RetrogeneDB ID: | retro_cjac_2211 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:19864384..19865002(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NUDT21 | ||
| Ensembl ID: | ENSCJAG00000012724 | ||
| Aliases: | None | ||
| Description: | nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870] |
Retrocopy-Parental alignment summary:
>retro_cjac_2211
GGGGTCGCCCAGTTCGGCAACGTGTACATCCAGCAGACCAACTCCCTCACCCTGGAGCGCACATGAACCTATACCCTCTC
ACCAATTATACTTTTGGTACAATAGAACCCCTCTATGAGCAGGACAGCTCTGTTGCAGCCAGATTTCGGAGCATGAGGGA
AGAATTTGATCCAATTGGAATGAGGAGGACTGCAGAAGGGGTTCTGATTGTACACGAGCACCAGCTACCCCATGCTGCTA
CAGCTGGAAACAACTTCTTTCAGACTGCCTGGTGGTGAACTTAACCCAGGAGATGATGAAGTTGAAGGACTAAAACGCTT
CATGACAGGGATACTGGGTAGTCAGGATGGAGTTCTGCAAGACTGGGTCATTGGGAACTGGTGGAGACCAAACTTTGAGC
TTCCCCAGAATCCATATATTCCTGCAGGTATTACAAAGTCTAAGGAACATAAGACGTTGCTTTTGGTTCAGCTTCAAGAA
AAAGCCTTGTTTGCAGTCCCCCAAAATTACAGGCTGGCACCTGCACCATTGTTTGAATTGCATGACACTGCACCAGGATA
TGGACCCGTCATTTCTAGTTTCCCTCAGCTGTTGAGCAGATTCGATTTTACACGCAAT
ORF - retro_cjac_2211 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.57 % |
| Parental protein coverage: | 93.39 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GVTQFGNKYIQQTKPLTLERT-INLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVL |
| GV.QFGN.YIQQT..LTLERT..NLYPLTNYTFGT.EPLYE.DSSVAARF..MREEFD.IGMRRT.EGVL | |
| Retrocopy | GVAQFGNVYIQQTNSLTLERT<MNLYPLTNYTFGTIEPLYEQDSSVAARFRSMREEFDPIGMRRTAEGVL |
| Parental | IVHEHRLPHVLLLQLGTTFF-KLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNF |
| IVHEH.LPH......G..FF..LPGGELNPG.DEVEGLKR.MT.ILG.QDGVLQDWVI....GNWWRPNF | |
| Retrocopy | IVHEHQLPHA--ATAGNNFF>RLPGGELNPGDDEVEGLKRFMTGILGSQDGVLQDWVI----GNWWRPNF |
| Parental | EPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFN |
| E.PQ.PYIPA.ITK.KEHK.L.LVQLQEKALFAVP.NY.L..APLFEL.D.APGYGP.ISS.PQLLSRF. | |
| Retrocopy | ELPQNPYIPAGITKSKEHKTLLLVQLQEKALFAVPQNYRLAPAPLFELHDTAPGYGPVISSFPQLLSRFD |
| Parental | FIYN |
| F..N | |
| Retrocopy | FTRN |
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 | 27 .18 RPM |
| SRP051959_heart | 0 .00 RPM | 27 .99 RPM |
| SRP051959_kidney | 0 .00 RPM | 31 .79 RPM |
| SRP051959_liver | 0 .00 RPM | 25 .36 RPM |
| SRP051959_lung | 0 .00 RPM | 28 .81 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 30 .09 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 21 .55 RPM |
| SRP051959_spleen | 0 .00 RPM | 30 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2211 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2211 was not experimentally validated.