RetrogeneDB ID: | retro_cjac_939 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 11:111250348..111250843(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSCJAG00000031644 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | IL32 | ||
| Ensembl ID: | ENSCJAG00000015506 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_939
CAGCCCTTTGAAAAATTTGCTGGTGTGATGGAAAATCCAGAATCAAAACTGGAGAGGTGAAGTTGAGCATGAAAGAGCTG
GAGGACAACGTCAAAGTGTGGTGTCTGGACACTGTGGTGGCTTAGTGTCAGAGATAGCGCCCGGAGCTCACTCCTCTACT
TGAGAAAGAAGGAGATGAATTACGGTGCAGAGGCAACAGACCCCCTGTCCTGGAAGTTGAGGATCCTGAAACCAAGGAGC
ACAGGAGCGCTTTTGTGACAAGGTCATGAGATGGTTCCAGGCCATGCTGCAGTGGCTGCGGACGTGGTGGCAGACGGTTG
TGGCCTGGGTGAAGGAGAAGGTGGAGGTCCTGGTCCATGCAGTGCAGGCCCTCTGGAAAGAGTTCGAGAGTTTCTGCTGC
TCTCTGACCGAGCTCTTCATGTCCTTTTTACAGTCCCAAGGAGCCCCCCAAAGGGGATGGAGGAGCTGACACCCCAGAAG
TACTCTGAACCCCAA
CAGCCCTTTGAAAAATTTGCTGGTGTGATGGAAAATCCAGAATCAAAACTGGAGAGGTGAAGTTGAGCATGAAAGAGCTG
GAGGACAACGTCAAAGTGTGGTGTCTGGACACTGTGGTGGCTTAGTGTCAGAGATAGCGCCCGGAGCTCACTCCTCTACT
TGAGAAAGAAGGAGATGAATTACGGTGCAGAGGCAACAGACCCCCTGTCCTGGAAGTTGAGGATCCTGAAACCAAGGAGC
ACAGGAGCGCTTTTGTGACAAGGTCATGAGATGGTTCCAGGCCATGCTGCAGTGGCTGCGGACGTGGTGGCAGACGGTTG
TGGCCTGGGTGAAGGAGAAGGTGGAGGTCCTGGTCCATGCAGTGCAGGCCCTCTGGAAAGAGTTCGAGAGTTTCTGCTGC
TCTCTGACCGAGCTCTTCATGTCCTTTTTACAGTCCCAAGGAGCCCCCCAAAGGGGATGGAGGAGCTGACACCCCAGAAG
TACTCTGAACCCCAA
ORF - retro_cjac_939 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.17 % |
| Parental protein coverage: | 73.33 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | QLVDKFTEKMGNKESEPEK-VKLSLDDLEDDFRECMLDTVVDCYQGQHLELIPLLEKERDELRLRGNRPP |
| Q...KF...M.N.ES..E..VKLS...LED......LDTVV...Q....EL.PLLEKE.DELR.RGNRPP | |
| Retrocopy | QPFEKFAGVMENPESKLER<VKLSMKELEDNVKVWCLDTVVA*CQR*RPELTPLLEKEGDELRCRGNRPP |
| Parental | ALEAEDPETQE-PEESFCDKVMRWFCAMMQRLQMWWQKFVAWVKKVVAALVDAAKAFWKELERFCCSLAE |
| .LE.EDPET.E...E.FCDKVMRWF.AM.Q.L..WWQ..VAWVK..V..LV.A..A.WKE.E.FCCSL.E | |
| Retrocopy | VLEVEDPETKE<AQERFCDKVMRWFQAMLQWLRTWWQTVVAWVKEKVEVLVHAVQALWKEFESFCCSLTE |
| Parental | LLRS-LFSTKEAHRGD-EELTAQKCYEPQ |
| L..S...S.KE...GD.EELT.QK..EPQ | |
| Retrocopy | LFMS>FYSPKEPPKGD>EELTPQKYSEPQ |
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 | 39 .74 RPM |
| SRP051959_heart | 0 .02 RPM | 3 .03 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .36 RPM |
| SRP051959_liver | 0 .00 RPM | 74 .08 RPM |
| SRP051959_lung | 0 .02 RPM | 69 .97 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 138 .62 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .44 RPM |
| SRP051959_spleen | 0 .00 RPM | 55 .17 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_939 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_939 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_939 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 | ENSCJAG00000015506 | 1 retrocopy |
retro_cjac_939 ,
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