RetrogeneDB ID: | retro_cjac_2809 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:47804635..47805894(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000006970 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ISYNA1 | ||
| Ensembl ID: | ENSCJAG00000014230 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2809
GCGCAATACGAGTACCGGACAACCCGCGTCAGCCGCGAGGGCGGCGTCCTCAAGGTGCACCCCACGACCACGTGCTTCAC
CTTCCGGACCGTCTGGCGGGTGCCCCGGCTCGGGGTCATGCTTGTCGGCTGGGGCGGGAACAATGGCTCCACGCTCACCA
CCGCGGTGCTGGCCAACCAACTGCTTCTGTACTGGCCCACGCGCAGCGGCCGCAAGGAGGCCAACTACTATGGCTCGCTG
ACTCAGGCGGGCACCCTGAGCCTGGGCTTGGATGCCGAGGGCCAGGAGGTGTTCGTGCCCTTCAGTGTGCTGCTGCCCAT
GGTGGCACCCAACGACCTCGTGTTTGATGGCTGGGACATCTCGTCACTGAACCTCGCCGAGGCGATGCGGCGCGCGAAGG
TGCTGGATTGGGAGCTGCAGGAGCAACTGTGGCCGCACATGGAAGCCGTACGGCCTCGGCCTTCCATCTGCATCCCCGAG
TTCATCCCGGCCAACCAGAGCACGCGCGCGGACAACCTCATCCCGGGCTCGGGCGCACAGCAGCTGGAGCAGATCCGCAA
GGACATCCGAGACTTCCGGTCTAGCGCGGGGCTGGACAAAGTCACCGTGCTGTGGACGGCCAACACAGAGCGCTTCTGTG
AGGTGGTTCCAGGTCTCAACAACACGGCCGAGAACCTGCTGCGCACCATTAAGCTTGGCCTGGAGGTGTCTCCCTCCACG
CTCTTCGCGGTCGCCAGCATCCTGGAGGGCTGCGCCTTCCTCAATGGGTCCCCGTAGAACACCCTGGTGCCAGAGCTCTT
GAGCTCGCGTGTCAGCGCCGGGTTTTCGTGGGCGGAGATGACTTTAAGTCTGGCCAGACCAAAGTCAAGTCCGTGCTCGT
GGACTTCTTCATCAGCTCTGGCCTCAAGACCATGTCCATCGTGAGTTACAACCACCTGGGCAACAACGATGGGCAGAACC
TGTCGGTGCCGTTGCAGTTCCGCTCTAAGGAGGTGTCCAAGAGCAACGTGGTGGACGACATGGTGCAGAGTAACCTAGTG
CTCTATATCCTCGGCGAGGAGCCCGACCACTGCGTGGTCATCAAGTACGTGCCATACGTGGGCGACAGCAAGCCCGCGCT
GGATAAGTATACATCGGAGCTAATGCTGGGTGGGACCAACACGCTGGTGCTGCACAACACTTGCGAGGACTCCCTGCTGG
CCGCACCCATCATGCTAGACCTGGCGCTGCTGACCGAGCTGTGCCAGCACGTGAGCTTC
ORF - retro_cjac_2809 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.11 % |
| Parental protein coverage: | 76.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AQYEYRTTRVSREGGVLKVHPTTTRFTFRTVRQVPRLGVMLVGWGGNNGSTLTAAVLANRLRLSWPTRSG |
| AQYEYRTTRVSREGGVLKVHPTTT.FTFRTV..VPRLGVMLVGWGGNNGSTLT.AVLAN.L.L.WPTRSG | |
| Retrocopy | AQYEYRTTRVSREGGVLKVHPTTTCFTFRTVWRVPRLGVMLVGWGGNNGSTLTTAVLANQLLLYWPTRSG |
| Parental | RKEANYYGSLTQAGTVSLGLDAEGQEVFVPFSALLPMVAPNDLVFDGWDISSMNLAEAMRRAKVLDWELQ |
| RKEANYYGSLTQAGT.SLGLDAEGQEVFVPFS.LLPMVAPNDLVFDGWDISS.NLAEAMRRAKVLDWELQ | |
| Retrocopy | RKEANYYGSLTQAGTLSLGLDAEGQEVFVPFSVLLPMVAPNDLVFDGWDISSLNLAEAMRRAKVLDWELQ |
| Parental | EQLWPHMEALRPRPSVYIPEFIAANQSTRADNLIPGSRAQQLEQIRKDIRDFRSSAGLDKVVVLWTANTE |
| EQLWPHMEA.RPRPS..IPEFI.ANQSTRADNLIPGS.AQQLEQIRKDIRDFRSSAGLDKV.VLWTANTE | |
| Retrocopy | EQLWPHMEAVRPRPSICIPEFIPANQSTRADNLIPGSGAQQLEQIRKDIRDFRSSAGLDKVTVLWTANTE |
| Parental | RFCEVVPGLNDTAENLLRTIELGLEVSPSTLFAVASILEGCAFLNGSPQNTLVP-GALELACQRRVFVGG |
| RFCEVVPGLN.TAENLLRTI.LGLEVSPSTLFAVASILEGCAFLNGSP.NTLVP..ALELACQRRVFVGG | |
| Retrocopy | RFCEVVPGLNNTAENLLRTIKLGLEVSPSTLFAVASILEGCAFLNGSP*NTLVP<RALELACQRRVFVGG |
| Parental | DDFKSGQTKVKSVLVDFLISSGLKTMSIVSYNHLGNNDGQNLSAPLQFRSKEVSKSNVVDDMVQSNPVLY |
| DDFKSGQTKVKSVLVDF.ISSGLKTMSIVSYNHLGNNDGQNLS.PLQFRSKEVSKSNVVDDMVQSN.VLY | |
| Retrocopy | DDFKSGQTKVKSVLVDFFISSGLKTMSIVSYNHLGNNDGQNLSVPLQFRSKEVSKSNVVDDMVQSNLVLY |
| Parental | MPGEEPDHCVVIKYVPYVGDSKRALDEYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQRVS |
| ..GEEPDHCVVIKYVPYVGDSK.ALD.YTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQ.VS | |
| Retrocopy | ILGEEPDHCVVIKYVPYVGDSKPALDKYTSELMLGGTNTLVLHNTCEDSLLAAPIMLDLALLTELCQHVS |
| Parental | F |
| F | |
| Retrocopy | F |
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 .00 RPM | 0 .55 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .49 RPM |
| SRP051959_kidney | 0 .00 RPM | 2 .64 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .93 RPM |
| SRP051959_lung | 0 .11 RPM | 7 .01 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 11 .21 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .76 RPM |
| SRP051959_spleen | 0 .04 RPM | 5 .17 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2809 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2809 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2809 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000014230 | 6 retrocopies |
retro_cjac_2768, retro_cjac_2803, retro_cjac_2809 , retro_cjac_2831, retro_cjac_3817, retro_cjac_435,
|
| Homo sapiens | ENSG00000105655 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000016939 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000006026 | 1 retrocopy |