RetrogeneDB ID: | retro_ecab_140 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:117880136..117881438(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NADK | ||
| Ensembl ID: | ENSECAG00000022883 | ||
| Aliases: | None | ||
| Description: | NAD kinase [Source:HGNC Symbol;Acc:29831] |
Retrocopy-Parental alignment summary:
>retro_ecab_140
ATGGAAGTGGAACAAGAGAAAGTCAACATGAGTAAGGAGCTGAGTGCAGATGCGGCCTCGTACCGCTGCTCCGCGTGTCA
TGGGGACGAGGACTGGGGGCTCAGCCACCCCCATGCGGGGGCGGGCCAAGTCCCGCAGCTTGTCTGCCGCGCTGGCCCTG
GCAAGCACCAAGGAGTTCAGGAGGACCCGCTCCCTGCACAGGCCGTGCCCAGTGACCACTTTTGGACCAAAGGCCTGCGT
GCTGCAGAACCCCCAGACCATCATGCACATCCAGGACCCTGCTAGCCAGTGGTTGACGTGGAACAAGTCCCCAAAGAGTG
TTCTCGTCATCAAGAAGATCCGTGACGCCAGCCTGCCCCAGCCCTTCAAGGAGCTCTGCATGTACCTGATGGAGGAGAAC
AACATGATTGTGTATGTGGAGAAGAAAGTTCTAGAAGACCCTGCCATAGTGAGTGACGACAGCTTTGGGCCAGTGAAGAG
GAAGTTCTGCACCTTCAGAGAAGATTATGACGACATCTCCAATCAGATCGACCTCATCATCTGCCTGGGTGGGGACGGGA
CCCTGCTCTACGCCTCCTCCCTCTTCTCGGGCAGCGTGCCTCGGGTCATGGCTTTTCACCTGGCCTCCCTGGGCTTCCTG
ACCCCCTTCAACTTTGAGAACTTTCAGTCCCAAGATACTCAGGTGATACAGGGGAATGCAGCTGTTGTTCTTCGGAGCCG
GCTGAAGGTCAGGGTCGTGAAGGAGCTTAGAGGGAAGATGGCCATCCCCAACGGGATCAGCGAGAACGGGGTGCTGGCTG
CAGACCTGGACACAGAGGTCGGGAAGCAGGTCATGCAGTACCAGGTCTTGAATGAGGTGTTGATCGACTGAGGTCCGTCC
TCGTACCTGTCCAACGTGGACGTCTACCTGGACGGGCACCTCATCACCACGGTGCAGGGCGACGGGGTGATTGTGTCCAC
CCCGACGGGCAGCACAGCGTATGCGGCGACAGCGGGGCCTCCATGATCCACCCCAACGTGCCAGCCATCATGATCACACC
TATCTGCCCCCACTCACTGTCATTCCGGCCCATCGTGGTCCCTGCGGGGGTCGAGCTGAAGATCATGCTATCACCGGAAG
CTAGAAACACCGCCTGGGTGTCCTTTGATGGACGAAAGAGACAGGAGATCCGCCGCGGAGACAGCATCAGCATTGCTACC
TCTTGCTACCCCGTGCCCTCCATCAGCGTCCGAGACCCCATGAGCAACTGGTTTGAGAGCTTGGCTCAGTGTCTGCACTG
GAACGTGCGGAAGAAGCAGGCC
ORF - retro_ecab_140 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.81 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MEVEQEKVNMSKELSADAASYRCSACHGDEDWGLSHP-MRGRAKSRSLSAAPAPASTKEFRRTRSLHGPC |
| MEVEQEKVNMSKELSADAASYRCSACHGDEDWGLSHP.MRGRAKSRSLSAA.A.ASTKEFRRTRSLH.PC | |
| Retrocopy | MEVEQEKVNMSKELSADAASYRCSACHGDEDWGLSHP>MRGRAKSRSLSAALALASTKEFRRTRSLHRPC |
| Parental | PVTTFGPKACVLQNPQTIMHIQDPASQRLTWNKSPKSVLVIKKIRDASLLQPFKELCMYLMEENNMIVYV |
| PVTTFGPKACVLQNPQTIMHIQDPASQ.LTWNKSPKSVLVIKKIRDASL.QPFKELCMYLMEENNMIVYV | |
| Retrocopy | PVTTFGPKACVLQNPQTIMHIQDPASQWLTWNKSPKSVLVIKKIRDASLPQPFKELCMYLMEENNMIVYV |
| Parental | EKKVLEDPAIVSDDSFGPVKRKFCTFRE-YDDISNQIDLIICLGGDGTLLYASSLFQGSVPPVMAFHLGS |
| EKKVLEDPAIVSDDSFGPVKRKFCTFRE.YDDISNQIDLIICLGGDGTLLYASSLF.GSVP.VMAFHL.S | |
| Retrocopy | EKKVLEDPAIVSDDSFGPVKRKFCTFREDYDDISNQIDLIICLGGDGTLLYASSLFSGSVPRVMAFHLAS |
| Parental | LGFLTPFNFENFQSQVTQVIQGNAAVVLRSRLKVRVVKELRGKMAIPNGISENGVLATDLDTEVGKQVMQ |
| LGFLTPFNFENFQSQ.TQVIQGNAAVVLRSRLKVRVVKELRGKMAIPNGISENGVLA.DLDTEVGKQVMQ | |
| Retrocopy | LGFLTPFNFENFQSQDTQVIQGNAAVVLRSRLKVRVVKELRGKMAIPNGISENGVLAADLDTEVGKQVMQ |
| Parental | YQVLNEVVIDRGPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAAAA-GASMIHPNVPAIMITPI |
| YQVLNEV.ID.GPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAA.A.GASMIHPNVPAIMITPI | |
| Retrocopy | YQVLNEVLID*GPSSYLSNVDVYLDGHLITTVQGDGVIVSTPTGSTAYAATA<GASMIHPNVPAIMITPI |
| Parental | CPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRHGDSISITTSCYPLPSICVRDPVSDW- |
| CPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIR.GDSISI.TSCYP.PSI.VRDP.S.W. | |
| Retrocopy | CPHSLSFRPIVVPAGVELKIMLSPEARNTAWVSFDGRKRQEIRRGDSISIATSCYPVPSISVRDPMSNWF |
| Parental | RAWLQCLHWNVRKKQA |
| ....QCLHWNVRKKQA | |
| Retrocopy | ESLAQCLHWNVRKKQA |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .47 RPM | 8 .80 RPM |
| SRP021940_cerebellum | 0 .36 RPM | 15 .63 RPM |
| SRP021940_embryo | 3 .48 RPM | 49 .30 RPM |
| SRP021940_placental_villous | 2 .74 RPM | 35 .70 RPM |
| SRP021940_synovial_membrane | 3 .18 RPM | 40 .71 RPM |
| SRP021940_testis | 7 .23 RPM | 50 .77 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_140 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_140 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_140 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000022883 | 1 retrocopy |
retro_ecab_140 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000012783 | 1 retrocopy |