RetrogeneDB ID: | retro_btau_458 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 12:9339869..9340475(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSBTAG00000039720 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 225-like [Source:RefSeq peptide;Acc:NP_001091490] |
Retrocopy-Parental alignment summary:
>retro_btau_458
GTAGCCTCCCTGGGCTACCTGCTTATCCTGCTGGTCTCCATCTTCCCCTTCTGGGTGCGGCTGGTGAACGAGGAGTCCCA
GGAAGTGTTCTTCAGTGGCCTGTTTGAGAACTGCTTCCATATCAAGTGCTGGAAGCCTCGACCCTTATCCATTTACGTCA
TCCTCGGCCGAGTCTCCCTGCTGTCCGCCGTTGTCTTGTCTTTCCTCACCACTTTCATCATGGTGTCCTTTGCGTCTCAG
CTCTTTCCGAGGACCCGGAAGCACAATTTTGTGTCAGCCTTCATCAGTTTCCTCACAGGGGCTTGTGCCTTCCTGGCCTT
GTTGCTGCATGCCCTGGAGATCCAGAGTCTGCGGATGAAGCCCAGCCCCCCGCAGTTCTCCATACAGTGGCCTTACTACG
TCCTGGGCTTCAGCATCCTTCTGTTCATGGTGGCTGGTGCCATCTGCCTCATCCAAGAAATAGCCTGCCCTAGATGCCAT
TTGTTGCCCATTTCCCAGAGTACTGAGGACACCCAAGAGATCTCGTACCTGGAAAACCTGGATAGTCTGGGAGGAGAACT
GAGCTCCATGCAGAAGGAGACGCTGCTGAAGGAAGAAACCATTATC
ORF - retro_btau_458 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.01 % |
| Parental protein coverage: | 89.38 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LTSLGYLLILLVSIFPFWVRLVNEESQEVFFSGLFENCFHIKCWKPRPLSIYVILGRVSLLSAVVLSFLT |
| ..SLGYLLILLVSIFPFWVRLVNEESQEVFFSGLFENCFHIKCWKPRPLSIYVILGRVSLLSAVVLSFLT | |
| Retrocopy | VASLGYLLILLVSIFPFWVRLVNEESQEVFFSGLFENCFHIKCWKPRPLSIYVILGRVSLLSAVVLSFLT |
| Parental | TFIMVSFASQLFPRTRKHNFVSAFISFLTGACAFLALLLHALEIQSLRMKPSPPQFSIQWPYYVLGFSIL |
| TFIMVSFASQLFPRTRKHNFVSAFISFLTGACAFLALLLHALEIQSLRMKPSPPQFSIQWPYYVLGFSIL | |
| Retrocopy | TFIMVSFASQLFPRTRKHNFVSAFISFLTGACAFLALLLHALEIQSLRMKPSPPQFSIQWPYYVLGFSIL |
| Parental | LFMVAGAICLIQEIACPRCHLLPISQSTEDTQEISYLENLDSLGGELSSMQKETLLKEETII |
| LFMVAGAICLIQEIACPRCHLLPISQSTEDTQEISYLENLDSLGGELSSMQKETLLKEETII | |
| Retrocopy | LFMVAGAICLIQEIACPRCHLLPISQSTEDTQEISYLENLDSLGGELSSMQKETLLKEETII |
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 | 1 .87 RPM |
| ERP005899_muscle | 0 .05 RPM | 4 .91 RPM |
| SRP017611_brain | 0 .09 RPM | 5 .25 RPM |
| SRP017611_kidney | 0 .06 RPM | 5 .51 RPM |
| SRP017611_liver | 0 .08 RPM | 1 .21 RPM |
| SRP030211_testis | 0 .95 RPM | 66 .06 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_458 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_458 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_458 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000039720 | 2 retrocopies |
retro_btau_1081, retro_btau_458 ,
|