RetrogeneDB ID: | retro_cjac_2174 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:114462317..114463716(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000015062 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000001720 | ||
| Aliases: | None | ||
| Description: | Annexin [Source:UniProtKB/TrEMBL;Acc:F6XT66] |
Retrocopy-Parental alignment summary:
>retro_cjac_2174
ATGTCATACCCAGGCTATCCCCCAACAGGCTACCCACCTTTCCCTGGATATCCTCCTGCAGGTCAGGAGTCATCTTTTCC
CCGTTCTGGTCAGTATCCTTATCCTAGTGGCTTTCCTCCAATGGGGGGGAGGTGCCTACCCACAAGGGCCAAGTGGTGGC
TATCCAGGAGCTGGAGGCTACCCTGCGCTTGGAGGTTATCCAGGCCCTGGAGGCTATCCTGGTGCCCCACAGCCAGGGGG
AGCTCCATCCTATCCCGGAGTTCCTCCAGGCTATGGATTTGGAGTCCCACCAGGTGGAGCAGGCTTTTCTGGCTATCCAC
AGCCACCCTCACAATCTTATGGAGGCGGTCCGGCACAGGTCCCACTACCTGGTGGCTTTCCTGAAGGACAGATGCCTTCC
CAGTATCCTGGAGGACAGCCTACTTACCCTAGTCAGCCTGCCGCAGTGACACAGGGCGCTCAAGGAACTATCCGACCAGT
TGCCAACTTCGATGCTATGAGAGATGCAGAAATTCTCCGTAAGGCAATGAAGGGTTTTGGGACAGACGAACAGGCGATTG
TGGATGTGGTGGCCAACCGTTCAAATGATCAGAGGCAAAAAATTAAAGCAGCATTTAAGACCTCGTATGGCAAGGATTTA
ATCAAAGATCTCAAATCAGAGTTAAGTGGAAATATGGAAGAACTGATCCTGGCCCTATTCATGCCTCCTACGTATTACGA
TGCCTGGAGCTTACGGAAAGCAATACAGGGAGCAGGAACTCAGGAACGTGTATTGATTGAAATTTTGTGCACGAGAACAA
ATCAGGAAATCCGAGAAATTGTCAGATGTTATCAGTCAGAATTTGGACGAGACCTTGAAAAGGACATTAGGTCAGATACA
TCAGGACATTTTGAATGCTTACTTGTGTCCATGTGCCAGGGAAATCGTGATGAAGACCAGAGTGTAAACCACCAAATGGC
TCAGGAAGATGCTCAGCGTCTCTATCAAGCTGGCGAGGGGAGACTAGGGACTGATGAATCTTGCTTTAACATGATCCTTG
CCACGAGAAGCTTTCCTCAGCTAAGAGCTACCATGGAGGCTTATTCCAGGATGACTAATCGAGATTTGTTAAGCAGTGTG
AGCCGTGAGTTTTCCGGATATGTGGAAAGTGGTTTGAAGACCATCTTGCAGTGTGCCCTGAACCGCCCTGCCTTCTTTGC
TGAGAGACTCTACTATGCTATGAAAGGTGCTGGTACAGATGACTCCACCCTGGTCAGGATTGTGGTCACTCGAAGTGAGA
TTGATCTTGTACAAATAAAACAAATGTTCGCTCAGATGTATCAGAAGACCCTGGGCACAATGATTGTAGGTGACACAAGT
GGAGATTACCGAAGACTTCTTCTGGCTATTGTGGGCCAG
ORF - retro_cjac_2174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.58 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSYPGYPPTGYPPFPGYPPAGQESSFPPSGQYPFPSGFPPMGG-GAYPQVPSGGYPGAGGYPAPGGYPAP |
| MSYPGYPPTGYPPFPGYPPAGQESSFP.SGQYP.PSGFPPMGG.GAYPQ.PSGGYPG............. | |
| Retrocopy | MSYPGYPPTGYPPFPGYPPAGQESSFPRSGQYPYPSGFPPMGG>GAYPQGPSGGYPGXXXXXXXXXXXXX |
| Parental | GGYPGAPQPGGAPSYPGVPPGHGFGVPPSGAGFSGYPQPPSQSYGGGPAQVPLPGGFPGGQMPSQYPGGQ |
| .....APQPGGAPSYPGVPPG.GFGVPP.GAGFSGYPQPPSQSYGGGPAQVPLPGGFP.GQMPSQYPGGQ | |
| Retrocopy | XXXXXAPQPGGAPSYPGVPPGYGFGVPPGGAGFSGYPQPPSQSYGGGPAQVPLPGGFPEGQMPSQYPGGQ |
| Parental | PTYPSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQKIKAAFKTSY |
| PTYPSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQKIKAAFKTSY | |
| Retrocopy | PTYPSQPAAVTQGAQGTIRPVANFDAMRDAEILRKAMKGFGTDEQAIVDVVANRSNDQRQKIKAAFKTSY |
| Parental | GKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAMQGAGTQERVLIEILCTRTNQEIREIVRCYQS |
| GKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKA.QGAGTQERVLIEILCTRTNQEIREIVRCYQS | |
| Retrocopy | GKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAIQGAGTQERVLIEILCTRTNQEIREIVRCYQS |
| Parental | EFGRDLEKDIRSDTSGHFERLLVSMCQGNRDENQSVNHQMAQEDAQRLYQAGEGRLGTDESCFNMILATR |
| EFGRDLEKDIRSDTSGHFE.LLVSMCQGNRDE.QSVNHQMAQEDAQRLYQAGEGRLGTDESCFNMILATR | |
| Retrocopy | EFGRDLEKDIRSDTSGHFECLLVSMCQGNRDEDQSVNHQMAQEDAQRLYQAGEGRLGTDESCFNMILATR |
| Parental | SFPQLRATMEAYSRMANRDLLSSVSREFSGYVESGLKTILQCALNRPAFFAERLYYAMKGAGTDDSTLVR |
| SFPQLRATMEAYSRM.NRDLLSSVSREFSGYVESGLKTILQCALNRPAFFAERLYYAMKGAGTDDSTLVR | |
| Retrocopy | SFPQLRATMEAYSRMTNRDLLSSVSREFSGYVESGLKTILQCALNRPAFFAERLYYAMKGAGTDDSTLVR |
| Parental | IVVTRSEIDLVQIKQMFAQMYQKTLGTMIAGDTSGDYRRLLLAIVGQ |
| IVVTRSEIDLVQIKQMFAQMYQKTLGTMI.GDTSGDYRRLLLAIVGQ | |
| Retrocopy | IVVTRSEIDLVQIKQMFAQMYQKTLGTMIVGDTSGDYRRLLLAIVGQ |
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 | 71 .73 RPM |
| SRP051959_heart | 0 .14 RPM | 50 .15 RPM |
| SRP051959_kidney | 0 .24 RPM | 58 .28 RPM |
| SRP051959_liver | 0 .15 RPM | 49 .82 RPM |
| SRP051959_lung | 0 .16 RPM | 48 .48 RPM |
| SRP051959_lymph_node | 0 .14 RPM | 49 .45 RPM |
| SRP051959_skeletal_muscle | 0 .11 RPM | 41 .71 RPM |
| SRP051959_spleen | 0 .13 RPM | 66 .53 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2174 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2174 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2174 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000014749 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000001720 | 3 retrocopies |
retro_cjac_1288, retro_cjac_2174 , retro_cjac_860,
|
| Microcebus murinus | ENSMICG00000013143 | 2 retrocopies | |
| Pteropus vampyrus | ENSPVAG00000013001 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000007136 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000012433 | 1 retrocopy |