjac_3873 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.7 % |
| Parental protein coverage: | 99.76 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVAT |
| MSASAV..LD.KGK.L...NY.GD...S..EHFMP.L...E.EG.L...L..G...F.WIK...LYLVAT | |
| Retrocopy | MSASAVFILDIKGKSLMSHNYKGD*PLSKMEHFMPLLVQWEDEGALTLLLSYGEAHFLWIKQSSLYLVAT |
| Parental | SKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYITQEGH |
| ..KNA..........K..Q.F.EYFKELEEESI.D.FVIIY.LL..LMDFG..Q.TDSKILQEYI.Q... | |
| Retrocopy | TLKNANATFFY----KTIQLFCEYFKELEEESIWDSFVIIYKLLNKLMDFGFLQSTDSKILQEYISQQSN |
| Parental | KLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIE-SVNLLVSANGN-ACSEIVGSIKMRVFLSGMPE |
| KLETG..R.P.TVTNAV.W.SEGIKY.KNEVF.D.IE..VNLLV.ANGN...SEIVG.IK..VFL.GMPE | |
| Retrocopy | KLETG-KRVPPTVTNAVWWHSEGIKY-KNEVFIDFIE<VVNLLVNANGNILLSEIVGTIKLKVFLLGMPE |
| Parental | LRLGLNDKVLFDNTG--RGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI |
| ..L.LN..VLF..TG....K.KS..L.DVKFHQ...LS.F.NDRT.SFIP.DG.F.LMSY.L.T.VK.LI | |
| Retrocopy | SWLSLNHCVLFELTGLSGSKNKSIKLKDVKFHQHMWLSCFGNDRTNSFIPSDGDFKLMSYLLSTQVKLLI |
| Parental | WIESVIEKHSHSRIEYMIKAKSQF-KRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSIK |
| WI.S.IEK.S.S..E.M.KAK.Q..K....A..V.I....P..A.SP.FKT.VGS.K.VPE.....WSIK | |
| Retrocopy | WIGSIIEKFSQSHVEIMVKAKGQL<KKQPVATSVDIPVTMPSNANSPRFKTSVGSTKYVPEKNVVIWSIK |
| Parental | S-FPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQN |
| S.FPGGKEY..RAHFGLPS.E.E..EG.PPI.VKFEIPYFT.SGIQVRY.KIIEKSGYQALP.V.YITQ. | |
| Retrocopy | S<FPGGKEYSLRAHFGLPSMEKEELEGWPPIGVKFEIPYFTISGIQVRYIKIIEKSGYQALPCVCYITQS |
| Parental | GDYQLRT |
| GDYQL.T | |
| Retrocopy | GDYQLCT |
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_3873 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3873 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3873 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 ,
|