RetrogeneDB ID: | retro_cjac_3159 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:100081660..100082467(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DAP3 | ||
| Ensembl ID: | ENSCJAG00000008125 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3159
ACACTACTGAAAGGAATAATAAGGCTTATCTCTAGGATCCATAAGTTGGACCCTGGGCTTTTGTTACACATGGGAACCCA
GGCACACCAAAGCATTGCTGCTCACCTAGATAACCAGGTTCCAGTTGAGAGTCCCAGAGCTATTTCCCACACCAATGAGA
ATGACCCAGCTAAGCATGGGGATCAGCATGAGGGTCAGCACTACAACATCTTCCCCCAGGATATGAAGACAGTAGTTCCC
CAGGGCCTTCCTCCTCGCTTTGTGATGCAGGTGAAGACATTCAGTGAAGCTTACCTGATGGAAAGGAAACCAGCCCTGGA
ACTTCTGCATTACCTGAAAAAACACCAATGTTGCTTATCCGACTGTATGATATCTTCTGTATGGGGAGAAGGGAACAGGA
AAAACTCTCAGTCTTTGCCATATTATTAATTTCTGTGCAAAACAGGACTGGATGATACTACATATTCCAGATGCTCATAA
TGGGGTAAAAAATTTCCGGGAACTTCTACAGTCGAACTACAACAAACAACTCTTTGATCAACCTTTAGAGGCTTCAACCT
GGCTGAAGAATTTCAAAACTACAAGTGATTGCTTCCTGAACCAGATAAAAATTCAAGAGAAGTATGTCTGGAATAAGAGA
GGAAGCACTGAGAAAGGCAGTCCTCTGGGAGAAGTGGTTGAACAGGGCATAACACAGGTGAGGAACGCCTCAGATGCATT
GGAATTGTGCTGAAAGAGCTAAAGAGGCAAAGTTCTTTGGGTATTTTTCACCTCCTGGTGGCCGTGGATAGAATAAAAGG
CACTTGG
ORF - retro_cjac_3159 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.24 % |
| Parental protein coverage: | 67.59 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TMLKGITRLISKIRKLDPGRSLHVGTQAHQSIAAHLDNQVPVGSPRAISRTNENDPAKHGDQHEGQHYNI |
| T.LKGI.RLIS.I.KLDPG..LH.GTQAHQSIAAHLDNQVPV.SPRAIS.TNENDPAKHGDQHEGQHYNI | |
| Retrocopy | TLLKGIIRLISRIHKLDPGLLLHMGTQAHQSIAAHLDNQVPVESPRAISHTNENDPAKHGDQHEGQHYNI |
| Parental | SPQDLKTVFPHGLPPRFVMQVKTFSEAYLMVRKPALELLHYLK-NTNFSYPAVRYLLYGEKGTGKTLSLC |
| .PQD.KTV.P.GLPPRFVMQVKTFSEAYLM.RKPALELLHYLK.NTN..YP.V.YLLYGEKGTGKTLSLC | |
| Retrocopy | FPQDMKTVVPQGLPPRFVMQVKTFSEAYLMERKPALELLHYLK>NTNVAYPTV*YLLYGEKGTGKTLSLC |
| Parental | HVIHFCAKQDWLILHIPDAHLWVKNCRELLQSNYNKQRFDQPLEASSWLKNFKTTNERFLNQIKVQEKYV |
| H.I.FCAKQDW.ILHIPDAH..VKN.RELLQSNYNKQ.FDQPLEAS.WLKNFKTT...FLNQIK.QEKYV | |
| Retrocopy | HIINFCAKQDWMILHIPDAHNGVKNFRELLQSNYNKQLFDQPLEASTWLKNFKTTSDCFLNQIKIQEKYV |
| Parental | WNKRESTEKGSPLGEVVEQGITRVRNATDA-VGIVLKELKRQSSLGIFHLLVAVDGINAVW |
| WNKR.STEKGSPLGEVVEQGIT.VRNA.DA..GIVLKELKRQSSLGIFHLLVAVD.I...W | |
| Retrocopy | WNKRGSTEKGSPLGEVVEQGITQVRNASDA<IGIVLKELKRQSSLGIFHLLVAVDRIKGTW |
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 .04 RPM | 13 .09 RPM |
| SRP051959_heart | 0 .12 RPM | 15 .65 RPM |
| SRP051959_kidney | 0 .04 RPM | 17 .62 RPM |
| SRP051959_liver | 0 .00 RPM | 17 .57 RPM |
| SRP051959_lung | 0 .03 RPM | 18 .27 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 22 .81 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 18 .13 RPM |
| SRP051959_spleen | 0 .00 RPM | 22 .96 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3159 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3159 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3159 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 | ENSCJAG00000008125 | 1 retrocopy |
retro_cjac_3159 ,
|
| Macropus eugenii | ENSMEUG00000015501 | 1 retrocopy |