RetrogeneDB ID: | retro_ecab_283 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 13:40083976..40084644(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000016714 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TWSG1 | ||
| Ensembl ID: | ENSECAG00000018189 | ||
| Aliases: | None | ||
| Description: | twisted gastrulation homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:12429] |
Retrocopy-Parental alignment summary:
>retro_ecab_283
GTGAAGTCACACCGTGTTGTTATGCTTACTCTAGCTGTCCTGGGGTTGCTGACATGGGTCCCCGTGTCACTGAGTTGCAA
TAAAGCTCTCTGTGCTGGTGATGTGAGCAAATGCCTAATTCAGGAGCTTTGCCAGTGCCGACCCGGAGAAGGGAATTGTT
CCTGCTGTAAGGAGTGCATGCTGTGTCTTGGAACCCTTTGGGATGAGTGCTGTGATTGCGTTGGTACGTGTAATCCTCGA
AATTATAGTGACATACCTCCAACTTCAAAGAGCACGGTGGAAGAGCTTCATGAGCCCATCCCTTCTCTCTCCCGGGCTCT
CACAGAAGGAGATACTCAGTTGAACTGGAACATCGTTTCCTTCCCTGTTGCAGAAGAACTTTCACATCATGAGAATCTGG
TTTCATTTTTAGAAACAGTGAACCAGCCACACCACCAAACTGTGTCTGTTCCCAGCAATATGTTCACGCACCTTATTCCA
GTGACAAAGAACACATGTGTATTGTGGTTTACTTTGATGACTGCGTGTCCATACATCGGTGTAAAATATTCTGTGAGTCC
ATGGGGGCAGCCAAATACCGCTGGTTCCATAACGCCTGCTGCGAGCGCATTGGTCCAGAGTGTATCGACTATGGTAGTAA
GACTGTCAAATGTATGAACTGCACGTTC
ORF - retro_ecab_283 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.41 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MKSHCVVMLTLAVLVLLTWVPVSLSCNKALCASDVSKCLIQELCQCRPGEGNCSCCKECMLCLGTLWDEC |
| .KSH.VVMLTLAVL.LLTWVPVSLSCNKALCA.DVSKCLIQELCQCRPGEGNCSCCKECMLCLGTLWDEC | |
| Retrocopy | VKSHRVVMLTLAVLGLLTWVPVSLSCNKALCAGDVSKCLIQELCQCRPGEGNCSCCKECMLCLGTLWDEC |
| Parental | CDCVGMCNPRNYSDTPPTSKSTVEELHEPIPSLFRALTEGDTQLNWNIVSFPVAEELSHHENLVSFLETV |
| CDCVG.CNPRNYSD.PPTSKSTVEELHEPIPSL.RALTEGDTQLNWNIVSFPVAEELSHHENLVSFLETV | |
| Retrocopy | CDCVGTCNPRNYSDIPPTSKSTVEELHEPIPSLSRALTEGDTQLNWNIVSFPVAEELSHHENLVSFLETV |
| Parental | NQPHHQNVSVPSN-NVHAPYSSDKEHMCTVVYFDDCMSIHQCKISCESMGASKYRWFHNACCECIGPECI |
| NQPHHQ.VSVPSN..VHAPYSSDKEHMC.VVYFDDC.SIH.CKI.CESMGA.KYRWFHNACCE.IGPECI | |
| Retrocopy | NQPHHQTVSVPSN<YVHAPYSSDKEHMCIVVYFDDCVSIHRCKIFCESMGAAKYRWFHNACCERIGPECI |
| Parental | DYGSKTVKCMNCMF |
| DYGSKTVKCMNC.F | |
| Retrocopy | DYGSKTVKCMNCTF |
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 | 48 .88 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 7 .43 RPM |
| SRP021940_embryo | 0 .00 RPM | 31 .51 RPM |
| SRP021940_placental_villous | 0 .19 RPM | 17 .27 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 30 .06 RPM |
| SRP021940_testis | 0 .00 RPM | 7 .23 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_283 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_283 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_283 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 | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000002791 | 1 retrocopy | |
| Equus caballus | ENSECAG00000018189 | 1 retrocopy |
retro_ecab_283 ,
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