RetrogeneDB ID: | retro_ecab_962 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 8:488206..489866(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000012704 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CNOT6 | ||
| Ensembl ID: | ENSECAG00000019325 | ||
| Aliases: | None | ||
| Description: | CCR4-NOT transcription complex, subunit 6 [Source:HGNC Symbol;Acc:14099] |
Retrocopy-Parental alignment summary:
>retro_ecab_962
GGCATGCCCAAAGACAAATGCGAGCCCCCTGACCCTGGGAGGATGTACACAATTATGTCCTCTGAGGAAGCAGCAAATGG
AAAGAAATCACATTGGGCAGAGCTTGAAATAAGTGGAAAAGTAAGAAGCTTAAGCTCATCTTTGTGGTCACTAACTCACC
TGACAGCTTTGCATCTGAGTGACAATTCCCTGTCCCGTATTCCTTCAGACATTGCCAAGCTTCACAATCTGGTGTATCTG
GACCTGTCTTCTAATAAAATCCGGAGTTTACCGGCAGAACTCGGAAACATGGTATCACTCAGGGAACTCCATTTAAATAA
CAACCTGTTACGAGTTCTACCTTTTGAGCTGGGAAAACTGTTTCAGTTGCAGACTTTAGGCCTGAAAGGAAATCCACTTA
CCCAAGATATATTGAACCTCTATTTGGAACTAGATGGAACAAGAAGGCTACTGAACTATTTGCTTGATAATTTGGCAGTT
TCAACAGAACAACCACCTCCAAGATCTTGGATTATGTTACAAGAACCAGACAGAACAAGGCCTTCTGCCTTGTTTTCTTT
CATGTGCTACAATGTTCTTTGTGATAAATATGCGACCCGGCAGTTATACGGCTACTGTCCGTCATGGGTGCTAAACTGGG
ACTACAGGAAAAAGGCCATTATTCAAGAAATCTTGAGCTGCAATGCTGATATCATAAGTCTTAAGGAGGTTGAAACAGAA
CAGTATTACAGTTTTTTTTCTGGTAGAACTGAAAGAACGTGGCTATAATGGATTCTTTAGTCCTAAATCTAGAGCTGGGA
CAATGTCAGAACAAGAAAGAAAACATGTTGATGGCTGTGCAATATTCTTCAAGACAGAAAAATTTACTTTGGTTCAGAAA
CACACTGTTGAATTTAATCAGCTAGCGATGGCAAATTCAGAAGGGTCTGAAGCTATGCTGAACAGAGTCATGACAAAAGA
TAACATTGGAGTTGCAGTACTGCTAGAACTTCGAAAGGAATTGATTGAAATGTCATCTGGAAAGCCACGTCTTGGAACAG
AAAAACAACTGATTCTCGTGCCTAATGCTCATATGCATTGGGACCCTGAATACTCTGATGTGAAGTTGGTTCAGACAATG
ATGTTCCTCTCAGAAGTGACGAACATTATTGACAAAGCCTCACGGAGCCTCCAGTCCAGTGTCTTGGGAGAGTTTGGAGC
TATTCCATTGGTGGTGTGTGCAGATCTTAATTCTTTGCCAGACTCTGGTGATGTAGAATATTTGAGCACTGGTGGAGTAG
AAACAAACCATAAAGACTTTAAGGAGCTGAGATATAATGAAAGTCTCACAAACTTCAGCTGCAATGGGAAAAATGGGACG
ACCAATGGCAGGATCACGCATGGGTTCAAGTTAAAGAGTGCCTACGAGAGTGGCCTGATGCCTTACACGAACTACACCTT
CGATTTCAAGGGTATAATTGACTACATCTTCTACTCTAAACCTCAGCTGAACACTTTAGGCATCCTGGGACCTCTGGACC
ACCATTGGCTAGTTGAGAATAATATCAGTGGTGGCCCACACCCACTCATCCCCTCTGATCACTGCTCACTTTTTGCACAA
CTGGAGCTCTTACTGCCTTTCCTGCCCCAAGTAAACGGCATTCACCTTCCCAGCAGGAGG
ORF - retro_ecab_962 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.28 % |
| Parental protein coverage: | 99.82 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GMPKEKYEPPDPRRMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLSRIPSD |
| GMPK.K.EPPDP.RMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLSRIPSD | |
| Retrocopy | GMPKDKCEPPDPGRMYTIMSSEEAANGKKSHWAELEISGKVRSLSSSLWSLTHLTALHLSDNSLSRIPSD |
| Parental | IAKLHNLVYLDLSSNKIRSLPAELGNMVSLRELHLNNNLLRVLPFELGKLFQLQTLGLKGNPLTQDILNL |
| IAKLHNLVYLDLSSNKIRSLPAELGNMVSLRELHLNNNLLRVLPFELGKLFQLQTLGLKGNPLTQDILNL | |
| Retrocopy | IAKLHNLVYLDLSSNKIRSLPAELGNMVSLRELHLNNNLLRVLPFELGKLFQLQTLGLKGNPLTQDILNL |
| Parental | YLEPDGTRRLLNYLLDNLAGTAKRISTEQPPPRSWIMLQEPDRTRPTALFSVMCYNVLCDKYATRQLYGY |
| YLE.DGTRRLLNYLLDNLA..........PP.RSWIMLQEPDRTRP.ALFS.MCYNVLCDKYATRQLYGY | |
| Retrocopy | YLELDGTRRLLNYLLDNLAVSTE----QPPP-RSWIMLQEPDRTRPSALFSFMCYNVLCDKYATRQLYGY |
| Parental | CPSWALNWDYRKKAIIQEILSCNADIVSLQEVETEQYY-SFFLVELKERGYNGFFSPKSRARTMSEQERK |
| CPSW.LNWDYRKKAIIQEILSCNADI.SL.EVETEQYY....LVELKERGYNGFFSPKSRA.TMSEQERK | |
| Retrocopy | CPSWVLNWDYRKKAIIQEILSCNADIISLKEVETEQYY>XXXLVELKERGYNGFFSPKSRAGTMSEQERK |
| Parental | HVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAVLLELRKELIEMSSGKPHL |
| HVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAVLLELRKELIEMSSGKP.L | |
| Retrocopy | HVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAVLLELRKELIEMSSGKPRL |
| Parental | GTEKQLILVANAHMHWDPEYSDVKLVQTMMFLSEVKNIIDKASRSLQSSVLGEFGAIPLVLCADLNSLPD |
| GTEKQLILV.NAHMHWDPEYSDVKLVQTMMFLSEV.NIIDKASRSLQSSVLGEFGAIPLV.CADLNSLPD | |
| Retrocopy | GTEKQLILVPNAHMHWDPEYSDVKLVQTMMFLSEVTNIIDKASRSLQSSVLGEFGAIPLVVCADLNSLPD |
| Parental | SGVVEYLSTGGVETNHKDFKELRYNESLTNFSCNGKNGTTNGRITHGFKLKSAYESGLMPYTNYTFDFKG |
| SG.VEYLSTGGVETNHKDFKELRYNESLTNFSCNGKNGTTNGRITHGFKLKSAYESGLMPYTNYTFDFKG | |
| Retrocopy | SGDVEYLSTGGVETNHKDFKELRYNESLTNFSCNGKNGTTNGRITHGFKLKSAYESGLMPYTNYTFDFKG |
| Parental | IIDYIFYSKPQLNTLGILGPLDHHWLVENNISGCPHPLIPSDHFSLFAQLELLLPFLPQVNGIHLPSRR |
| IIDYIFYSKPQLNTLGILGPLDHHWLVENNISG.PHPLIPSDH.SLFAQLELLLPFLPQVNGIHLPSRR | |
| Retrocopy | IIDYIFYSKPQLNTLGILGPLDHHWLVENNISGGPHPLIPSDHCSLFAQLELLLPFLPQVNGIHLPSRR |
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 | 6 .38 RPM |
| SRP021940_cerebellum | 0 .21 RPM | 9 .04 RPM |
| SRP021940_embryo | 0 .31 RPM | 16 .16 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 8 .08 RPM |
| SRP021940_synovial_membrane | 0 .05 RPM | 6 .40 RPM |
| SRP021940_testis | 0 .00 RPM | 4 .99 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_962 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_962 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_962 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000019325 | 1 retrocopy |
retro_ecab_962 ,
|
| Microcebus murinus | ENSMICG00000013018 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000011083 | 1 retrocopy |