RetrogeneDB ID: | retro_cjac_4102 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:95177833..95179316(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STAU1 | ||
| Ensembl ID: | ENSCJAG00000016233 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4102
GAAAGCATAACCCCTACCGTAGAACTAAATGCACTGTGCATGAAACTTGGAAAAAAACCAATATATAAGCCTGTTGACCC
TTACTCTCTGATGCAATCCACCTATAACTACAACATGAGAGGAGGTGTTTATCCCCTGAGGTACTTTTACCCATTTCCAG
TTCCACCTTTACTTTATCAAGTGGAGCTTTCTGTGGGAGGACAGCAATTTAATGGGAAAGGAAAGACAAGACAGGCTGCA
AAACATACTGCTGCTGCCAAAGCGTTGAGGATCCTGCAGAATGAGCCCCCACCAGAGAGGATGGAGGTGAATGGAAGAGA
ATCAGAAGAAAATCTCAATAAATCTGAAATAAGTCAAGTGTTTGAGATTGCACTTAAATGAAACTTGCCTGTGAATTTTG
AGGTGGCCTGGGAGAGTGGCGCACCCCACATGAAGGATTCTGTGACCAAGGTTTCGGTTGGGGAGTTTGTGGAGGAAGGT
GAAGGGAAAAGCAAGAAGATTTCAAAGAAAAATGCCGCCATAACTGTCCTTGAGGAGCTGAAGAAGTTACCGCCCCTGCC
TGCAGTTGAACAAGTAAAGCCTAGAATCAAAAAGAAAACAAAACCTATAGTAAAGCCACAGACAACCCCAGAATATGGCC
AGGGGATCTATCGGATTAGCAGACTGGCCCAGATCCAGCAGGCAAAAAAGGAGAGGGAGCTAGAGTACATGCTTCTCACA
GAGCTAGGCCTTCCATGCCACAGGGAGTTCGCAATGCAGGTAAAGGTTGGAAACCACACTGCAGAAGGAACAGGCACCAA
CAAGAAGGTGGCCAGGTGCAATGCAGCTGAGAACATGCTGGAGGTCCTTGGTCTCAAAGTCCCGCAGGCACAGCCCACCA
AGCCAGCACTCAAGTCAGAGGAGAAGACACCCATAAAGAAACGAGGGGATGGAAGAAAAGTAACCTTTTTTGAACCTGGC
TCTGGGGATGAAAATGGGACTAGTAATAAAGAGGATGAGTTCAAGATGCCTTATCTAAGTCATCAGCAGCTGCCTGCTGG
AATTCTTCCCATGGTGCCCGAGGTCGCTCAGGCTGTAGGAGTTAGTCAAGGACATCACACCAAAGATTTCACCAGGGCAG
CTCCCAATCCTTCCAGGGCCACAGTAACTGCCATGATAGCCCGAGAGTTGTTGTATGGGGGCACCTCGCCCATAGCCAAG
ACCATTTTAAAGAATAACATCTCTTCAGGCCATGTACCCCATGGACCTCACAAGACCCTCTGAGGAACTGGACTATCTTT
TCAGAGTTTAGGGATTTCAGGTTGACTACAAAGACTTCCCCCAAAACAACAAGAATGAATTTGTATCTCTTATCAATTGC
TCCTCTCAGCCGTCTCTGATCAGCCATGGTATTGGCAAGGATGTGGAGTCCTGCCATGATATGGCTGCACTGAACATCTT
AAAGTTGTTGTCTGAGTTGGACCAACAAAGTACAGAGATGCCT
ORF - retro_cjac_4102 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.76 % |
| Parental protein coverage: | 85.96 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPFPVPPLLYQVELSVGGQQF |
| ESITPTVELNALCMKLGKKP.YKPVDPYS.MQSTYNYNMRGG.YP.RYFYPFPVPPLLYQVELSVGGQQF | |
| Retrocopy | ESITPTVELNALCMKLGKKPIYKPVDPYSLMQSTYNYNMRGGVYPLRYFYPFPVPPLLYQVELSVGGQQF |
| Parental | NGKGKTRQAAKHDAAAKALRILQNEPPPERLEVNGRESEEENLNKSEISQVFEIALKRNLPVNFEVARES |
| NGKGKTRQAAKH.AAAKALRILQNEPPPER.EVNGRESEE.NLNKSEISQVFEIALK.NLPVNFEVA.ES | |
| Retrocopy | NGKGKTRQAAKHTAAAKALRILQNEPPPERMEVNGRESEE-NLNKSEISQVFEIALK*NLPVNFEVAWES |
| Parental | GPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTT |
| G.PHMK..VTKVSVGEFV.EGEGKSKKISKKNAAI.VLEELKKLPPLPAVE.VKPRIKKKTKPIVKPQTT | |
| Retrocopy | GAPHMKDSVTKVSVGEFVEEGEGKSKKISKKNAAITVLEELKKLPPLPAVEQVKPRIKKKTKPIVKPQTT |
| Parental | PEYGQGINPISRLAQIQQAKKEKEPEYMLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENM |
| PEYGQGI..ISRLAQIQQAKKE.E.EYMLLTE.GLP..REF.MQVKVGNHTAEGTGTNKKVA..NAAENM | |
| Retrocopy | PEYGQGIYRISRLAQIQQAKKERELEYMLLTELGLPCHREFAMQVKVGNHTAEGTGTNKKVARCNAAENM |
| Parental | LEILGFKVPQAQPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGIL |
| LE.LG.KVPQAQPTKPALKSEEKTPIKK.GDGRKVTFFEPGSGDENGTSNKEDEF.MPYLSHQQLPAGIL | |
| Retrocopy | LEVLGLKVPQAQPTKPALKSEEKTPIKKRGDGRKVTFFEPGSGDENGTSNKEDEFKMPYLSHQQLPAGIL |
| Parental | PMVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGP-LT |
| PMVPEVAQAVGVSQGHHTKDFTRAAPNP..ATVTAMIARELLYGGTSP.A.TILKNNISSGHVPHGP... | |
| Retrocopy | PMVPEVAQAVGVSQGHHTKDFTRAAPNPSRATVTAMIARELLYGGTSPIAKTILKNNISSGHVPHGP<SQ |
| Parental | RPSEQLDYLSRVQGFQVEYKDFPK-NNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSEL |
| .P.......S....F....K..PK.NNKNEFVSLINCSSQP.LISHGIGKDVESCHDMAALNILKLLSEL | |
| Retrocopy | DPLRNWTIFSEFRDFRLTTKTSPK<NNKNEFVSLINCSSQPSLISHGIGKDVESCHDMAALNILKLLSEL |
| Parental | DQQSTEMP |
| DQQSTEMP | |
| Retrocopy | DQQSTEMP |
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 | 35 .17 RPM |
| SRP051959_heart | 0 .00 RPM | 37 .34 RPM |
| SRP051959_kidney | 0 .04 RPM | 50 .12 RPM |
| SRP051959_liver | 0 .02 RPM | 34 .87 RPM |
| SRP051959_lung | 0 .03 RPM | 41 .64 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 25 .84 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 28 .83 RPM |
| SRP051959_spleen | 0 .08 RPM | 33 .47 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4102 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4102 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4102 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016233 | 1 retrocopy |
retro_cjac_4102 ,
|
| Monodelphis domestica | ENSMODG00000016276 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000027444 | 1 retrocopy |