RetrogeneDB ID: | retro_cjac_12 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 20:12518710..12519526(-) | ||
| Located in intron of: | ENSCJAG00000011550 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000034991 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RFC2 | ||
| Ensembl ID: | ENSCJAG00000003985 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_12
ACCACAAGAATTCTATGCTTGGCACGAGCTCTGCTGGGCCCAGCACTCAAGGATGCTGTGTTGGAACTCAATGCTTCAAA
TGACAGGGGCATTGACGTTGTGAGGAATAAAATTAAAATGTTTGCTCAACAAAAAGTCACCCTTCCCAAAGGCCAACATA
AGATCATCATTCTGGATGAAGCCGACAGCATGACTGACGGAGCCCAGCAAGCCTTGAGGAGAACCATGGAAATCTACTCC
AAAACCACGTGCTTTGCCCTTGCTTGTAATGCTTCGGATAAGATCATTGAGCCCATTCAGTCCCGCTGCGCTGTCCTCCG
CTACACGAAGCTGACCGATGCCCAGATCCTCACCAGGCTGATGAGTGTTATCGAAAAGGAGAGGGTGCCCCACACTGATG
ACGGCCTGGAAGCCATCATCTTCATGGCGCAGGGAGACATGAGGCAGGCACTGAACAACCTGCAGTCCACCTTCTCAGGA
TTTGGCTTCATTAACAGTGAGAATGTTTTCAAGGTCTGTGATGAGCCCCACCCACTGCTGGTGAAGGAGATGATCCAGCA
CTGTGTGAACACCAGCATCGATGAAGCTTACAAGATTCTCGCTCACCTGTGGCATCTGGGCTACTCACCAGAAGATATCA
TTGGCAACATCTTTCGAGTGTCTAAAGCTTTCCAAATGGCAGAATACCTGAAACTGGAGTTTATCAAGGAAATTGGATAC
ACTCATATGAAAATCGCAGGAGTGAACTCCCTTTTGCAGATGGCAGGCCTCCTGGCCAGGCTGTGTCAGAAGACAATGGC
CCCGGTGGCCAGTTAG
ORF - retro_cjac_12 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.96 % |
| Parental protein coverage: | 77.27 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TTSILCLARALLGPALKDAVLELNASNDRGIDVVRNKVKMFAQHKVTLPKGRHKIIILDEADSMTDGAQQ |
| TT.ILCLARALLGPALKDAVLELNASNDRGIDVVRNK.KMFAQ.KVTLPKG.HKIIILDEADSMTDGAQQ | |
| Retrocopy | TTRILCLARALLGPALKDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGQHKIIILDEADSMTDGAQQ |
| Parental | ALRRTMEIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMSVIEKERVPHTDDGLEAII |
| ALRRTMEIYSKTT.FALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMSVIEKERVPHTDDGLEAII | |
| Retrocopy | ALRRTMEIYSKTTCFALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMSVIEKERVPHTDDGLEAII |
| Parental | FTAQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEAYKILAHLWHLGYSP |
| F.AQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVN..IDEAYKILAHLWHLGYSP | |
| Retrocopy | FMAQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNTSIDEAYKILAHLWHLGYSP |
| Parental | EDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNSLLQMAGLLARLCQKTMAPVAS |
| EDIIGNIFRV.K.FQMAEYLKLEFIKEIGYTHMKIA.GVNSLLQMAGLLARLCQKTMAPVAS | |
| Retrocopy | EDIIGNIFRVSKAFQMAEYLKLEFIKEIGYTHMKIA-GVNSLLQMAGLLARLCQKTMAPVAS |
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 .16 RPM | 8 .54 RPM |
| SRP051959_heart | 2 .28 RPM | 6 .45 RPM |
| SRP051959_kidney | 0 .31 RPM | 5 .64 RPM |
| SRP051959_liver | 0 .02 RPM | 7 .39 RPM |
| SRP051959_lung | 0 .07 RPM | 8 .43 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 10 .55 RPM |
| SRP051959_skeletal_muscle | 0 .07 RPM | 4 .89 RPM |
| SRP051959_spleen | 0 .02 RPM | 7 .65 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_12 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_12 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_12 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003985 | 1 retrocopy |
retro_cjac_12 ,
|
| Otolemur garnettii | ENSOGAG00000014927 | 1 retrocopy |