RetrogeneDB ID: | retro_cjac_1990 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 20:10623900..10624244(+) | ||
| Located in intron of: | ENSCJAG00000035823 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SUPT4H1 | ||
| Ensembl ID: | ENSCJAG00000017369 | ||
| Aliases: | None | ||
| Description: | suppressor of Ty 4 homolog 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:11467] |
Retrocopy-Parental alignment summary:
>retro_cjac_1990
ATGGCCCGGGAGACGGTGCTGAAGAACTTGCAGCATCTATGGGCTTGTCTGCTGTGTTTGCTGGTCAAGTCTATAGACCA
GTTTGAATATGATGGTTGTGACAACTGTGATGCCTATGTACAGATGAAGAATAATAACCGAGAGATGGTATATGACCACA
CTAGCTCTTCCTTTGATGGAATCATTGCAATGATGAGTCCAGAGGACAGCTAGGTCTCCAAGTGGCAGCGAGTCAGTAAC
TTTAAGCCAAGTGTATATGCAGTGTCATTCACTGGTTGCCTGCCCCAAGGAATCGTGTGGAAGTGAAAAGTTGAGGAGTG
ATCTCCAAATCCAGAGACACAGCT
ORF - retro_cjac_1990 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.9 % |
| Parental protein coverage: | 97.44 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGN-REMVYDCTSSSFDGIIAMMSPEDS |
| MA.ETV.K.L.HL.ACLLC.LVK.IDQFEYDGCDNCDAY.QMK.N.REMVYD.TSSSFDGIIAMMSPEDS | |
| Retrocopy | MARETVLKNLQHLWACLLCLLVKSIDQFEYDGCDNCDAYVQMKNNNREMVYDHTSSSFDGIIAMMSPEDS |
| Parental | WVSKWQRVSNFKPGVYAVSVTGRLPQGIV-RELKSRGVAYKSRDTA |
| .VSKWQRVSNFKP.VYAVS.TG.LPQGIV..E.KS.GV..KSRDTA | |
| Retrocopy | *VSKWQRVSNFKPSVYAVSFTGCLPQGIV<VEVKS*GVISKSRDTA |
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 .02 RPM | 6 .77 RPM |
| SRP051959_heart | 0 .02 RPM | 6 .33 RPM |
| SRP051959_kidney | 0 .11 RPM | 8 .32 RPM |
| SRP051959_liver | 0 .02 RPM | 8 .17 RPM |
| SRP051959_lung | 0 .03 RPM | 9 .13 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 9 .89 RPM |
| SRP051959_skeletal_muscle | 0 .07 RPM | 6 .86 RPM |
| SRP051959_spleen | 0 .04 RPM | 12 .77 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1990 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1990 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1990 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017369 | 3 retrocopies |
retro_cjac_1196, retro_cjac_1990 , retro_cjac_4216,
|
| Dipodomys ordii | ENSDORG00000002826 | 2 retrocopies | |
| Macropus eugenii | ENSMEUG00000010164 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000025583 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000031972 | 1 retrocopy |