RetrogeneDB ID: | retro_cjac_4103 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:96436224..96436671(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NCBP2 | ||
| Ensembl ID: | ENSCJAG00000013735 | ||
| Aliases: | None | ||
| Description: | nuclear cap binding protein subunit 2, 20kDa [Source:HGNC Symbol;Acc:7659] |
Retrocopy-Parental alignment summary:
>retro_cjac_4103
CTGAAAATTCTGTGTAAAGACCCTGCTTTGGAGCTGAGCTGCTACCAGGACTACCAGTTCAGTGGCAGTAAATCTGAGCA
GGAAAAATTACTGAGGGAAAGCTCCACATTGTATGTGGAGAATCTTTCCTTTTATACAACTGAAGAGCAAATACATGAGC
TCTTTAGTAGATGCGGTGATGTCAGGAATATATTTATGGGCCTGGATAAAATAACGAAAACAGCATGCTGTTTCTGTTTT
GTAGAATACTATAACAGAGCCGATGCTGAAAATGCCATGTGGTTTCTAAATGGGACCTGCCTAGATGAACGTATTATCCA
CACTGATCGGGATATAGGTTTTAGAGAGGGTTGACAGTATAGTCACGGTGTATCTGGGGGTCAGGTAATGGGTGAGTTTC
ACGAAGATTTTGATCCTGGTAGAGGAGGCTCTGGAAGACAGGCTCAG
ORF - retro_cjac_4103 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.1 % |
| Parental protein coverage: | 95.51 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK |
| LK.L..D...ELS.Y.D..F.G...EQEKLL..S.TLYV.NLSFYTTEEQI.ELFS..GD...I.MGLDK | |
| Retrocopy | LKILCKDPALELSCYQDYQFSGSKSEQEKLLRESSTLYVENLSFYTTEEQIHELFSRCGDVRNIFMGLDK |
| Parental | MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAG |
| ..KTAC.FCFVEYY.RADAENAM...NGT.LD.RII.TD.D.GF.EG.QY..G.SGGQV..E...D.D.G | |
| Retrocopy | ITKTACCFCFVEYYNRADAENAMWFLNGTCLDERIIHTDRDIGFREG*QYSHGVSGGQVMGEFHEDFDPG |
| Parental | RGGYGKLAQ |
| RGG.G..AQ | |
| Retrocopy | RGGSGRQAQ |
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 | 15 .80 RPM |
| SRP051959_heart | 0 .00 RPM | 24 .38 RPM |
| SRP051959_kidney | 0 .00 RPM | 25 .71 RPM |
| SRP051959_liver | 0 .00 RPM | 15 .70 RPM |
| SRP051959_lung | 0 .00 RPM | 26 .60 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 34 .18 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 25 .44 RPM |
| SRP051959_spleen | 0 .00 RPM | 34 .33 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4103 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4103 was not experimentally validated.