RetrogeneDB ID: | retro_cjac_1697 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 19:12183414..12184740(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000015738 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CRBN | ||
| Ensembl ID: | ENSCJAG00000015479 | ||
| Aliases: | None | ||
| Description: | cereblon [Source:HGNC Symbol;Acc:30185] |
Retrocopy-Parental alignment summary:
>retro_cjac_1697
ATGGCCGGCGAGGGAGACCAGCAGGACGCTGCGCACAACATGGGCAAACACCTGCCGCTCCTGCCTGCAGAGAGTGAGGA
AGAAGATGAAATGGAAGTTGAAGACCAGGATAGTAAAGAAGCCAAAAAACCAAACATTGTAAATTTTGACACCAGCCTGC
CAACATCACATACATACCTAGGCGCTGATATGGAAGAATTTCATGGCAGGACTTTGCACGATGACGACAGCTGTCAGGTG
ATTCCAGTTCTGCCACAGGTGATGATGATTCTGATGCCTGGACAGACATTACCTCTTCAACTTTTTCACCCTCAAGAAGT
CAGTATGGTGCGGAATTTAATTCAGAAAGATAGAACCTTTGCTGTTCTTGCATACAGCAATATACAAGAAAGGGAAGCAC
AGTTTGGAACAACAGCAGAGATATATGCCTATCGAGAAGAACAGGATTTTGGAATTGAGATAGTGAAAGTGAAAGCAATT
GGAAGACAAAGGTTCAAAGTCCTTGAGCTAAGAACACAGTCAGATGGAATCCAGCAAGCTAAAGTGCAAATTCTTCCCGA
ATGTGTGTTGCCTTCAACCATGTCTGCAGTTCAGTTAGAATCCCTCAATAAATGCCAGATATTTCCTTCAAAACCTGTCT
CATGGGAAGACCAGTGTTCATATAAATGGTGGCAGAAATACCAGAAGAGAAAGTTTCATTGTGCAAATCTAACTTCATGG
CCTCGCTGGCTGTATTCCTTATATGATGCTGAAACCTTAATGGACAGAATCAAGAAACAGCTACGTGAATGGGATGAAAA
TCTAAAAGATGATTCTCTTCCTTCAAATCCAATAGATTTTTCTTACAGAGTAGCTGCTTGTCTTCCTATTGATGATGTAT
TGAGAATTCAGCTCCTTAAAATTGGCAGTGGTATCCAGCGACTTCGCTGTGAATTAGACATTATGAATAAATGCACCTCC
CTTTGCTGTAAACAATGTCAAGAAACAGAAATAACAACGAAAAATGAAATATTCAGTTTATCCTTATGTGGGCCGATGGC
AGCTTATGTGAATCCTCATGGATATGTGCATGAGACACTTACTGTGTATAAGGCTTGCAACTTGAATCTGATAGGCCGGC
CTTCTACGGAACACAGCTGGTTTCCTGGGTATGCCTGGACTGTTGCCCAGTGTAAGATCTGTGCAAGCCATATTGGATGG
AAGTTTACAGCCACCAAAAAAGACATGTCACCTCCAAAATTTTGGGGCTTAACGCGATCTGCTCTGTTGCCTACAATCCC
AGACACGGAAGATGAAATAAGTCCAGACAAAGTAATACTTTGCTTG
ORF - retro_cjac_1697 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.87 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGR |
| MAGEGDQQDAAHNMG.HLPLLPAESEEEDEMEVEDQDSKEAKKPNI.NFDTSLPTSHTYLGADMEEFHGR | |
| Retrocopy | MAGEGDQQDAAHNMGKHLPLLPAESEEEDEMEVEDQDSKEAKKPNIVNFDTSLPTSHTYLGADMEEFHGR |
| Parental | TLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNIQEREAQFGTTAE |
| TLHDDDSCQVIPVLPQVMMIL.PGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNIQEREAQFGTTAE | |
| Retrocopy | TLHDDDSCQVIPVLPQVMMILMPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNIQEREAQFGTTAE |
| Parental | IYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPS |
| IYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPS | |
| Retrocopy | IYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPS |
| Parental | KPVSWEDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDF |
| KPVSWEDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDF | |
| Retrocopy | KPVSWEDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDF |
| Parental | SYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYV |
| SYRVAACLPIDDVLRIQLLKIGS.IQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYV | |
| Retrocopy | SYRVAACLPIDDVLRIQLLKIGSGIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYV |
| Parental | NPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRS |
| NPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSP.KFWGLTRS | |
| Retrocopy | NPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPPKFWGLTRS |
| Parental | ALLPTIPDTEDEISPDKVILCL |
| ALLPTIPDTEDEISPDKVILCL | |
| Retrocopy | ALLPTIPDTEDEISPDKVILCL |
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 | 11 .71 RPM |
| SRP051959_heart | 0 .04 RPM | 23 .40 RPM |
| SRP051959_kidney | 0 .07 RPM | 23 .16 RPM |
| SRP051959_liver | 0 .04 RPM | 13 .65 RPM |
| SRP051959_lung | 0 .21 RPM | 20 .66 RPM |
| SRP051959_lymph_node | 0 .16 RPM | 20 .71 RPM |
| SRP051959_skeletal_muscle | 0 .13 RPM | 19 .76 RPM |
| SRP051959_spleen | 0 .15 RPM | 22 .44 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1697 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1697 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1697 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015479 | 1 retrocopy |
retro_cjac_1697 ,
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