RetrogeneDB ID: | retro_cjac_3197 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:21286642..21287191(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM76A | ||
| Ensembl ID: | ENSCJAG00000009327 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 76, member A [Source:HGNC Symbol;Acc:28530] |
Retrocopy-Parental alignment summary:
>retro_cjac_3197
TGCTGGCTGTGCACACTTTCATACAAGCGGGTCCTTCAGAAGACCAAAGAGCAGAGGAAACACCTGAGTAGCTCTTCTCG
TGCTGACCACCAGGAGAAGGAGCAGTATAGTCGCCTGAGTGGTGGTGGCCATTATAACAGCCAGAAAACACTTTCTACAT
ATTCAACTCAAAATGAAATCCCAAAGAAAAAGTCCACGTTTGAGTCAATCACAACTAATGGAGACAGCTTCTCCCCAGAC
CTGGCTCTGGACTCACCAGACACTGACCACTTTGTCATCATTGCCTAACTGAAGGAAGAAGTAGCTACCCTAAAGAAGAT
GTTGCATCAAAAGGATCAAATGATTTTAGAGAAAGAGAAGAAGATTACAGAGGTGAAGGCTGATTTTCAGTACCAGGAAT
CACAGATGAGAGCCAAAATGAACCAGATGGAGAAAACCGACAAAGAAGTCACAGAACAATTGCAGGCCAAAAACCGAGAG
CTCCTGAATCAGGCAGCTGCCTTGTCCGAGAGCAAGAAGTCAGAGAAGTCAGGAGCTATAACCTCTCCG
ORF - retro_cjac_3197 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.54 % |
| Parental protein coverage: | 59.61 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | CWLCTLSYKRVLQKTKEQRKHLSSSSRAGHQEKEQYSRLSGGGHYNSQKTLSTSSIQNEIPKKKSKFESI |
| CWLCTLSYKRVLQKTKEQRKHLSSSSRA.HQEKEQYSRLSGGGHYNSQKTLST.S.QNEIPKKKS.FESI | |
| Retrocopy | CWLCTLSYKRVLQKTKEQRKHLSSSSRADHQEKEQYSRLSGGGHYNSQKTLSTYSTQNEIPKKKSTFESI |
| Parental | TTNGDSFSPDLALDSPGTDHFVIIAQLKEEVATLKKMLHQKDQMILEKEKKITELKADFQYQESQMRAKM |
| TTNGDSFSPDLALDSP.TDHFVIIA.LKEEVATLKKMLHQKDQMILEKEKKITE.KADFQYQESQMRAKM | |
| Retrocopy | TTNGDSFSPDLALDSPDTDHFVIIA*LKEEVATLKKMLHQKDQMILEKEKKITEVKADFQYQESQMRAKM |
| Parental | NQMEKTHKEVTEQLQAKNRELLKQAAALSKSKKSEKSGAITSP |
| NQMEKT.KEVTEQLQAKNRELL.QAAALS.SKKSEKSGAITSP | |
| Retrocopy | NQMEKTDKEVTEQLQAKNRELLNQAAALSESKKSEKSGAITSP |
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 .24 RPM | 10 .16 RPM |
| SRP051959_heart | 0 .84 RPM | 20 .61 RPM |
| SRP051959_kidney | 0 .91 RPM | 21 .12 RPM |
| SRP051959_liver | 0 .35 RPM | 9 .99 RPM |
| SRP051959_lung | 0 .99 RPM | 18 .04 RPM |
| SRP051959_lymph_node | 0 .66 RPM | 15 .55 RPM |
| SRP051959_skeletal_muscle | 0 .90 RPM | 22 .60 RPM |
| SRP051959_spleen | 0 .57 RPM | 17 .54 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3197 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3197 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3197 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000009327 | 1 retrocopy |
retro_cjac_3197 ,
|
| Mus musculus | ENSMUSG00000028878 | 2 retrocopies | |
| Ochotona princeps | ENSOPRG00000017049 | 1 retrocopy |