RetrogeneDB ID: | retro_ecab_801 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 4:8471708..8472497(-) | ||
| Located in intron of: | ENSECAG00000018422 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GLRB | ||
| Ensembl ID: | ENSECAG00000019011 | ||
| Aliases: | None | ||
| Description: | glycine receptor, beta [Source:HGNC Symbol;Acc:4329] |
Retrocopy-Parental alignment summary:
>retro_ecab_801
TTGATAGCCAACCTTTTTATTAACAGTTTTGGATCCATTCAAGAGACAACAATGGACTGTAGAGTTAACATCTTCCTGAG
ACAAAAATGGAACGATCCCAGGCTGAAGCTCCCTGGAGATTTTCGGGGCTTAGATGCACTGACAGTGGATCCCACAACAT
ACAAGTGTCCGTGGAAACTTAATTAGTTTTTTCCAAATGAAAAAAGTGCCAATTTTTATGATGTAACACAGGAAAACATC
CTCTTTATTTTGGGGGATGGAGATGTCCTCGTCAGCGTGAGGTTATCTATTGTCTTTCACGCCCTTTGAACTTGACTTTG
TTTCCCGTGCACACACAACATTGTAAGACACAATTTAAGAGCTTTGTTTACACAACTGATGATTTACGATTTGTCTGGCA
GTCAGGGGATCCTCTCAGTTAGAAAAAATTGTGCTGCCTCAATTTGATATTAAAAAGGAGGATGTTGAATATGGTGTAAC
TGTACAAAATACTATGAAGGTACTGGCTACTACACACATGTAGAAGTCATCCTCACCCTAAGGAGACAGATAGGGTTTTC
CACGATGGGTGTCTATACCCCAACCCTGCTGATTGTGGTTCTCTCTTGGCTTTCCTTCTGGATCAATCCAGATACCAGTG
CTGCCGGAATGCCCCTGGGTATCTTCTCAGTACTCAGCTTGGCCTCTGAGTGCACAACCCTTGCTGCTGAACTCCCCAAA
GTATCGTACACTAAGGCTCTTGATGAATGACTCGTTGCTTGTCTTCTCTTTGGGTTTGCCTCACTAGTG
ORF - retro_ecab_801 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.94 % |
| Parental protein coverage: | 53.12 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VVVNIFINSFGSIQETTMDYRVNIFLRQKWNDPRLKLPSDFRGSDALTVDPTMYKCLWKPDLFFANEKSA |
| ...N.FINSFGSIQETTMD.RVNIFLRQKWNDPRLKLP.DFRG.DALTVDPT.YKC.WK...FF.NEKSA | |
| Retrocopy | LIANLFINSFGSIQETTMDCRVNIFLRQKWNDPRLKLPGDFRGLDALTVDPTTYKCPWKLN*FFPNEKSA |
| Parental | NFHDVTQENILLFIFRDGDVLVSMRLSIT-LSCPLDLTLFPMDTQRCKMQLESFGYTTDDLRFIWQSGDP |
| NF.DVTQENIL.FI..DGDVLVS.RLSI..LS.PL.LTLFP..TQ.CK.Q..SF.YTTDDLRF.WQSGDP | |
| Retrocopy | NFYDVTQENIL-FILGDGDVLVSVRLSIV<LSRPLNLTLFPVHTQHCKTQFKSFVYTTDDLRFVWQSGDP |
| Parental | VQLEKIALPQFDIKKEDIE-YGNCTKYYKGTGYYTCVEVIFTLRRQVGFYMMGVYAPTLLIVVLSWLSFW |
| ....K........K........NCTKYY.GTGYYT.VEVI.TLRRQ.GF..MGVY.PTLLIVVLSWLSFW | |
| Retrocopy | LS*KKLCCLNLILKRRMLN>WCNCTKYYEGTGYYTHVEVILTLRRQIGFSTMGVYTPTLLIVVLSWLSFW |
| Parental | INPDASAARVPLGIFSVLSLASECTTLAAELPKVSYVKALDVWLIACLLFGFASLV |
| INPD.SAA..PLGIFSVLSLASECTTLAAELPKVSY.KALD..L.ACLLFGFASLV | |
| Retrocopy | INPDTSAAGMPLGIFSVLSLASECTTLAAELPKVSYTKALDE*LVACLLFGFASLV |
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 | 7 .50 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 31 .00 RPM |
| SRP021940_embryo | 0 .00 RPM | 3 .27 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 3 .13 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 3 .84 RPM |
| SRP021940_testis | 0 .00 RPM | 1 .02 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_801 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_801 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_801 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 | ENSECAG00000019011 | 1 retrocopy |
retro_ecab_801 ,
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