RetrogeneDB ID: | retro_ecab_563 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 21:10036356..10037698(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMCC3 | ||
| Ensembl ID: | ENSECAG00000011697 | ||
| Aliases: | None | ||
| Description: | transmembrane and coiled-coil domain family 3 [Source:HGNC Symbol;Acc:29199] |
Retrocopy-Parental alignment summary:
>retro_ecab_563
GTAGAGCGTCATGACATGAATACCCTAAGCCTGCCCCTCAACATACGCCGAGGGGGCTCAGACACCAACCTCAACTTCGA
CGTACCAGATGGCATCCTGGACTTCCACAAGGTCAAACTCAGCGCGGACAGCCTGAAGCAGAAAATCCTAAAGGTAACAG
AGCAGATAAAAATAGAGCAGACGTCCCGTGATGGGAACGTGGCGGAGTATCTGAAGCTGGTCAGCAGCGCGGACAAGCAG
CAGGCCGGCCGGATCAAGCAAGTCTTTGAGAAGAAGAATCAGAAGTCAGCTCACTCGATCGCCCAGCTGCAGAAGAAGTT
AGAAAAGTATCATAGAAAGCTCAAGGAGATCGAACAGAACGGAGCCTCCAAAAGCTCAAAGGACTTTTCCAAAGACCACC
TGGAGGACATCCAGCACTCTCTGAAAGATGCCCACGCCAAGTCTCGAACGGCGCCCGGCAACATGGAGAGCGGTAAATCG
GGCATGCCAGGGGTGTCCCTCACTCCCCCCGTGTTCGTCTTTAATAAGTCCAGGGAGTTTGCCAACCTGATCCGTAATAA
GTTTGGCAGCGCCGACAACATCGCTCACTTAAAAAATTCCTTAGAGGAGTTTAGGCCCAAGGCGAGTGCCAGGGTCTACG
GGGACAGCGCGACCATTGTGAACAAGCCCAAGTATGGCAGTGACGACGAGTGTTCAAGTGGCACCTCGGGTTCCACCGAC
AGTAATGGGAACCAGTCGTCCGGGCTGGTGGAGCCAGCACGCTGGACAGCCAGGGGAAGCTCACCATGATCCTGGAGGAG
CTGTGGGAGATCAAGGACACCCAGGCACAGCTGGCTGAGGACATCGAGGTGCTGAAGGTGCAGTTTAAGAGAGAATATGG
TTTTATTTCTCAGACCCTGCAAGAAGAGAGATACAGGTACAAGTGACTGGAAGACCAGCTCCATGACATGACGGACCTGC
ATCAGCACGAGACAGCCAACCTGAAACAGGAGCTGGCCAGCATCGAGGACAAGGTGGCCTACCAGGCCTAGGAGCGCTCG
CGGGACATCCAGGGAGCCTTGGAGTCCTGCCAGACTCGCATCTCGAAGCTGGAGCTGCACCAGCAGGAGCAGCAGACGGA
CACCGTGAATGCCAAAGTTCTCCTGGCAAGTGCATCAACATGGTCCTGGCCTTCATGACTGTGATCTTGGTGTGTGTGTC
TACCATCACCAAGTTCGTCTCGCCCATGATGAAGAGCCGCTTCCACATTGTCGGCACCTTCTTTGCTGTGACTCTTCTTG
CAATATTTTGTAAAAACTGGGACCATATTCTGTGTGCCATAGAAAGGATAATAATACCAAGA
ORF - retro_ecab_563 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.48 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VERHDMNTLSLPLNIRRGGSDTNLNFDVPDGILDFHKVKLSADSLKQKILKVTEQIKIEQTSRDGNVAEY |
| VERHDMNTLSLPLNIRRGGSDTNLNFDVPDGILDFHKVKLSADSLKQKILKVTEQIKIEQTSRDGNVAEY | |
| Retrocopy | VERHDMNTLSLPLNIRRGGSDTNLNFDVPDGILDFHKVKLSADSLKQKILKVTEQIKIEQTSRDGNVAEY |
| Parental | LKLVSSADKQQASRIKQVFEKKNQKSAHSIAQLQKKLEQYHRKLKEIEQNGASKSSKDFSKDHLKDIQHS |
| LKLVSSADKQQA.RIKQVFEKKNQKSAHSIAQLQKKLE.YHRKLKEIEQNGASKSSKDFSKDHL.DIQHS | |
| Retrocopy | LKLVSSADKQQAGRIKQVFEKKNQKSAHSIAQLQKKLEKYHRKLKEIEQNGASKSSKDFSKDHLEDIQHS |
| Parental | LKDAQAKSRTAPGNMESSKSGMPGVSLTPPVFVFSKSREFANLIRNKFGSADNIAHLKNSLEEFRPEASA |
| LKDA.AKSRTAPGNMES.KSGMPGVSLTPPVFVF.KSREFANLIRNKFGSADNIAHLKNSLEEFRP.ASA | |
| Retrocopy | LKDAHAKSRTAPGNMESGKSGMPGVSLTPPVFVFNKSREFANLIRNKFGSADNIAHLKNSLEEFRPKASA |
| Parental | RVYGGSATIVNKPKYGSDDECSSGTSGSADSNGNQSFG-AGGAGTLDSQGKLTMILEELREIKDTQAQLA |
| RVYG.SATIVNKPKYGSDDECSSGTSGS.DSNGNQS.G.AGGA.TLDSQGKLTMILEEL.EIKDTQAQLA | |
| Retrocopy | RVYGDSATIVNKPKYGSDDECSSGTSGSTDSNGNQSSG<AGGASTLDSQGKLTMILEELWEIKDTQAQLA |
| Parental | EDIEALKVQFKREYGFISQTLQEERYRYERLEDQLHDMTDLHQHETANLKQELASIEEKVAYQAYERSRD |
| EDIE.LKVQFKREYGFISQTLQEERYRY..LEDQLHDMTDLHQHETANLKQELASIE.KVAYQA.ERSRD | |
| Retrocopy | EDIEVLKVQFKREYGFISQTLQEERYRYK*LEDQLHDMTDLHQHETANLKQELASIEDKVAYQA*ERSRD |
| Parental | IQEALESCQTRISKLELHQQEQQVLQTDTVNAKVLL-GKCINVVLAFMTVILVCVSTIAKFVSPMMKSRF |
| IQ.ALESCQTRISKLELHQQEQQ...TDTVNAKVLL.GKCIN.VLAFMTVILVCVSTI.KFVSPMMKSRF | |
| Retrocopy | IQGALESCQTRISKLELHQQEQQ---TDTVNAKVLL<GKCINMVLAFMTVILVCVSTITKFVSPMMKSRF |
| Parental | HIVGTFFAVTLLAIFCKNWDHILCAIERIIIPR |
| HIVGTFFAVTLLAIFCKNWDHILCAIERIIIPR | |
| Retrocopy | HIVGTFFAVTLLAIFCKNWDHILCAIERIIIPR |
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 .00 RPM | 0 .53 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 10 .39 RPM |
| SRP021940_embryo | 0 .03 RPM | 5 .45 RPM |
| SRP021940_placental_villous | 0 .10 RPM | 34 .21 RPM |
| SRP021940_synovial_membrane | 0 .05 RPM | 4 .23 RPM |
| SRP021940_testis | 0 .19 RPM | 48 .41 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_563 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_563 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_563 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000011697 | 1 retrocopy |
retro_ecab_563 ,
|