RetrogeneDB ID: | retro_btau_1725 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:592202..592810(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDXK | ||
| Ensembl ID: | ENSBTAG00000018186 | ||
| Aliases: | None | ||
| Description: | Pyridoxal kinase [Source:UniProtKB/Swiss-Prot;Acc:Q0II59] |
Retrocopy-Parental alignment summary:
>retro_btau_1725
CTGAAGCTGAACAATTCCAATCAGGATGATTACATTCTCAGGGGCTATAGGTGAGACAAGTCCTTCCTGGCCATGGTGGT
GAACATCCTGAGGGAGCTTTAACAGCAGAACTCCAGGCTCATGTACATGTGTGACCCTGAGATGGGAGACCAGCATAATG
GAGAAGGCACCATGTACATCCCCAGAGGACCTCCTTCCCGTTTACAGAGAGAAGGTGGTGCCAGTTGCAGACATCATCAC
CCCCAACCAGTTTGAGGCTGAGTTGCTGACCAGGAGAAAGATCCACAGCCAGGAAGAAGTCTTTAGAGGTTATGGACAAG
CTATACTCCACGGGGCCCAACACGGTGGTCATCACCAGCTCTGACCTGCTGTCCTCGAGCGGCACTGACTACCTGATGGC
ACTGGGGAGCCAGAGGACATGGACCCCTGACAGCTCCACGGTGATGTAGTGCATCCCCAGGGAGACACACAAGGTGGACA
CCATCTTCGTCGGCACTGGGGATGGCTTCGCCGCCATGCTCTTGGCGTGGATGCACAAGCACCCCAACAACCTCAAGGTG
GCCTGTGAGAAGACCCTGTCAGCTACGCACCATGTTCTGCAGTGGACC
ORF - retro_btau_1725 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.98 % |
| Parental protein coverage: | 64.74 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LKLNSVNQYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVMGDQRDGEGAMYVP-DDLLPVYR |
| LKLN..NQ.DY.L.GY..DKSFLAMVV.I..EL.QQN.RL.Y.CDP.MGDQ..GEG.MY.P..DLLPVYR | |
| Retrocopy | LKLNNSNQDDYILRGYR*DKSFLAMVVNILREL*QQNSRLMYMCDPEMGDQHNGEGTMYIP>EDLLPVYR |
| Parental | EKVVPVADIITPNQFEAELLTGRKIHTQEE-ALEVMDMLHSMGPDTVVITSSDLLSPRGSDYLMALGSQR |
| EKVVPVADIITPNQFEAELLT.RKIH.QEE..LEVMD.L.S.GP.TVVITSSDLLS..G.DYLMALGSQR | |
| Retrocopy | EKVVPVADIITPNQFEAELLTRRKIHSQEE>SLEVMDKLYSTGPNTVVITSSDLLSSSGTDYLMALGSQR |
| Parental | TRAPDGSMVTQRIRMEMHKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSAMHHVLQRT |
| T..PD.S.V...I..E.HKVD..FVGTGD.FAAMLLAW.HKHPNNLKVACEKT.SA.HHVLQ.T | |
| Retrocopy | TWTPDSSTVM*CIPRETHKVDTIFVGTGDGFAAMLLAWMHKHPNNLKVACEKTLSATHHVLQWT |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 3 .75 RPM |
| ERP005899_muscle | 0 .00 RPM | 114 .76 RPM |
| SRP017611_brain | 0 .00 RPM | 113 .42 RPM |
| SRP017611_kidney | 0 .00 RPM | 38 .76 RPM |
| SRP017611_liver | 0 .00 RPM | 5 .81 RPM |
| SRP030211_testis | 0 .00 RPM | 20 .92 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1725 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1725 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1725 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000018186 | 1 retrocopy |
retro_btau_1725 ,
|
| Myotis lucifugus | ENSMLUG00000004931 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000011152 | 1 retrocopy |