RetrogeneDB ID: | retro_cjac_475 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:153002549..153004003(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000017296 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZYG11A | ||
| Ensembl ID: | ENSCJAG00000004369 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_475
GACTCAACAAGCATCTCTCAAAATTCAAGAGTACTGTTCTTTGGTCAGCTCACTGGTCTTTGCATTTTAAGTGTTTTTAA
TGTTTGTTTTCATACTGAAGACCTGGCTAATGTTTCTCAGTTACCAAGACTGGAAAGCTTGGGTATCTCTAGTACTCTGG
TCACGGATATTTCTGCACTGCTTACCTGTAAGGATCGATTGAAGCCTCTCACAATGCACTATCTGAAATGCCTGACCATG
ACCAAACCACAAATTCTTGCAGTCATTAGAGAACTTAAATGTCTGCTTCACCTTGACATTTCTGATCACAAGCAACTCAA
ATCAGACCTAGCTTTTCATTTGCTACAGCAGAAGGATATCCTGCCCAATGTCGTGTCACTGGGTATTTCTGGGAGCAATT
GCATCACTGATGCAGCTGTAGAACTGTTTATGCGACAGTGGCCTGCCATGCAATTTGTGGGACTATTGGCCACAGATGCT
GGCTATTCTGACTTCTTTACTACAAAGCAAGGCTTGAGGGTTGCTGGAGGAGTCAATATGAGTCAGATTTCAGAAGCACT
GAGCCGATACAGGAACAGATCATGTTTTATGAAGGAAGCCCTCTACAGGCTATTCACAGAGACATTGTCAATGAAGGTAA
CCATGCCTGCTATTTTAAAGCTTGTGACTGTAGGAATGAGGAATCACCGTTGGATTTGCCAGTGCAATTCACAGCTAGTG
CTTGCGCTCTCAACCTAACACACCACGGCCTGGCCAAGGGGATGCCTGTTCGCCTGTTGTCAGAGGTCACCTGTCTACTT
TTCAAGGCTCTGAAAAATTTCCCTTGTTACCAACAGTTACAGAAGAATTGTCTTCTCTCCTTAACCAATTCCAGGATTCT
TGTGGATGTTCTGTTTGACAGGTTTGGTGCTGCCAAGTTTGTTATGAGATGGCTCAGTAAGCATGAAAACCCCAAGATGA
AAACAATAGCAGCGAGTGTCACCTCTATTCTAGCTCTGCAGCTTTCACCTCAGCAAACGGCAGAGCTTGAAGAGCTTTTC
ATGGCAGTTAAGGAACTTCTAGCAATAGTAAAACAAAAGACTACTGAGAATTTAGATGATGTCACCCTCTTGTTTACTTC
AAAAGCACTTTGGAATCTTACAGACGAGTCTCCAGCTGCCTGCAAGCACTTTATTGAAAATCAAGGATTGGAAATCTTCA
TCCAAGTCTTGGAGACCTTTTCAAAGTCAGCAATACAAAGCAAAGTACTTGGTCTTTTGAACAACATAGCAGAAGTCAGA
GAGCCTTCTGCCAAGCTGGTGACTGAAGACGTGCTGAAGCATATCAACAATTTACTCTGTAGCAGGGAAATGGAAGTCAG
CTATTTTGCTGCAGGTATCATAGCCCACCTGACATCTGACAGACAACTTTGGATATCCCATGACTTCCAGAGGCATTTTC
TTCTGCAAGATCTG
ORF - retro_cjac_475 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.21 % |
| Parental protein coverage: | 71.85 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DSTSISQNSRVLFFGQLTGLCVLSVFNVCFHTEDLANVSQLPRLESLDISSTLVTDISALLTCKDRLKSL |
| DSTSISQNSRVLFFGQLTGLC.LSVFNVCFHTEDLANVSQLPRLESL.ISSTLVTDISALLTCKDRLK.L | |
| Retrocopy | DSTSISQNSRVLFFGQLTGLCILSVFNVCFHTEDLANVSQLPRLESLGISSTLVTDISALLTCKDRLKPL |
| Parental | TMHYLKCLTMTKPQILAVIRQLKCLLHLDISDHKQLKSHLAFHLLQQKDILPNIVSLDISGSNCITDAAV |
| TMHYLKCLTMTKPQILAVIR.LKCLLHLDISDHKQLKS.LAFHLLQQKDILPN.VSL.ISGSNCITDAAV | |
| Retrocopy | TMHYLKCLTMTKPQILAVIRELKCLLHLDISDHKQLKSDLAFHLLQQKDILPNVVSLGISGSNCITDAAV |
| Parental | ELFIRQRPAMQFVGLLATDAGYSDFFTTKQGLRVAGGANMSQISEALSRYRNRSCFMKEALYRLFTETLS |
| ELF.RQ.PAMQFVGLLATDAGYSDFFTTKQGLRVAGG.NMSQISEALSRYRNRSCFMKEALYRLFTETLS | |
| Retrocopy | ELFMRQWPAMQFVGLLATDAGYSDFFTTKQGLRVAGGVNMSQISEALSRYRNRSCFMKEALYRLFTETLS |
| Parental | MKVTMPAILKLVTVGMRNH-PLDLPVQFTASACALNLTRHGLAKGMPVRLLSEVTCLLFKALKNFPHYQQ |
| MKVTMPAILKLVTVGMRNH.PLDLPVQFTASACALNLT.HGLAKGMPVRLLSEVTCLLFKALKNFP.YQQ | |
| Retrocopy | MKVTMPAILKLVTVGMRNH<PLDLPVQFTASACALNLTHHGLAKGMPVRLLSEVTCLLFKALKNFPCYQQ |
| Parental | LQKNCLLSLTNSRILVDVPFDRFDAARFVMRWLCKHENPKMQTMAVSVTSILALQLSPQQTAHLEELFMA |
| LQKNCLLSLTNSRILVDV.FDRF.AA.FVMRWL.KHENPKM.T.A.SVTSILALQLSPQQTA.LEELFMA | |
| Retrocopy | LQKNCLLSLTNSRILVDVLFDRFGAAKFVMRWLSKHENPKMKTIAASVTSILALQLSPQQTAELEELFMA |
| Parental | VKELLAIVKQKTTENLDDVTLLFTLKALWNLTDESPAACKHFIENQGLEIVIQVLETFSESAIQSKVLGL |
| VKELLAIVKQKTTENLDDVTLLFT.KALWNLTDESPAACKHFIENQGLEI.IQVLETFS.SAIQSKVLGL | |
| Retrocopy | VKELLAIVKQKTTENLDDVTLLFTSKALWNLTDESPAACKHFIENQGLEIFIQVLETFSKSAIQSKVLGL |
| Parental | LNNIAEVRELSSKLVTEDVLKHINSLLWSREMEVSYFAAGIIAHLTSDRWLWISRDVQRRILLQDL |
| LNNIAEVRE.S.KLVTEDVLKHIN.LL.SREMEVSYFAAGIIAHLTSDR.LWIS.D.QR..LLQDL | |
| Retrocopy | LNNIAEVREPSAKLVTEDVLKHINNLLCSREMEVSYFAAGIIAHLTSDRQLWISHDFQRHFLLQDL |
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 .04 RPM | 0 .18 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .46 RPM |
| SRP051959_kidney | 0 .27 RPM | 3 .99 RPM |
| SRP051959_liver | 0 .04 RPM | 0 .41 RPM |
| SRP051959_lung | 0 .08 RPM | 1 .09 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .23 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 0 .28 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .32 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_475 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_475 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_475 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 | ENSCJAG00000004369 | 1 retrocopy |
retro_cjac_475 ,
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