RetrogeneDB ID: | retro_cjac_2362 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:105920760..105921984(+) | ||
| Located in intron of: | ENSCJAG00000006246 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000006301 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MKRN2 | ||
| Ensembl ID: | ENSCJAG00000016733 | ||
| Aliases: | None | ||
| Description: | makorin ring finger protein 2 [Source:HGNC Symbol;Acc:7113] |
Retrocopy-Parental alignment summary:
>retro_cjac_2362
AGGTACTTTATGCATGGTGTGTGTCGGGAAGGAAGCCAGTGCTTATTCTCACATGACTTGGCAAGCAGCAAGCCGTCCAC
CATCTGCAAGTACTACCAGAAAGGCTACTGTGCCTATGGAACTCGGTGCAGATATGACCACACAAGGCCCTCTGCTGCAG
CTGGAGGTGCTGTGGGCACCATGGCCCACAATGTACCCTCTCCGACTTTTCACAGTCCTCACCCTCCTTCTGAGGTCACT
GCATCCATTGTGAAAACTAACTCACATGAACCTGGGAATCGTGAAAAGAGAACATTGGTTCTCAGAGACCGAAATCTCTC
TGGCATGGCTGAAGGAAAGACTAACCCGAGCATGGTGAGTAATCTAGGCAGCTGCAGTGACTCCCAGCCCAGCCCCGAGA
TGAAGCCGACTTCCTACCTAGATGCCATTAGGAGTGGCCTTGATGACCTGGAGGCCAGCAGCTCCTACAACAATAAGCAG
CAGCTGTGCCCCTATGCAGCTGCTGGGGAGTGCCGATTTGGGGATGCCTGTGTCTACCTGCACAGGGAGGTCTGTGAAAT
CTGTAGGCTGCGAGTCTTGCACCCCTTCGACCCAGAGCAGAGGAAGGCTCACGAAAAGATCTGCATGTTGACATTCGAAC
ATGAGATGGAGAAGGCCTTTGCCTTCCAAGCAAGCCAGGACAAAGTGTGCAGTATCTGCATGGAAGTGATCCTGGAGAAG
GCCTCTGCTTCTGAGAGGAGATTTGGGATTCTCTCCAATTGCAATCACACGTACTGCTTGTCCTGCATCCGACAGTGGCG
GTGTGCCAAACAATTTGAAAACCAAATCATTAAGTCTTGTCCAGAATGCTGTGTGATATCAGAGTTTGTAATTCCAAGTG
TGTATTGGGTGGAAGATCAGAATAAAAAGAACGAGTTGATTGAAGCTTTCAAACAGGGGATGGGGAAAAAAGCCTGTAAA
TACTTTGAGCAAGGCAAGGGGACCTGCCCATTTGGAAGCAAATGCCTTTATCGACATGCTTACCCTGATGGGCAGCTAGC
AGAGCCTGAGAAACCTCAGAAACAGCTCAGTTCTCAAGGCACTGTGAGGTTCTTTAATTCAGTGCGGCTCTGGGATTTCA
TTGAGAACCGAGAAAGCCAGCATGTCCCCAACAATGAAGATGTCGACATGACAGAGCTTGGGGACCTCTTCATGCACCTT
TCTGGAGTGGAGTCATCAGAACCC
ORF - retro_cjac_2362 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.28 % |
| Parental protein coverage: | 98.07 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RYFMHGVCREGSQCLFSHDLANSKPSTICKYYQKGYCAYGTRCRYDHTRPSAAAGGAVGTMAHNVPSPTF |
| RYFMHGVCREGSQCLFSHDLA.SKPSTICKYYQKGYCAYGTRCRYDHTRPSAAAGGAVGTMAHNVPSPTF | |
| Retrocopy | RYFMHGVCREGSQCLFSHDLASSKPSTICKYYQKGYCAYGTRCRYDHTRPSAAAGGAVGTMAHNVPSPTF |
| Parental | HSPHPPSEVTASIVKTNSHEPGKREKRTLVLRDRNLSGMAEGKTNPSMVSNLGSCSDSQPSPEMKPTSYL |
| HSPHPPSEVTASIVKTNSHEPG.REKRTLVLRDRNLSGMAEGKTNPSMVSNLGSCSDSQPSPEMKPTSYL | |
| Retrocopy | HSPHPPSEVTASIVKTNSHEPGNREKRTLVLRDRNLSGMAEGKTNPSMVSNLGSCSDSQPSPEMKPTSYL |
| Parental | DAIRSGLDDLEASSSYNNKQQLCPYAAAGECRFGDACVYLHGEVCEICRLRVLHPFDPEQRKAHEKICML |
| DAIRSGLDDLEASSSYNNKQQLCPYAAAGECRFGDACVYLH.EVCEICRLRVLHPFDPEQRKAHEKICML | |
| Retrocopy | DAIRSGLDDLEASSSYNNKQQLCPYAAAGECRFGDACVYLHREVCEICRLRVLHPFDPEQRKAHEKICML |
| Parental | TFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCNHTYCLSCIRQWRCAKQFENQIIKSC |
| TFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCNHTYCLSCIRQWRCAKQFENQIIKSC | |
| Retrocopy | TFEHEMEKAFAFQASQDKVCSICMEVILEKASASERRFGILSNCNHTYCLSCIRQWRCAKQFENQIIKSC |
| Parental | PECRVISEFVIPSVYW-EDQNKKNELIEAFKQGMGKKACKYFEQGKGTCPFGSKCLYRHAYPDGRLAEPE |
| PEC.VISEFVIPSVYW.EDQNKKNELIEAFKQGMGKKACKYFEQGKGTCPFGSKCLYRHAYPDG.LAEPE | |
| Retrocopy | PECCVISEFVIPSVYWVEDQNKKNELIEAFKQGMGKKACKYFEQGKGTCPFGSKCLYRHAYPDGQLAEPE |
| Parental | KPRKQLSSQGTVRFFNSVRLWDFIENRESQHVPNNEDVDMTELGDLFMHLSGVESSEP |
| KP.KQLSSQGTVRFFNSVRLWDFIENRESQHVPNNEDVDMTELGDLFMHLSGVESSEP | |
| Retrocopy | KPQKQLSSQGTVRFFNSVRLWDFIENRESQHVPNNEDVDMTELGDLFMHLSGVESSEP |
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 .73 RPM | 6 .94 RPM |
| SRP051959_heart | 2 .07 RPM | 17 .17 RPM |
| SRP051959_kidney | 1 .29 RPM | 8 .52 RPM |
| SRP051959_liver | 0 .58 RPM | 6 .82 RPM |
| SRP051959_lung | 1 .20 RPM | 9 .65 RPM |
| SRP051959_lymph_node | 0 .91 RPM | 10 .02 RPM |
| SRP051959_skeletal_muscle | 2 .42 RPM | 23 .63 RPM |
| SRP051959_spleen | 1 .28 RPM | 10 .44 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2362 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2362 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2362 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013474 | 2 retrocopies | |
| Callithrix jacchus | ENSCJAG00000016733 | 1 retrocopy |
retro_cjac_2362 ,
|
| Mus musculus | ENSMUSG00000000439 | 2 retrocopies | |
| Otolemur garnettii | ENSOGAG00000003255 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000005822 | 1 retrocopy |