RetrogeneDB ID: | retro_cjac_2472 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:122862202..122863319(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RABEPK | ||
| Ensembl ID: | ENSCJAG00000006849 | ||
| Aliases: | None | ||
| Description: | Rab9 effector protein with kelch motifs [Source:HGNC Symbol;Acc:16896] |
Retrocopy-Parental alignment summary:
>retro_cjac_2472
GTGAAGCAGCTGCCAGTCTTGGAACCTGGACACAAGCCCAGGAAAGCAGTGTCGTACACCTTGACTCTCCCTGGAGACAG
CTCCTGTGCTTGAGCTGGCCACAGCTGTTCATAGTTACCCCCAGTTGGTAATGCCAAGAGAGGGAAGGTCTTCATTGTTG
GGGGAGCAAATCCAAACAGAAGCTTCTCAGATGTGCACACCATGAATCTCGGAAAACACCAGTGGGACTTAGTTACCTGC
AGGGACCTCTTGCCCCGGTATAAACATGCTAGCTTCATTCCCTCCTGCACACCTGACAGTATTTGGGTATTTGGAGGTGC
CAGCCAATCAGGAAATCTAAATTGTCTACAAGTCCTGAATCCTGAAACCAGGACATGGACCACGTCAGAAGTGACCAGCC
CCCTACCATCCCCAAGAACATTCTACACGTCATCGGCAGCCATTGGAAACCAGCTGTATGCCTTTGGGGTTGGAGAGAGA
GGTGTCTAGCCTGGTGCAGGACATGAAGCTGCATGTGTCTGATGCAAACACTCTGACCTGGTCACAGCCAGAGACACTTG
GAAATCCTCCATACCCCAGGCATGGTCATGTGATAGTGGCAGCAGGGACAAAGCTCTTCATCCATGGAGCCTTGGCGATA
GACAAATTCTATGTTAATCTCCATTACATTGATATAAGTGACATGAAACGGCAGAAACTAAGTCCCACGGAGGCTGCTCT
AGCAGGCTGTGCTGCCCACTCAGCTGTGGCCTTGGGAAAACACTTGTACATCTTTGGTGGAATGACTCCTGCAGGAGCGC
TGGACACAACGTACTAGTATCACACAGAAAAGCAGCATTGGACCTTGCTTAAGTTTGATACTTTTCCACGCCCTGGACGA
TTGGGCCACTCCTTGGGTATCATTCCGTGGCCAGTGACATGTGCTTCTGAGAAGGAAGATTCCAATTCTCTCACTCTGAA
TCATGAAGCTGAGGAAGGAGATTCAGCTGACACAGTAATGACCCACAGTAGTGACTCACACAAGGAAAGCCAGGCTGATA
CACTGCTCTGTTTTGTGTTTGGTGGGATGAGTACAGAAGGGGAAATCTATGATGATTGTGTTGTGACTGTAGTTGAC
ORF - retro_cjac_2472 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.45 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MKQLPILEPGDKPRKASWYTLTLQGDSPCARVGHSCSYLPPVGNAKRGKVFIVGGANPNRSFSDVHAMDL |
| .KQLP.LEPG.KPRKA..YTLTL.GDS.CA..GHSCS.LPPVGNAKRGKVFIVGGANPNRSFSDVH.M.L | |
| Retrocopy | VKQLPVLEPGHKPRKAVSYTLTLPGDSSCA*AGHSCS*LPPVGNAKRGKVFIVGGANPNRSFSDVHTMNL |
| Parental | GKHQWDLVTCKGLLPRYEHASFIPSCTPDSIWVFGGANQSGNRNCLQVLNPETRTWTMPEVTSPPPSPRT |
| GKHQWDLVTC..LLPRY.HASFIPSCTPDSIWVFGGA.QSGN.NCLQVLNPETRTWT..EVTSP.PSPRT | |
| Retrocopy | GKHQWDLVTCRDLLPRYKHASFIPSCTPDSIWVFGGASQSGNLNCLQVLNPETRTWTTSEVTSPLPSPRT |
| Parental | FHTSSAAIGNQLYVFGGGERGAQP-VQDVKLHVFDASTLTWSQPETLGNPPSPRHGHVMVAAGTKLFIHG |
| F.TSSAAIGNQLY.FG.GERG..P.VQD.KLHV.DA.TLTWSQPETLGNPP.PRHGHV.VAAGTKLFIHG | |
| Retrocopy | FYTSSAAIGNQLYAFGVGERGV*P>VQDMKLHVSDANTLTWSQPETLGNPPYPRHGHVIVAAGTKLFIHG |
| Parental | GLAGDKFYDDFHCIDISDMKWQKLSPTGATPAGCAAHSAVAVGKHLYIFGGMTPAGALDTMYQYHTEKQH |
| .LA.DKFY...H.IDISDMK.QKLSPT.A..AGCAAHSAVA.GKHLYIFGGMTPAGALDT.Y.YHTEKQH | |
| Retrocopy | ALAIDKFYVNLHYIDISDMKRQKLSPTEAALAGCAAHSAVALGKHLYIFGGMTPAGALDTTY*YHTEKQH |
| Parental | WTLLKFDTFLPPGRLDHSMCIIPWPVTCASEKEDSNSLSLNHEAEKVDSADTVMTHSGDSHEESRADTLL |
| WTLLKFDTF..PGRL.HS..IIPWPVTCASEKEDSNSL.LNHEAE..DSADTVMTHS.DSH.ES.ADTLL | |
| Retrocopy | WTLLKFDTFPRPGRLGHSLGIIPWPVTCASEKEDSNSLTLNHEAEEGDSADTVMTHSSDSHKESQADTLL |
| Parental | CFVFGGMNTEGEIYDDCIVTAVD |
| CFVFGGM.TEGEIYDDC.VT.VD | |
| Retrocopy | CFVFGGMSTEGEIYDDCVVTVVD |
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 | 3 .95 RPM |
| SRP051959_heart | 0 .05 RPM | 3 .32 RPM |
| SRP051959_kidney | 0 .00 RPM | 5 .06 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .03 RPM |
| SRP051959_lung | 0 .03 RPM | 3 .58 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 3 .49 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .29 RPM |
| SRP051959_spleen | 0 .02 RPM | 3 .51 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2472 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2472 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2472 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000020201 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000006849 | 1 retrocopy |
retro_cjac_2472 ,
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