RetrogeneDB ID: | retro_cjac_2416 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:22540151..22541908(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SLC4A10 | ||
| Ensembl ID: | ENSCJAG00000005614 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2416
CCTCAGTCCGTTCCAACTACAAGTCTTGAAGTAAAAAATGGAGTGAATTGTGAACATAGTCCTGTGGATTTAAGCAAGGT
AGACCTTCATTTCATGAAAAAAATTCCTACTGGGGCTGAGGCCTTCAATGTCCTGGTTGGAGAGGTGGATATTTTGGACC
ATCCCATTGTTGCCTTTGTGAGACTGTCTCCAGCTGTTCTTCTCTCAGGCCTAACAGAAGTTCCAATCCCAACAAGATTT
TTGTTTATCTTATTGGGTCCAGTAGGGAAAGGTCAGCAGTACCATGAGATTGGCAGATCCATGGCCACCTTCATGACAGA
TGAGATTTTTCATGACGTAGCATATAAGGCAAAAGAGCGAGATGATCTCCTGGCGGGGATTGACGAGTTCCTTGACCAGG
TGACGGTGCTCCCTCCAGGAGAGTGGGATCCCTCCATTAGAATTGAGCCACCCAAAAATGTCCCTTCCCAGGAGAAAAGG
AAAATACCTGGAGTTCCAAATGAAACTATTTGCCACATAGAACAGGAACCACATGGGGGTCACAGTGGGCCAGAACTTCA
GCTCACTGGGCGGCTATTTGGGGGCTTGGTGTTGGACATCAAGTGGAAGGCCCCCTGGTACTGGAGCGGCTACCGGGATG
CACTCAGCTTACAGTGTTTGGCCTCCTTTCTGTTCCTGTACTGTGCCTGCATGTCACCTGTCATCACCTTTGGGGGATTG
CTTGGAGAAGCCACTGAGGGACGCGTAAGTGCAATTGAATCCTTGTTTGGAGCCTCCATGACTGGGATTGCTTATTCCTT
GTTTGCGGGACAGGCTCTCACCATCCTGGGAAGTACTGGGCCAGTGCTTGTGTTTGAAAAGATTTTGTTCAAATTCTGCA
AAGACTATGCTCTTCCATACCTCTCCCTGCAAGCTTGTATTGGACTGTGGACTGCTTTCCTGTGTATTGTCCTTGTGGCA
ACTGATGCCAGTTCCCTTGTCTGCTACATTACCCGTTTCACTGAAGAAGCATTTACCTCCCCAATTTGCATTATTTTCAT
CTACGAAGCAATAGAAAAACTGATTCACCTGGCAGAGACCTATCCCATCCACATGCACAGCCAGCTGGACCACCCTAGCC
TCTATTACTGCAGGTGTACTCTCCCAGAGAATCCAAACAATCACACTCTGCAGTACTGGAAGGACCACAACATCGTGACA
GCAGAAGTCCACTGGGCTAATCTGACTGTCAGTGAATGCCAGGAGATGCATGGAGAGTTCATGGGATCTGCGTGCGGTCA
TCATGGACCCTACACTCCTGATGTCCTCTTTTGGTCCTGTATTCTCTTCTTCACCACCTTCATTCTCTCAAGCACCTTAA
AGACATTTAAGATGAGCCATTATTTCCCGACCAGAGTACGTTCCATGGTGAGTGACTTTGCTGTTTTCCTCACTATCTTC
ACAATGGTGATTATTGATTTTTTGATTGGAGTTCCACCACCAAAGCTTCAAGTTCCCAGTGTGTTCGAGCCAACAAGGGA
TGATCGAGGATGGATTATTAATCCTATTGGCCCCAATCCCTGGTGGACTGTGATAGCTGCAATTATCCCAGCTCTTCTCT
GCACTAGCTTGATATTCATGGATCAGCAGATCACAGCCGTCATTATTAATAGAAAGGAACATAAGCTCAAGAAAGGCTGT
GGCTACCACCTGGACCTACTGGTGGTGGCAATCATGCTGGGTGTCTGCTCCATCATGGGCTGCCTTGGTTTGTAGCT
ORF - retro_cjac_2416 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.71 % |
| Parental protein coverage: | 53.77 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PQSAPAC-VENKNDVSRENSTVDFSKVDLHFMKKIPPGAEASNILVGELDFLDRTVVAFVRLSPAVLLQG |
| PQS.P....E.KN.V..E.S.VD.SKVDLHFMKKIP.GAEA.N.LVGE.D.LD...VAFVRLSPAVLL.G | |
| Retrocopy | PQSVPTTSLEVKNGVNCEHSPVDLSKVDLHFMKKIPTGAEAFNVLVGEVDILDHPIVAFVRLSPAVLLSG |
| Parental | LAEVPIPTRFLFILLGPLGKGQQYHEIGRSIATLMTDEVFHDVAYKAKDRNDLVSGIDEFLDQVTVLPPG |
| L.EVPIPTRFLFILLGP.GKGQQYHEIGRS.AT.MTDE.FHDVAYKAK.R.DL..GIDEFLDQVTVLPPG | |
| Retrocopy | LTEVPIPTRFLFILLGPVGKGQQYHEIGRSMATFMTDEIFHDVAYKAKERDDLLAGIDEFLDQVTVLPPG |
| Parental | EWDPSIRIEPPKNVPSQEKRKIPAVPNGTAAHGEAEPHGGHSGPELQRTGRIFGGLILDIKRKAPYFWSD |
| EWDPSIRIEPPKNVPSQEKRKIP.VPN.T..H.E.EPHGGHSGPELQ.TGR.FGGL.LDIK.KAP..WS. | |
| Retrocopy | EWDPSIRIEPPKNVPSQEKRKIPGVPNETICHIEQEPHGGHSGPELQLTGRLFGGLVLDIKWKAPWYWSG |
| Parental | FRDAFSLQCLASFLFLYCACMSPVITFGGLLGEATEGRISAIESLFGASMTGIAYSLFGGQPLTILGSTG |
| .RDA.SLQCLASFLFLYCACMSPVITFGGLLGEATEGR.SAIESLFGASMTGIAYSLF.GQ.LTILGSTG | |
| Retrocopy | YRDALSLQCLASFLFLYCACMSPVITFGGLLGEATEGRVSAIESLFGASMTGIAYSLFAGQALTILGSTG |
| Parental | PVLVFEKILFKFCKEYGLSYLSLRASIGLWTATLCIILVATDASSLVCYITRFTEEAFASLICIIFIYEA |
| PVLVFEKILFKFCK.Y.L.YLSL.A.IGLWTA.LCI.LVATDASSLVCYITRFTEEAF.S.ICIIFIYEA | |
| Retrocopy | PVLVFEKILFKFCKDYALPYLSLQACIGLWTAFLCIVLVATDASSLVCYITRFTEEAFTSPICIIFIYEA |
| Parental | LEKLFELSEAYPINMHNDLELLTQYSCNCVEPHNPSNDTLKEWRESNISASDIIWENLTVSECKSLHGEY |
| .EKL..L.E.YPI.MH..L.....Y.C.C..P.NP.N.TL..W...NI......W.NLTVSEC...HGE. | |
| Retrocopy | IEKLIHLAETYPIHMHSQLDHPSLYYCRCTLPENPNNHTLQYWKDHNIVTAEVHWANLTVSECQEMHGEF |
| Parental | VGRACGHDHPYVPDVLFWSVILFFSTVTLSATLKQFKTSRYFPTKVRSIVSDFAVFLTILCMVLIDYAIG |
| .G.ACGH..PY.PDVLFWS.ILFF.T..LS.TLK.FK.S.YFPT.VRS.VSDFAVFLTI..MV.ID..IG | |
| Retrocopy | MGSACGHHGPYTPDVLFWSCILFFTTFILSSTLKTFKMSHYFPTRVRSMVSDFAVFLTIFTMVIIDFLIG |
| Parental | IPSPKLQVPSVFKPTRDDRGWFVTPLGPNPWWTVLAAIIPALLCTILIFMDQQITAVIINRKEHKLKKGC |
| .P.PKLQVPSVF.PTRDDRGW...P.GPNPWWTV.AAIIPALLCT.LIFMDQQITAVIINRKEHKLKKGC | |
| Retrocopy | VPPPKLQVPSVFEPTRDDRGWIINPIGPNPWWTVIAAIIPALLCTSLIFMDQQITAVIINRKEHKLKKGC |
| Parental | GYHLDLLMVAVMLGVCSIM-GLPWFVA |
| GYHLDLL.VA.MLGVCSIM.GLPWFVA | |
| Retrocopy | GYHLDLLVVAIMLGVCSIM<GLPWFVA |
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 | 0 .07 RPM |
| SRP051959_heart | 0 .00 RPM | 20 .98 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .02 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 0 .02 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .04 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2416 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2416 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2416 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 | ENSCJAG00000005614 | 1 retrocopy |
retro_cjac_2416 ,
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