RetrogeneDB ID: | retro_cjac_992 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:82280391..82282299(+) | ||
| Located in intron of: | ENSCJAG00000015969 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022962 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GTPBP4 | ||
| Ensembl ID: | ENSCJAG00000008494 | ||
| Aliases: | None | ||
| Description: | nucleolar GTP-binding protein 1 [Source:RefSeq peptide;Acc:NP_001240708] |
Retrocopy-Parental alignment summary:
>retro_cjac_992
ATGGCGCACTACAACTTCAAGAAAATTACGGTGGTACCGTCCGCCAAGGACTTTATTGACCTGACATTGTCGAAGACTCA
ACGAAAGACTCCAACCGTTATTCATAAACATTACCAAATTCATCACATTAGACATTTTTACATGAGAAAAGTCAAATTTA
CTCAACAGAATTACCACGATAGACTTTCACAAATTCTAACAGATTTTCCTAAGTTGGATGACATTCATCCATTCTACGCA
GACTTGATGAATATTCTGTACGACAAAGATCACTACAAGTTGGCTCTGGGGCAAATAAATATTGCCAAAAATTTAGAGGA
CAATGTTGCTAAAGATTATGTGCGGTTGATGAAGTACGGCGACTCTCTCTACCGCTGCAAGCAGTTGAAGAGTGCGCCCC
TGGGGCGGATGTGCACCGTGATCAAGAGGCAGAAGCAGAGTTTGGAGTATTTGGAGCAAGTGCGTCAGCATTTATCCCGT
TTGCCAACCATTGATCCAAATACCAGGACTCTGCTTTTGTGTGGGTACCCAAATGTAGGCAAGTCCAGCTTCATCAATAA
GGTGACAAGAGCAGATGTGGATGTCCAACCCTATGCGTTCACAACCAAGTCTCTGTTTGTTGGGCACATGGATTATAAGT
ATCTACGTTGGCAGGTTGTAGACACTCCTGGGATACTGGACCACCCTCTGGAGGATAGGAACACCATCGAGATGCAGGCC
ATCACTGCCCTGGCCCACCTCCGTGCTGCGGTCCTGTACGTGATGGATTTGTCTGAGCAGTGTGGGCACCGGCTGAGGGA
GCAGCTAGAACTCTTCCAGAACATCAGACCTCTCTTCATCAACAAGCCTCTTATAGTTGTAGCCAACAAATGTGATGTGA
AGAGAATAGCTGAACTTTCTGAAGATGATCAGAAAATATTTACAAATTTGCAGGCTGAAGGATTCCCTGTAATAGAGACC
AGCACCTTGACTGAGGAAGGTGTTATTAAAGTTAAAACAGAGGCTTGTGATAGGCTTTTGGCTCATCGAGTGGAAACCAA
AATGAAGGGAAATAAAGTGAATGAGGTGCTGAATAGACTACACCTGGCTGTCCCAACCAGGAGGGACGATAAGGAGAGGC
CGCCTTTCATCCCTGAAGGAGTGGTGGCACGCAGGAAGAGAATGGAAATGGAGGAGCCCAAGAAAAAGAGGGAACGAGAT
CTTGAGCTGGAAATGGGAGATGATTATATTTTGGATCTTCAGAAGTACTGGGATTTAATGAATTCATCTGAAAAACATGA
TAAGATACTAGAAATCTGGCAAGGCCATAATATAGCTGATTATATTGATCCAGCCATCATGAAGAAATTGGAAGAATTAG
AAAAAGAAGAAGAGCTGAGAACAGCTGCTGGAGAGTATGACAGTGACTCTGAGAGTGAAGATGAGGAGATGCTGGAGATT
CGACAGCTGGCAAAGCAGATTAGAGAGAAGAAGAAGTTGAAAATTCTGGAGTCCAAAGAAAAGAATACACAGGGACCCAG
GATGCCTCGAACTGTTAAGAAGGTTCAGAGGACAGTTTTGGAGAATGAGATGCGTAGTCTTGGTGTTGACATGGACGATA
AAGACAACGCCCACTACGCAGTCCAGGCAAGAAGATCCCGGAGTGTCACTAGGAAAAGAAAGCGGGAAGACTCTGCTCCC
CGCTCCTCTGTGGCCCGGAGTCGGAGTCGGAGTTGCTCTCGAACTCCACGTGACGTTTCTGGTCTTCGGGATGTCAAGAT
GGTGAAGAAAGCCAAGACTATGATGAAGAATGCTCAGAAGAAGATGAATCGGTTGGGGAAGAAAGGGGAGGCAGATAAAC
ATGTGTTTGATATGAAGCCCAAGCACTTACTCTCTGGAAAGAGGAAAGCTGGCAAAAAGGACAGGAGA
ORF - retro_cjac_992 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.71 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHRIRHFYMRKVKFTQQNYHDRLSQILTDFP |
| MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIH.IRHFYMRKVKFTQQNYHDRLSQILTDFP | |
| Retrocopy | MAHYNFKKITVVPSAKDFIDLTLSKTQRKTPTVIHKHYQIHHIRHFYMRKVKFTQQNYHDRLSQILTDFP |
| Parental | KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLVDNVAKDYVRLMKYGDSLYRCKQLKRAALGRMCTV |
| KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNL.DNVAKDYVRLMKYGDSLYRCKQLK.A.LGRMCTV | |
| Retrocopy | KLDDIHPFYADLMNILYDKDHYKLALGQINIAKNLEDNVAKDYVRLMKYGDSLYRCKQLKSAPLGRMCTV |
| Parental | IKRQKQSLEYLEQVRQHLS-VATLIP-ITGLC-FVWVPKCR-KSS-INKVTRADVDVQPYAFTTKSLFVG |
| IKRQKQSLEYLEQVRQHLS...T..P.I.GLC.FVWVPKCR.KSS.INKVTRADVDVQPYAFTTKSLFVG | |
| Retrocopy | IKRQKQSLEYLEQVRQHLSRLPTIDP>IPGLC>FVWVPKCR>KSSFINKVTRADVDVQPYAFTTKSLFVG |
| Parental | HMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGHGLREQLELFQNIRPL |
| HMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGH.LREQLELFQNIRPL | |
| Retrocopy | HMDYKYLRWQVVDTPGILDHPLEDRNTIEMQAITALAHLRAAVLYVMDLSEQCGHRLREQLELFQNIRPL |
| Parental | FINKPLIVVANKCDVKRIAELSEDDQKIFTNLQAEGFPVIETSTLTEEGVIKVKTEACNRLLAHRVETKM |
| FINKPLIVVANKCDVKRIAELSEDDQKIFTNLQAEGFPVIETSTLTEEGVIKVKTEAC.RLLAHRVETKM | |
| Retrocopy | FINKPLIVVANKCDVKRIAELSEDDQKIFTNLQAEGFPVIETSTLTEEGVIKVKTEACDRLLAHRVETKM |
| Parental | KGNKVNEVLNRLHLAVPTRRDDKERPPFIPEGVVARRKRMEMEEPKKKRERDLELEMGDDYILDLQKYWD |
| KGNKVNEVLNRLHLAVPTRRDDKERPPFIPEGVVARRKRMEMEEPKKKRERDLELEMGDDYILDLQKYWD | |
| Retrocopy | KGNKVNEVLNRLHLAVPTRRDDKERPPFIPEGVVARRKRMEMEEPKKKRERDLELEMGDDYILDLQKYWD |
| Parental | LMNSSEKHDKIPEIWEGHNIADYIDPAIMKKLEELEKEEELRTAAGEYDSDSESEDEEMLEIRQLAKQIR |
| LMNSSEKHDKI.EIW.GHNIADYIDPAIMKKLEELEKEEELRTAAGEYDSDSESEDEEMLEIRQLAKQIR | |
| Retrocopy | LMNSSEKHDKILEIWQGHNIADYIDPAIMKKLEELEKEEELRTAAGEYDSDSESEDEEMLEIRQLAKQIR |
| Parental | EKKKLKILESKEKNTQGPRMPRTAKKVQRTVLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREDS |
| EKKKLKILESKEKNTQGPRMPRT.KKVQRTVLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREDS | |
| Retrocopy | EKKKLKILESKEKNTQGPRMPRTVKKVQRTVLENEMRSLGVDMDDKDNAHYAVQARRSRSVTRKRKREDS |
| Parental | APPSSVARSRSRSCSRTPRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEADRHVFDMKPKHLLSGKR |
| AP.SSVARSRSRSCSRTPRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEAD.HVFDMKPKHLLSGKR | |
| Retrocopy | APRSSVARSRSRSCSRTPRDVSGLRDVKMVKKAKTMMKNAQKKMNRLGKKGEADKHVFDMKPKHLLSGKR |
| Parental | KAGKKDRR |
| KAGKKDRR | |
| Retrocopy | KAGKKDRR |
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 | 3 .17 RPM | 14 .29 RPM |
| SRP051959_heart | 2 .35 RPM | 17 .47 RPM |
| SRP051959_kidney | 2 .33 RPM | 21 .08 RPM |
| SRP051959_liver | 2 .25 RPM | 17 .48 RPM |
| SRP051959_lung | 2 .34 RPM | 19 .59 RPM |
| SRP051959_lymph_node | 2 .12 RPM | 25 .30 RPM |
| SRP051959_skeletal_muscle | 2 .62 RPM | 19 .06 RPM |
| SRP051959_spleen | 2 .82 RPM | 20 .92 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_992 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_992 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_992 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 | ENSCJAG00000008494 | 2 retrocopies |
retro_cjac_2592, retro_cjac_992 ,
|
| Cavia porcellus | ENSCPOG00000013736 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000016217 | 2 retrocopies | |
| Sarcophilus harrisii | ENSSHAG00000014713 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000010042 | 1 retrocopy |