RetrogeneDB ID: | retro_cjac_1794 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:59089762..59090389(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GINS3 | ||
| Ensembl ID: | ENSCJAG00000011635 | ||
| Aliases: | None | ||
| Description: | GINS complex subunit 3 (Psf3 homolog) [Source:HGNC Symbol;Acc:25851] |
Retrocopy-Parental alignment summary:
>retro_cjac_1794
ATGTCCGGAGCTTATTTCCGGAAGGAGTCGGGTGCACTGGAGCCTGAGGAGAACTTTCTGTCCTTGCACGACATCCGGAT
GTCGCAGGAGACGCTCCCACTGCGCTCGTAGACCCGCCTGCCTCGCCTGGCGTTTTCTTCCTGGAGCGCAGGCGCAGAGA
CTGACAATGCAGTGCCGCCGCGCTCAAAGCCTGAACTCCCCTTGTGGCTGCAAAAGGACGTTTTGACAAGCGACGGATTC
GTTCTGTGGACTTCCCAAAATATAAGGGGAGGGTTGGAGGACCGTGTTCCGTGCGGATGCCAGTGTGACGGACCGCCACA
AAATGAGGCCCCATTTCTACGGGTTTGGCTCCCAGCTCCCGCATTTTGACAGTCTTGAGAATGCAACTATTTCCCAGTCT
CTGCTGCAGAACTTTTATTGGACTTGCCGCATCATGGACTCCTCCCCAAAAACTTACAACGGAGACACTTCAGCTCTGGT
AGCCAGGCTAGAAGAGATGGAGAGGGGCTTATTTCAAACAAGGCAGAAAGGACTGAATGACTTTCAGAGAAAGGGCAGGC
TTCTTGGATCACAGCTTCCAACCTCGTTTAGAATTACAAAAAGGGAAAATTCACTGACATGGAAGAA
ORF - retro_cjac_1794 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.69 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MSEAYFRVESGALGSEENFLSLDDILMSHEKLPVRMETAMPRLGAFFLERSGGAETDNAVPQGSKLELPL |
| MS.AYFR.ESGAL..EENFLSL.DI.MS.E.LP.R..T..PRL...F...S.GAETDNAVP..SK.ELPL | |
| Retrocopy | MSGAYFRKESGALEPEENFLSLHDIRMSQETLPLRS*TRLPRLA--FSSWSAGAETDNAVPPRSKPELPL |
| Parental | WL-AKGLFDNKRRILSVE-LPKIYQEGWRTVFSADANVVDLHKIGPHFYGFGSQLLHFDSPENADISQSL |
| WL.AKG.FD.KRRI.SV..LPKI..EGWRTVF.ADA.V.D.HK..PHFYGFGSQL.HFDS.ENA.ISQSL | |
| Retrocopy | WL<AKGRFD-KRRIRSVD<LPKI*GEGWRTVFRADASVTDRHKMRPHFYGFGSQLPHFDSLENATISQSL |
| Parental | LQTFIGRFRRIMDSSQNAYNEDTSALVARLDEMERGLFQTGQKGLNDFQCWEKG-QASQITVSTLVQNYK |
| LQ.F.....RIMDSS...YN.DTSALVARL.EMERGLFQT.QKGLNDFQ...KG.QAS.IT.S.LV.NYK | |
| Retrocopy | LQNFYWTC-RIMDSSPKTYNGDTSALVARLEEMERGLFQTRQKGLNDFQ--RKG<QASWITASNLV*NYK |
| Parental | KRKFTDMED |
| K.KFTDME. | |
| Retrocopy | KGKFTDMEE |
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 .07 RPM | 1 .02 RPM |
| SRP051959_heart | 0 .47 RPM | 1 .21 RPM |
| SRP051959_kidney | 0 .04 RPM | 0 .22 RPM |
| SRP051959_liver | 0 .09 RPM | 0 .11 RPM |
| SRP051959_lung | 0 .26 RPM | 0 .28 RPM |
| SRP051959_lymph_node | 0 .23 RPM | 0 .25 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 0 .04 RPM |
| SRP051959_spleen | 0 .36 RPM | 0 .34 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1794 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1794 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1794 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011635 | 1 retrocopy |
retro_cjac_1794 ,
|