RetrogeneDB ID: | retro_cjac_558 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:81166889..81168215(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022053 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZNF277 | ||
| Ensembl ID: | ENSCJAG00000016891 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_558
GTCGCCCGACTGGAGGAAGACCGTGATGGAAGCTGCAGCACAGTCGGGGGTGTAGGTTATGGGGACAGTAAGGATTGTAT
CCTGGAGCCACTTTCCCTGCCAGAAAGTCCAGGTGGCACCACCACTTTAGAAGGTTCTCCATCTGTGCCTTTTATTTTCT
GTGAAGAACATTTTCATGTGGCTGAGCAAGACAAACTTCTGAAGCACATGATTATTGAGCATAAGATTGTCATAGCTGAT
GTCAAATTGGTCGCTGATTTCCAAAGGTACATTTTGTATTGGAGGAAAAGGTTCACTGAACAGCCCATCACAGATTTTTG
TAGTGTGATAAGAATTAATTCCACTGCTCCATTTGAAGAACAAGAGAATTATTTTTTGTTATGTGACGTTTTACCAGAAG
ATAGAATTCTTCGAGAAGAGCTTCAGAAACAGAAACTGAAAGAAATTCTGGAACAACAGCAGCAAGAACGAAATGATAAC
AATTTTCATGGCATTTGTATGTTTTGCAATGAAGAATTCCTTGGAAACAGATCTGTTCTTTTGAACCACATGGCCAGAGA
ACATGCTTTCAACATTGGATTGCCAGACAACATTGTAAACTGCAATGAATTTTTGTGTACATTACAGAAAAAGCTTGACA
ATTTGCAGTGCTTGTACTGTGAGAAGACCTTCAGGGACAAAAATACACTTAAAGATCACATGAGGAAAAAACAGCAACGT
AAGATTAATCCTAAGAACAGAGAATATGATCGATTTTATGTCATCAATTATTTGGAACTTGGAAAATCATGGGAAGAAGT
TCAGTTGGAAGATGATCGGGAGTTGCTGGACAATCAGGAAGATGACTGGTCTGACTGGGAAGAACACCCTGCCTCTGCCG
TCTGCTTATTTTGTGAAAAGCAAGCAGAAACAATTGAGAAATTGTATGTCCACATGGAGGATGCAAACGAATTTAATCTT
CTCAAAATAAAGTCAGAACTTGGATTAAATTTCTATCAGCAAGTGAAACTGGTCAATTTTATTCGGAGGCAAGTTCACCA
GTGCAGATGTTATGGCTGCCATGTGAAGTTCAAATCCAAAGCAGACTTAAGAACTCACATGGAAGAAACTAAACACACTT
CACTTCTCCCTGATAGAAAGACGTGGGATCAACTGGAGTATTATTTTCCAACCTATGAAAACGACACTCTCCTGTGTACA
CTGTCTGACAGTGAAAGTGACCTGACAGCTCAAGAACAAAATGAGGATGTTCCCATCATCAGTGAAGATACATCTAAACT
GTATGCTTTGAAACAAAGCAGTATTTTGAACCAGTTGCTACTACAA
ORF - retro_cjac_558 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.32 % |
| Parental protein coverage: | 98.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVPCIFCEEHFHVAEQDKLLKHM |
| VARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVP.IFCEEHFHVAEQDKLLKHM | |
| Retrocopy | VARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVPFIFCEEHFHVAEQDKLLKHM |
| Parental | IIEHKIVIADVKLVADFQRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDVLPEDRILREE |
| IIEHKIVIADVKLVADFQRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDVLPEDRILREE | |
| Retrocopy | IIEHKIVIADVKLVADFQRYILYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDVLPEDRILREE |
| Parental | LQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHAFNIGLPDNIVNCNEFLCTLQK |
| LQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHAFNIGLPDNIVNCNEFLCTLQK | |
| Retrocopy | LQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHAFNIGLPDNIVNCNEFLCTLQK |
| Parental | KLDNLQCLYCEKTFRDKNTLKDHMRKKQHRKINPKNREYDRFYVINYLELGKSWEEVQLEDDRELLDNQE |
| KLDNLQCLYCEKTFRDKNTLKDHMRKKQ.RKINPKNREYDRFYVINYLELGKSWEEVQLEDDRELLDNQE | |
| Retrocopy | KLDNLQCLYCEKTFRDKNTLKDHMRKKQQRKINPKNREYDRFYVINYLELGKSWEEVQLEDDRELLDNQE |
| Parental | DDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDAHEFNLLKIKSELGLNFYQQVKLVNFIRRQVHQCRC |
| DDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDA.EFNLLKIKSELGLNFYQQVKLVNFIRRQVHQCRC | |
| Retrocopy | DDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDANEFNLLKIKSELGLNFYQQVKLVNFIRRQVHQCRC |
| Parental | YGCHVKFKSKADLRTHMEETKHTSLLPDRKTWDQLEYYFPTYENDTLLCTLSDSESDLTAQEQNEDVPII |
| YGCHVKFKSKADLRTHMEETKHTSLLPDRKTWDQLEYYFPTYENDTLLCTLSDSESDLTAQEQNEDVPII | |
| Retrocopy | YGCHVKFKSKADLRTHMEETKHTSLLPDRKTWDQLEYYFPTYENDTLLCTLSDSESDLTAQEQNEDVPII |
| Parental | SEDTSKLYALKQSSILNQLLLQ |
| SEDTSKLYALKQSSILNQLLLQ | |
| Retrocopy | SEDTSKLYALKQSSILNQLLLQ |
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 .60 RPM | 6 .79 RPM |
| SRP051959_heart | 1 .09 RPM | 9 .79 RPM |
| SRP051959_kidney | 1 .02 RPM | 15 .18 RPM |
| SRP051959_liver | 1 .49 RPM | 15 .05 RPM |
| SRP051959_lung | 0 .76 RPM | 13 .83 RPM |
| SRP051959_lymph_node | 0 .75 RPM | 7 .49 RPM |
| SRP051959_skeletal_muscle | 0 .59 RPM | 9 .06 RPM |
| SRP051959_spleen | 1 .01 RPM | 12 .54 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_558 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_558 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_558 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016891 | 2 retrocopies |
retro_cjac_558 , retro_cjac_698,
|
| Mus musculus | ENSMUSG00000055917 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000005326 | 1 retrocopy |