RetrogeneDB ID: | retro_cjac_3277 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:20276987..20277755(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000001031 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3277
ATGGCCAGACCCGGCATGGAGCTGTGGCACGACCGGCTGGCGCTGGTGAAGGAAGCCTCAGTGGGCATTGGCGCGGCCGT
GGCCCGGGCCCTGGTCCAGCAGGGGCTGAAGGTGGTGGGCTGCGCCCACACCGTGGGCAACATCGAGGAGCTGGCTGCTG
AATGTTAAGAGTGCATGCTACCCCTGGACTTTGATCCCCTACAGATGTGACCTGTCAAATGAGGAGGACATCCTCTCCAT
GTTCTCGGCTATCCGTTCTCAGCACAGTGGCATAGACATCTGCATCAACAATACCGCTTGGGCCGGCCTGACTCCCTGCT
CTCAGGCAGCACCAGCGGTTGGAAGAAGATGCTCAATGTGAACGCGCTGGCCCTCAGCATCTGCACGCGGGAAGCCTACC
AGTCCATGAAGGAGTGAAATGTGGACCATGGGCACATCATTAACATCAATAGCATGTCTGGCCACCGAGTGGTCCCCCAG
TCTGTGACCCACTTCTATAGTGCCACCAAGTATGCTGTCACTACACTGACGGAGGGACTGAGGCAAGAGCTTCGGGAGGC
CCAGACCCACAACTGAGCCACATGCATCTTTCCAGGTGTTGTGGAAACACAATTTGCCTTCAGACTCCACGACAAGGACC
CTGAGAAGGCAGCTGCCACCTATGAGCACATGAAATGTCTCCAACCTGAGGATGTGGCCGAGGCTGTTATCTACGTCCTC
AGCACCCCCGCAAACGTCCAGATTGGAGACATCCAGATGAGGCCCACG
ORF - retro_cjac_3277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.0 % |
| Parental protein coverage: | 98.47 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MARRGMERWRDRLALVTGASVGIGAAVARALVQQGLKVVGCARTVGNIEELAAEC-KSAGYPGTLIPYRC |
| MAR.GME.W.DRLALV..ASVGIGAAVARALVQQGLKVVGCA.TVGNIEELAAEC.KSA.YP.TLIPYRC | |
| Retrocopy | MARPGMELWHDRLALVKEASVGIGAAVARALVQQGLKVVGCAHTVGNIEELAAEC>KSACYPWTLIPYRC |
| Parental | DLSNEEDILSMFSAIRSQHSGVDICINNAG-LGRPDSLLSGSTSGWKEMLNVNVLALSICTREAYQSMKE |
| DLSNEEDILSMFSAIRSQHSG.DICINN...LGRPDSLLSGSTSGWK.MLNVN.LALSICTREAYQSMKE | |
| Retrocopy | DLSNEEDILSMFSAIRSQHSGIDICINNTA<LGRPDSLLSGSTSGWKKMLNVNALALSICTREAYQSMKE |
| Parental | RNVDDGHIININSMSGHRVVPQSVTHFYSATKYAVTALTEGLRQELREAQTHIRATAQCISPGVVETQFA |
| .NVD.GHIININSMSGHRVVPQSVTHFYSATKYAVT.LTEGLRQELREAQTH..AT..CI.PGVVETQFA | |
| Retrocopy | *NVDHGHIININSMSGHRVVPQSVTHFYSATKYAVTTLTEGLRQELREAQTHN*AT--CIFPGVVETQFA |
| Parental | FRLHDKDPEKAAATYEHMKCLQPEDVTEAVIYVLSTPPHVQIGDIQMRPT |
| FRLHDKDPEKAAATYEHMKCLQPEDV.EAVIYVLSTP..VQIGDIQMRPT | |
| Retrocopy | FRLHDKDPEKAAATYEHMKCLQPEDVAEAVIYVLSTPANVQIGDIQMRPT |
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 | 17 .75 RPM |
| SRP051959_heart | 0 .02 RPM | 11 .47 RPM |
| SRP051959_kidney | 0 .00 RPM | 13 .36 RPM |
| SRP051959_liver | 0 .00 RPM | 12 .26 RPM |
| SRP051959_lung | 0 .00 RPM | 9 .30 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 16 .12 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 3 .80 RPM |
| SRP051959_spleen | 0 .00 RPM | 11 .79 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3277 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3277 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3277 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001031 | 2 retrocopies |
retro_cjac_3276, retro_cjac_3277 ,
|
| Oryctolagus cuniculus | ENSOCUG00000021228 | 1 retrocopy |