RetrogeneDB ID: | retro_cjac_228 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 17:19385090..19386539(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022309 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000021200 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_228
GCGGTTCTGCTACCCGGGGTGCGGCGGCGGTTGTGGGGTTTCAGCGAGAGGCTGCTGATCCGAGGTGCTGCAGGACGGTC
ATCATATTTTGGAGAGAATAGATTGAGGAGTACACAGGCTGCTACACAAGTTGTTCTGAATGTTCCTGAAACAAGAGTAA
CATGTTTAGAAAGTGGACTTAGAGTGGCCTCTGAAGACTCTGGGCTCTCAACATGCACAGTTGGACTCTGGATTGATGCT
GGAAGTAGATATGAAAATGAGAAGAATAATGGAACAGCTCACTTTCTGGAGCATATGGCTTTCAAGGGCACCAAAAAGAG
ATCCCAGTTAGATTTGGAACTTGAGATTGAAAACATGGGTGCTCATCTCAATGCCTATACCTCCAGAGAGCAGACCGTAT
ACTATGCCAAAGCATTCTCTAAAGACTTGCCAAGAGCTGTAGAAATTCTTGCTGATATCATACAAAACAGCACACTGGGA
GAAGCAGAGATTGAACGTGAGCGTGGAGTAATCCTTAGAGAGATGCAAGAAGTTGAAACCAATTTACAAGAAGTTGTTTT
TGATTATCTTCATGCCACAGCTTATCAAAATACTGCACTTGGACGGACAATTTTGGGACCAACTGAAAATATCAAATCTA
TAAGTCGTAAGGACTTAGTGGATTATATAACCACACATTACAAGGGGCCAAGAATAGTTCTTGCTGCTGCTGGAGGTGTT
TCCCATGATGAATTGCTTGACTTAGCAAAGTTGCATTTTGGTGACTCTTTATGCACACACAAAGGAGAAATACCAGCTCT
GCCTCCCTGCAAATTCACAGGAAGTGAGATTCGTATGAGGGATGACAAGATGCCTTTGGCACACCTTGCAATAGCTGTTG
AAGCTGTTGGTTGGGCACATCCAGATACAATATGTCTTATGGTTGCAAACACGCTGATTGGCAACTGGGATCGCTCTTTT
GGAGGAGGAATGAATTTATCTAGCAAGCTGGCCCAGCTCACTTGTCAGGGCAACCTTTGCCATAGCTTTCAGTCTTTCAA
CACTTCCTACACAGATACAGGATTATGGGGACTGTATATGGTTTGTGAACCAGCCACCGTTGGAGACATGCTACATGTTG
TTCAGAAAGAATGGATGCGACTCTGTACAAGTGTCACTGAAAGTGAGGTTGCACGAGCCAGAAATCTTCTGAAAACAAAC
ATGTTGTTGCAGCTTGATGGTTCAACTCCAATTTGTGAAGATATTGGTAGGCAGATGTTATGCTATAATAGAAGGATTCC
CATCCCTGAGCTTGAAGTAAGAATTGATGCTGTGAATGCTGAGACAATTCGAGAAGTATGTACCAAATATATTTATAATA
AGAGTCCAGCTATTGCTGCTGTTGGTCCCATTGAGCAACTACCAGATTTTAATCAGATTTGCAGTAACATGTGTTGGCTT
CGTGATTAA
ORF - retro_cjac_228 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 98.57 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AVLLPGVRRRLWGFSERLLIRGAAGRSSYFGENRLRSTQAATQVVLNVPETRVTCLESGLRVASEDSGLS |
| AVLLPGVRRRLWGFSERLLIRGAAGRSSYFGENRLRSTQAATQVVLNVPETRVTCLESGLRVASEDSGLS | |
| Retrocopy | AVLLPGVRRRLWGFSERLLIRGAAGRSSYFGENRLRSTQAATQVVLNVPETRVTCLESGLRVASEDSGLS |
| Parental | TCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFS |
| TCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFS | |
| Retrocopy | TCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFS |
| Parental | KDLPRAVEILADIIQNSTLGEAEIERERGVILREMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTEN |
| KDLPRAVEILADIIQNSTLGEAEIERERGVILREMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTEN | |
| Retrocopy | KDLPRAVEILADIIQNSTLGEAEIERERGVILREMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTEN |
| Parental | IKSISRKDLVDYITTHYKGPRIVLAAAGGVSHDELLDLAKLHFGDSLCTHKGEIPALPPCKFTGSEIRMR |
| IKSISRKDLVDYITTHYKGPRIVLAAAGGVSHDELLDLAKLHFGDSLCTHKGEIPALPPCKFTGSEIRMR | |
| Retrocopy | IKSISRKDLVDYITTHYKGPRIVLAAAGGVSHDELLDLAKLHFGDSLCTHKGEIPALPPCKFTGSEIRMR |
| Parental | DDKMPLAHLAIAVEAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCQGNLCHSFQSFNTSY |
| DDKMPLAHLAIAVEAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCQGNLCHSFQSFNTSY | |
| Retrocopy | DDKMPLAHLAIAVEAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCQGNLCHSFQSFNTSY |
| Parental | TDTGLWGLYMVCEPATVGDMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICEDIGRQML |
| TDTGLWGLYMVCEPATVGDMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICEDIGRQML | |
| Retrocopy | TDTGLWGLYMVCEPATVGDMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICEDIGRQML |
| Parental | CYNRRIPIPELEVRIDAVNAETIREVCTKYIYNKSPAIAAVGPIEQLPDFNQICSNMCWLRD |
| CYNRRIPIPELEVRIDAVNAETIREVCTKYIYNKSPAIAAVGPIEQLPDFNQICSNMCWLRD | |
| Retrocopy | CYNRRIPIPELEVRIDAVNAETIREVCTKYIYNKSPAIAAVGPIEQLPDFNQICSNMCWLRD |
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 .02 RPM | 12 .34 RPM |
| SRP051959_heart | 0 .05 RPM | 19 .29 RPM |
| SRP051959_kidney | 0 .09 RPM | 25 .14 RPM |
| SRP051959_liver | 0 .09 RPM | 19 .95 RPM |
| SRP051959_lung | 0 .05 RPM | 14 .53 RPM |
| SRP051959_lymph_node | 0 .09 RPM | 16 .37 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 24 .63 RPM |
| SRP051959_spleen | 0 .06 RPM | 14 .73 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_228 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_228 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_228 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003132 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000021200 | 1 retrocopy |
retro_cjac_228 ,
|
| Myotis lucifugus | ENSMLUG00000008798 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000012693 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000010699 | 1 retrocopy |