RetrogeneDB ID: | retro_btau_1316 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 4:33283177..33283465(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GTSF1 | ||
| Ensembl ID: | ENSBTAG00000018085 | ||
| Aliases: | GTSF1, FAM112B | ||
| Description: | Gametocyte-specific factor 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZU0] |
Retrocopy-Parental alignment summary:
>retro_btau_1316
CACCAGATTAGGGCCTGCAGGTTTCCTTATCATCTCATCAAGTGGAGAAAGAATCATCCTGACGTCACAAACACATGGGC
TACTTGTCCCTTCAGTGCTCTCCATCAGCTTCCCCAGGCTGAAATCAGTCACCATATATCAAGCTGTGATGACAAAAGGC
GTATTGAGCAGGATGTAGTCAGCCAAATCAGGGACCTTGGACAAGAGACTCTGGCCAAGAGCACGTGGCAGTGCCCTCCT
TGTGATGAAGACTAGGATAAAGATTTCTGGGGAAAGACCAGCACCCCA
ORF - retro_btau_1316 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.17 % |
| Parental protein coverage: | 57.49 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | HQIRACRFPYHLIKCRKNHPDVANKLATCPFNARHQVPRAEISHHISSCDDKSCIEQDVVNQTRSLGQET |
| HQIRACRFPYHLIK.RKNHPDV.N..ATCPF.A.HQ.P.AEISHHISSCDDK..IEQDVV.Q.R.LGQET | |
| Retrocopy | HQIRACRFPYHLIKWRKNHPDVTNTWATCPFSALHQLPQAEISHHISSCDDKRRIEQDVVSQIRDLGQET |
| Parental | MAESTWRCPPCDEDWDKDLWEQTSTP |
| .A.STW.CPPCDED.DKD.W..TSTP | |
| Retrocopy | LAKSTWQCPPCDED*DKDFWGKTSTP |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 0 .07 RPM |
| ERP005899_muscle | 0 .00 RPM | 0 .05 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .06 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .08 RPM |
| SRP030211_testis | 0 .01 RPM | 158 .43 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1316 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1316 was not experimentally validated.