RetrogeneDB ID: | retro_btau_1192 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 29:20297259..20298062(-) | ||
| Located in intron of: | ENSBTAG00000001043 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ATPAF1 | ||
| Ensembl ID: | ENSBTAG00000000094 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_btau_1192
AGTGGGAACGGCCGTGGCTCCTGCGGTGATAGGGGGCCCGGCCTCTAGGGCGGCCTGTGCGCAGTTCGCAGCCCCGCCCT
GGGCCTGGGGCTCCTGTCGCCTCGCAGTGATCCCGGTGCGCGCCGCAGCTCCAGCTGGCCCGCCAGGGGCGCCATTGGTA
GCGGGGGTCAGAAAGGCGCTCGAAGCCAACCCCTTCTAGGACCGCTACTGCAAAAAGATCCAGCAGTTGTGCAGGTCTGA
CTCAGCTGCTTTTGAGTCCTGACTAGAGAAGTGCAGTGAGTTTAGCAAGCAGCCAGTGGGGCACTCCAAGCAAGGGGACT
TTATCCCATGTGTGGCACGGAAGACACTGGGGAAACGGCCTGTGAGCCGAGGATTCACTAAGGACTAGACTCTCAGTTCA
ATCTTCAACATTGAGATGGTGAAAGACAAAACTGCCGAAGAAATAAAACAGATTTGGCAGCAGTATTTTGCAGCAAAAGA
GAACAGTCTACGCAGTTATTCCTAAAAAGTTTGATTTGATTTGGAACCGGGCTTAGTCCTGTCCAACATTTCTGTGTGGC
CTACCAAGAAGGGAAGGTTATGAGTTTTTTGTCCGGCAATGGACAGGTACTGAACTCCACTTCACTGCACTTATAAATAT
TCAGATCCCAGGGGAAGCTGCGGCCAGTCAGCTGATTCTATATCATTACCCTGAACTTAAGGAAGAAAATAGTATAGTGC
TAATGACAGCAGAAATGGATTCCACATTTCTGAATGATGCTGAGGCACAGTGCCTGGCCAACAAAGTTCAGCTCTTCTAT
GCA
ORF - retro_btau_1192 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.1 % |
| Parental protein coverage: | 83.59 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AAGGAGPAVLQVAGLYRGLCAVRSRALGLGLVSAAQLRVFPVRRSSGRPAGGADGSA-VGDELEANPFYD |
| ...G.G.......GL..GLCAVRS.A..LGL...........RRSS..PA.GA.GS..V...LEANPF.D | |
| Retrocopy | SGNGRGSCGDRGPGL*GGLCAVRSPA--LGLGLLSPRSDPGARRSSSWPARGAIGSG>VRKALEANPF*D |
| Parental | RYRDKIQQLRRSDPAAFESRLEKRSEFRKQPVGHSRQGDFIKCVEQKTLGKQPVSRGFTKDKTLSSIFNI |
| RY..KIQQL.RSD.AAFES.LEK.SEF.KQPVGHS.QGDFI.CV..KTLGK.PVSRGFTKD.TLSSIFNI | |
| Retrocopy | RYCKKIQQLCRSDSAAFES*LEKCSEFSKQPVGHSKQGDFIPCVARKTLGKRPVSRGFTKD*TLSSIFNI |
| Parental | EMVKGKTAEEIKQIWQQYFAAKD-TVYAVIPKEKFDLIWNRAQSCPTFLCALPRREGYEFFVGQWTGTEL |
| EMVK.KTAEEIKQIWQQYFAAK..TVYAVIPK.KFDLIWNRA.SCPTFLC.LPRREGYEFFV.QWTGTEL | |
| Retrocopy | EMVKDKTAEEIKQIWQQYFAAKE>TVYAVIPK-KFDLIWNRA*SCPTFLCGLPRREGYEFFVRQWTGTEL |
| Parental | HFTALINIQTRGEAAASQLILYHYPELKEEKGIVLMTAEMDSTFLSVAEAQCMANQVQLFYA |
| HFTALINIQ..GEAAASQLILYHYPELKEE..IVLMTAEMDSTFL..AEAQC.AN.VQLFYA | |
| Retrocopy | HFTALINIQIPGEAAASQLILYHYPELKEENSIVLMTAEMDSTFLNDAEAQCLANKVQLFYA |
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 | 22 .49 RPM |
| ERP005899_muscle | 0 .00 RPM | 15 .78 RPM |
| SRP017611_brain | 0 .00 RPM | 20 .42 RPM |
| SRP017611_kidney | 0 .00 RPM | 34 .44 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .86 RPM |
| SRP030211_testis | 0 .04 RPM | 50 .80 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1192 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1192 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1192 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000094 | 1 retrocopy |
retro_btau_1192 ,
|
| Cavia porcellus | ENSCPOG00000003349 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000012737 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000028710 | 1 retrocopy |