RetrogeneDB ID: | retro_ecab_167 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:65164155..65165954(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000004117 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IFT74 | ||
| Ensembl ID: | ENSECAG00000021030 | ||
| Aliases: | None | ||
| Description: | intraflagellar transport 74 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:21424] |
Retrocopy-Parental alignment summary:
>retro_ecab_167
ATGGCCAGTAATCACAAACCTTCAGCAGCTCGCCCTGTGTCACGAGGTGGAATTGGGTTGACAGGAAGGCCTCCTTCTGG
AGTACGACCTCCATCAGGAAATATTCGAGTGGCAACTGGAATGCCCCCTGGAACAGCAAGACCAGGCTCTCGTAGTGGTC
CCATAGGAACAGGAGGAGTTCTGTCTTCTCAAATCAAAGTTGCTGATCGTCCTGTAACACAGCAAGGTTTGAGTGGAATG
AAAACTGGGATGAAAGGTCCCCAGAGGCAAATATTAGACAAATCTTACTATCTTGGGCTTCTTCGAAGTAAAATAAGTGA
ACTTACAACAGAAATTAATAAACTTCAGAAAGAAATAGAAATGTACAATCAAGAGAATTCAGTATATTTGTCATATGAAA
AGAGAGCTGAGACTTTAGCTGTTGAAATCAAAGAGTTCCAAGGACAAATAGCAGACTACAACATGTTGGTAGATAAACTT
AATACCAATACTGAAATGGAAGAAGTAATGAATGATTACAACATGCTTAAAGCTCAAAATGATCAAGAAACACAAAGTAT
GGATATCATATTTACTGAAAGACAAGCGAAGGAAAAACATATTAGAAGTGTAGAAGAAGAAATTGAACAGGAAAAACAAG
CAGCAGATGGCATTATCAAAAATATGTCTCCTGAAAAGCAAGTCAAATACATGGAGATGAAAACAACAAATGAAAAATTG
TTGCAGGAACTAGATACACTTCAGCAACAACTAGATTCACTGAACATGAAAAAAGAGAGTCTGGAAGCTGAAATAGCACA
CTCCCAGGTAAAACAGGAGGCTGTATTGCTGCATGAAAAGCTTTATGAGTTGGAGTCCCATCGAGATCAAATGATTGCGG
AAGACAAAAGCATGGGATCTCCGATGGAAGAGAGAGAGAGATTACTTAAGCAGGTTAAAGAAGATAATCAGGAAATAGCC
AGCGTGGAGTGACAGTTAACAGATATAAGAGAAAAAATAAATCAATTTAATGAAGAAATTAGACAGCTTGACATGGATTT
AGAAGAACACCAAGGTGAAATGAATCAGAAGTACAAAGAGCTCAAAGAAAGGAAGGAAAGTATGGACACTTTTATTGAGA
CTTTTGAGGAAACTAAGAATCAGGAGCTGGCACGGAAGGCACAGTAGAAGCCCACATCATCGCCCTTCTGGAGCACTGTA
GTCGAAATATAAATTGTATGAAACAGATATCCTCTATCACCAATCAAGAGCTGAAGATGATGCAGGATGATCTCAATTTT
AAATCTACTGAGATGCAGAAATCACAAAGTACAGCTAGGAATTTGACTTCGGATAGTCAGCGTCTACAGTTGGATCTACA
GAAAATGGAACTTCTGGAAAGTAAGATGACTGAGGAACAACAGTCTCTGAAAAGCAAAATTAAGCAAATGACAACTGATC
TGGAGACGTATAATGATTTGCCAGCTTTAAAATCATCAGGTGAAGAAAAGAAAAAGAAATTACATCAGGAGAGAACAGTA
TTATTGACCCGCAGAAATGCCTTTAAGAAATTAATGGAGAAGCTAAACATAGAATATGAGGCACTAAAAACACAATTGCA
AGAAAATGAGACGCAGTCTCAGCTTACAAATTTGGAGAGGAAGTGGCAACACCATGAGCAAAATAATTTTGTGATGAAAG
AATTCATAGCAACCAAGAGTCAAGAGAGTGATTACCGGCCAATTATGAAGAATGTGACCAAGCAGATTGCAGAGTACAAT
AAAACCATTGTGGAAGCTCTGCGTAGCATGAGCAGAACC
ORF - retro_ecab_167 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.34 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MASNHKPSAARPVSRGGIGLTGRPPSGVRPPSGNIRVATGMPPGTARPGSRSGPIGTGGVLSSQIKVADR |
| MASNHKPSAARPVSRGGIGLTGRPPSGVRPPSGNIRVATGMPPGTARPGSRSGPIGTGGVLSSQIKVADR | |
| Retrocopy | MASNHKPSAARPVSRGGIGLTGRPPSGVRPPSGNIRVATGMPPGTARPGSRSGPIGTGGVLSSQIKVADR |
| Parental | PVTQQGLSGMKTGMKGPQRQILDKSYYLGLLRSKISELTTEINKLQKEIEMYNQENSVYLSYEKRAETLA |
| PVTQQGLSGMKTGMKGPQRQILDKSYYLGLLRSKISELTTEINKLQKEIEMYNQENSVYLSYEKRAETLA | |
| Retrocopy | PVTQQGLSGMKTGMKGPQRQILDKSYYLGLLRSKISELTTEINKLQKEIEMYNQENSVYLSYEKRAETLA |
| Parental | VEIKEFQGQLADYNMLVDKLNTNTEMEEVMNDYNMLKAQNDRETQSMDIIFTERQAKEKQIRSVEEEIEQ |
| VEIKEFQGQ.ADYNMLVDKLNTNTEMEEVMNDYNMLKAQND.ETQSMDIIFTERQAKEK.IRSVEEEIEQ | |
| Retrocopy | VEIKEFQGQIADYNMLVDKLNTNTEMEEVMNDYNMLKAQNDQETQSMDIIFTERQAKEKHIRSVEEEIEQ |
| Parental | EKQAADGIIKNMSPEKQVKYMEMKTTNEKLLQELDTLQQELDSLNMKKESLEAEIAHSQVKQEAVLLHEK |
| EKQAADGIIKNMSPEKQVKYMEMKTTNEKLLQELDTLQQ.LDSLNMKKESLEAEIAHSQVKQEAVLLHEK | |
| Retrocopy | EKQAADGIIKNMSPEKQVKYMEMKTTNEKLLQELDTLQQQLDSLNMKKESLEAEIAHSQVKQEAVLLHEK |
| Parental | LYELESHRDQMIAEDKSMGSPMEERERLLKQVKEDNQEIASMERQLTDIREKINQFNEEIRQLDMDLEEH |
| LYELESHRDQMIAEDKSMGSPMEERERLLKQVKEDNQEIAS.E.QLTDIREKINQFNEEIRQLDMDLEEH | |
| Retrocopy | LYELESHRDQMIAEDKSMGSPMEERERLLKQVKEDNQEIASVE*QLTDIREKINQFNEEIRQLDMDLEEH |
| Parental | QGEMNQKYKELKKREESMDTFIETFEETKNQELERKAQ-LEAHIVALLEHCSRNINRMKQISSITNQELK |
| QGEMNQKYKELK.R.ESMDTFIETFEETKNQEL.RKAQ..EAHI.ALLEHCSRNIN.MKQISSITNQELK | |
| Retrocopy | QGEMNQKYKELKERKESMDTFIETFEETKNQELARKAQ<VEAHIIALLEHCSRNINCMKQISSITNQELK |
| Parental | MMQDDLNFKSTEMQKSQSTARNLTSDSQRLQLDLQKMELLESKMTEEQHSLKSKIKQMTTDLETYNDLPA |
| MMQDDLNFKSTEMQKSQSTARNLTSDSQRLQLDLQKMELLESKMTEEQ.SLKSKIKQMTTDLETYNDLPA | |
| Retrocopy | MMQDDLNFKSTEMQKSQSTARNLTSDSQRLQLDLQKMELLESKMTEEQQSLKSKIKQMTTDLETYNDLPA |
| Parental | LKSSGEEKKKKLHQERTVLLTRRNAFKKLMEKLNVEYEALKTQLQENETHSQLTNLERKWQHHEQNNFVM |
| LKSSGEEKKKKLHQERTVLLTRRNAFKKLMEKLN.EYEALKTQLQENET.SQLTNLERKWQHHEQNNFVM | |
| Retrocopy | LKSSGEEKKKKLHQERTVLLTRRNAFKKLMEKLNIEYEALKTQLQENETQSQLTNLERKWQHHEQNNFVM |
| Parental | KEFIATKSQESDYRPIMKNVTKQIAEYNKTIVEALRSMSRT |
| KEFIATKSQESDYRPIMKNVTKQIAEYNKTIVEALRSMSRT | |
| Retrocopy | KEFIATKSQESDYRPIMKNVTKQIAEYNKTIVEALRSMSRT |
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 .24 RPM | 3 .19 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .78 RPM |
| SRP021940_embryo | 0 .31 RPM | 7 .31 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 1 .59 RPM |
| SRP021940_synovial_membrane | 0 .05 RPM | 1 .15 RPM |
| SRP021940_testis | 0 .00 RPM | 2 .24 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_167 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_167 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_167 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 | ENSECAG00000021030 | 1 retrocopy |
retro_ecab_167 ,
|
| Felis catus | ENSFCAG00000026070 | 1 retrocopy |