RetrogeneDB ID: | retro_cjac_2994 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:78919062..78919598(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MTX3 | ||
| Ensembl ID: | ENSCJAG00000019700 | ||
| Aliases: | None | ||
| Description: | metaxin 3 [Source:HGNC Symbol;Acc:24812] |
Retrocopy-Parental alignment summary:
>retro_cjac_2994
AATAACATTGTTTCTTAGCTGGTAAAAGTGTTAAACTTTTAAAGAAAACAGAAATATAATGCTGATTATGAACCTCCAGC
AAAAGGAAGGACAGATAGATACACTGGCTTTCACTGCTCTCCTCAAACAGAAGCTGTCTCCTTCTAGTGCTTCGCACACA
ATCAGTTGAAAGCAACAATCAGTTTACTGTGACTAAGCTGTGGTGTTGGTTTGCTTCATAGATTCCTTTTCCCTTGGGTT
TGATCCTGCCTGGAAAAATACCTGAAAGAGCACTATTAGAATTCTCCTGACCAGAAGAGAGCCTCTCCGCCTGTGCGAAG
CAGAATCACGGATCTGCAGAGACACTAAGAAGTGCCTAAATCTTCTGTCAGATAAATTGTGACCATCTCAGTTTCTCCTT
GGGGATACCCATTCTACTTTGGTTACCCACATTTGGTTTCCTTGCACCTCTGCATACGGCGCCCTCTCCTAAAGTTCAGT
TACAGGAACATTTGAAACATGTCTCCAACCTGCGATCCTTTTGCAATGCTATCCTA
ORF - retro_cjac_2994 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.92 % |
| Parental protein coverage: | 57.05 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | DNIVSQPAKILNFLRKQKYNADYE-LSAKQGA-DTLAYIALLEEKLLPA-VLHTFWVESDNYFTVTKPW- |
| .NIVS...K.LNF.RKQKYNADYE.L..K.G..DTLA..ALL..KL.P..VL.T..VES.N.FTVTK.W. | |
| Retrocopy | NNIVS*LVKVLNF*RKQKYNADYE>LQQKEGQIDTLAFTALLKQKLSPS>VLRTQSVESNNQFTVTKLWC |
| Parental | -FASQIPFPLSLILPGRMSRGALN-RILLTRGQPPLYHLREVEAQIYRDAKECLNLLSNRLGTSQ-FFFG |
| .FAS.IPFPL.LILPG.....AL..RILLTR..P....L.E.E..I.RD.K.CLNLLS..L..SQ.F..G | |
| Retrocopy | WFAS*IPFPLGLILPGKIPERALL<RILLTRREP--LRLCEAESRICRDTKKCLNLLSDKL*PSQ>FSLG |
| Parental | NTPSTLDAYVFGFLAPLYKVRFPKIQLQEHLKQLSNLCRFCDDIL |
| ..P..L....FGFLAPL.....PK.QLQEHLK..SNL..FC..IL | |
| Retrocopy | -IPILLWLPTFGFLAPLHTAPSPKVQLQEHLKHVSNLRSFCNAIL |
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 | 2 .55 RPM |
| SRP051959_heart | 0 .00 RPM | 3 .75 RPM |
| SRP051959_kidney | 0 .00 RPM | 2 .73 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .06 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .20 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .36 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .70 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .97 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2994 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2994 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2994 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000010893 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000019700 | 1 retrocopy |
retro_cjac_2994 ,
|
| Macaca mulatta | ENSMMUG00000021104 | 1 retrocopy | |
| Vicugna pacos | ENSVPAG00000009404 | 1 retrocopy |