RetrogeneDB ID: | retro_ecab_960 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 7:74632838..74633996(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GSTCD | ||
| Ensembl ID: | ENSECAG00000009590 | ||
| Aliases: | None | ||
| Description: | glutathione S-transferase, C-terminal domain containing [Source:HGNC Symbol;Acc:25806] |
Retrocopy-Parental alignment summary:
>retro_ecab_960
GATACTTCACTACTTAAAAATGTATTGTCCCAGCATGTTCAAATCCAGATTATCTCGAGGCAAGAGCTTCCACAGATAGT
CCAGAATTGCTGTTTACCTGCAGTGGTAGAAGGACCAGACAGTTTCTACAGAGCAGGGCTCGCTGTTGTGCTGAGACACA
TCGTCCAGAAAGCATATGACGCAGAGCCCTCAAAGAAGGGGATCTTCGAGCTGCTGGATTTTAAGAAGACTTGTTTGAAG
GCCTGTGTTGAAGTTAGTCAGTAGACCAGGCTATGTAAACTTACCATCCCTTTAGCTATTGAGAATTTTGTCAAAGAGTC
TTGTGACCTGCACGCAGCTATCCCCACAGAAGTACTACAGCTAGAGAAAAAGCTCAGCGAGCCTGTTGGAGTGCGCAACG
ATGACAAACTCTGTGAGCAAAAGCTGAAGCAGCAGAAGGCTGCTGCAGTGGTGCCTGCTCTTGCCCAGGAGAAATTGAAG
GCCTGTAGACAGGAAACATCTGAGGACCAAGACCCTTCATCCCGCAGCCTGGAGCTGCAAGTGGCCTTCTCAACGCTCAC
GGTACAGGGGCACCCAGCTGCTCCCAACAGGGAGCCTGCTCACATCATACGAGCAGGCACCTGCGCGCTTCTGCTCCTGG
AGCACCTGTTTGCAGAAGGCCTGTACTTCGCCTTGGTAGACCTCGTACTTCTGCCCTGCAGCCATCACTTTTTGGTAATT
ATCCTCGAGAAGCTTTCTGAAAGGCTGGTAGAATTTCTGCTGCTGGCTGCCTGGTACCAGAGGGCTCAGGAGGTGCCAGG
AGTGAGAACAGCAGCTTCTTGCCATGGGACCTAGTTTCTCCACTTACCAGAGTTGCCGACCACCTCCAGCGAACAGCATC
CAAAATTCAGCAAGGCCCAGGAGCAGAGGAGCACAGCGACCCTTCGTTTATGTTTAGTGGGCCCAAGACCCACTATGACC
AAGTTAATGGAAAAGGGCATTGAAGTGATGTTTTCTCCCCACCCTTGCTCTGCTTGGACCCTTGACTGGAATAGACTTCC
TGCAGCAGTGAGCCCAAAAGATGGGAAGACGTCCAGTGATTGAGCGCTGAGGAAGCAGCAGGAGTTAAGCAACCTCGTCT
ACGTGGTGACACATCAGGCCAGGCCTGGGGACAGAATC
ORF - retro_ecab_960 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.85 % |
| Parental protein coverage: | 60.37 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DTSLLKNVLSQHVEIQIISRQELPLIVQNCCLPAVVESPDSFCRAGLAVVLRHIVQRAYDAEPSKKGILE |
| DTSLLKNVLSQHV.IQIISRQELP.IVQNCCLPAVVE.PDSF.RAGLAVVLRHIVQ.AYDAEPSKKGI.E | |
| Retrocopy | DTSLLKNVLSQHVQIQIISRQELPQIVQNCCLPAVVEGPDSFYRAGLAVVLRHIVQKAYDAEPSKKGIFE |
| Parental | LLGFKKTCLKACAEVSQWTRLCELTIPLSIENFLKESCDQHPAIPTEILQLEKKLSEPVRVHNDDKLRRQ |
| LL.FKKTCLKAC.EVSQ.TRLC.LTIPL.IENF.KESCD.H.AIPTE.LQLEKKLSEPV.V.NDDKL..Q | |
| Retrocopy | LLDFKKTCLKACVEVSQ*TRLCKLTIPLAIENFVKESCDLHAAIPTEVLQLEKKLSEPVGVRNDDKLCEQ |
| Parental | KLKQQKAAGAGPTLAQEKLKSQAHMQETSEDQDPSSQSLELQVAFSKLTVQEHPAAPNREPAHIRRAGAC |
| KLKQQKAA...P.LAQEKLK..A..QETSEDQDPSS.SLELQVAFS.LTVQ.HPAAPNREPAHI.RAG.C | |
| Retrocopy | KLKQQKAAAVVPALAQEKLK--ACRQETSEDQDPSSRSLELQVAFSTLTVQGHPAAPNREPAHIIRAGTC |
| Parental | ALPPLEHVFAEGLYFTLADLVLLPCIHHFLVVICKKLSKRLVEFPLLAAWYQRVQEVPGVKTAASRCGIQ |
| AL..LEH.FAEGLYF.L.DLVLLPC.HHFLV.I..KLS.RLVEF.LLAAWYQR.QEVPGV.TAAS..G.. | |
| Retrocopy | ALLLLEHLFAEGLYFALVDLVLLPCSHHFLVIILEKLSERLVEFLLLAAWYQRAQEVPGVRTAASCHGT* |
| Parental | FLHLPELPTTSIEQHPKFSEA-AGAEEHSDPSFI-GGP-RPTMTKLMEKGIEVMFSPHPCPAWTLDWNRL |
| FLHLPELPTTS.EQHPKFS.A..GAEEHSDPSF...GP.RPTMTKLMEKGIEVMFSPHPC.AWTLDWNRL | |
| Retrocopy | FLHLPELPTTSSEQHPKFSKA<PGAEEHSDPSFMFSGP>RPTMTKLMEKGIEVMFSPHPCSAWTLDWNRL |
| Parental | PAAVSPKEGKMSSDRALRKQQQLNNLVYVVTHQARPGDRI |
| PAAVSPK.GK.SSD.ALRKQQ.L.NLVYVVTHQARPGDRI | |
| Retrocopy | PAAVSPKDGKTSSD*ALRKQQELSNLVYVVTHQARPGDRI |
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 | 6 .38 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 11 .74 RPM |
| SRP021940_embryo | 0 .13 RPM | 24 .17 RPM |
| SRP021940_placental_villous | 0 .29 RPM | 6 .30 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 9 .20 RPM |
| SRP021940_testis | 0 .32 RPM | 81 .98 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_960 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_960 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_960 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 | ENSECAG00000009590 | 1 retrocopy |
retro_ecab_960 ,
|