RetrogeneDB ID: | retro_cjac_4100 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:90299613..90300291(+) | ||
| 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_4100
ATGTCTGTGGTACCTCCGAATCACTCACAGACCGGCTGGTCCCCGGGGGTCACTCAGTTAGGCAACAAGTACATCCAGCA
GACCAAGCCCCTCACCCTGGCATGTACCATCAATCTGTACCCTCTTACCAATCATACTTCTGGTACAAAAGAGCCTCTCT
ACAAGAAGGACAGCTCTGTTGCAGCCAGATTTCAGCACATGAGGGAAGAATTTGATTAAATTGGAATGAGGAGGACTGTA
GAAGAGGTTCTGATTGTACACAAGCATCGGTTACCCCATGTGTTACTGCTATAGCTGGGAACAACTTTCTTCAAACTACC
TGGTGGTAAACTTAACCCGGGAGAAGATGAAGTTGAAGGACTGAAATGCTTAATGACAGAGATGCTGCGTCGTCAGGATA
GAGTTCTGCAAGACTGGGTCATTGATGACTGCATTGGTAACTGGTGAATGACTTTTGAACCTCCTCAGTATCCATATATT
CCTGCACATGTTACACAACCTAAGGAACATAAAAAGTTGTTTCTGGTTCAGCTACAAGAAAAAGCTTTGTTTGCAGTCCC
TAAAAATTACAAGCTGGTAGCTGCACCATTGTTTGAATTGTATGACAAAACACCGAGATATGGACCCATCATTTCTAGTC
TCCCTCAGCTGTTGAACACGTTAAATTTTATGCACAAC
ORF - retro_cjac_4100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.46 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSVVPPNRSQTGWPRGVTQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREE |
| MSVVPPN.SQTGW..GVTQ.GNKYIQQTKPLTL..TINLYPLTN.T.GTKEPLY.KDSSVAARFQ.MREE | |
| Retrocopy | MSVVPPNHSQTGWSPGVTQLGNKYIQQTKPLTLACTINLYPLTNHTSGTKEPLYKKDSSVAARFQHMREE |
| Parental | FDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV |
| FD.IGMRRTVE.VLIVH.HRLPHVLLL.LGTTFFKLPGG.LNPGEDEVEGLK.LMTE.L.RQD.VLQDWV | |
| Retrocopy | FD*IGMRRTVEEVLIVHKHRLPHVLLL*LGTTFFKLPGGKLNPGEDEVEGLKCLMTEMLRRQDRVLQDWV |
| Parental | IDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP |
| IDDCIGNW....FEPPQYPYIPAH.T.PKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYD..P.YGP | |
| Retrocopy | IDDCIGNW*M-TFEPPQYPYIPAHVTQPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDKTPRYGP |
| Parental | IISSLPQLLSRFNFIYN |
| IISSLPQLL...NF..N | |
| Retrocopy | IISSLPQLLNTLNFMHN |
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_4100 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4100 was not experimentally validated.