RetrogeneDB ID: | retro_btau_679 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 17:45268628..45269733(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000006758 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BCAT2 | ||
| Ensembl ID: | ENSBTAG00000009172 | ||
| Aliases: | None | ||
| Description: | Branched-chain-amino-acid aminotransferase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5EA40] |
Retrocopy-Parental alignment summary:
>retro_btau_679
GGCGGATCCAAAGAGGCGGTGGAGACTTTCAAGGCTGAAGATCTAATAATCACACGAGCCACCGTTTTAAAGGAAAAACC
AGACTCCAGTACTCCGGTTTTTGGAACGGTTTTTACAGATCACATGTTAACAGTGGAGTGGTCCTTGGAGCTTGGATGGG
AGAAACCACGCATCAAACCTCTTCAAAACCTCTCACTGCATCCGGGTTCACCGGCTTTCCATTATGCTGTGGAATTATTT
GAAGGGTTGAAGGCATTTCGGGGAGTAGATAATAAAATTCGTCTGTTTTGGCCAAACCTCAACATGGATAGGATGTACCG
ATCTGCTATGAGGGCAACTTTGCCGGCGTTTGACAAGAAAGAGCTTTTAGAGTGTATTCAGCAGCTTGTGAAATTGGATG
AGGAATGGGTCCCCTACTCAACATTTGCGAGTCTATATATCCGTCCTACGTTCATTGGAACTGAGTCTTCTCTGGGAATC
AAGAAGCCGACTAAAGCCCTGCTCTTTGTAATCTTGAGCCCAGTGGGACCTTATTTTTCCACTGGAAGCTTTAATCCTGT
GTCCCTGTGGGCCGAAGTATGTAAGAGCCTGGAAAGGTGGGACCGGAGACTGCAAGATGGGAGGGAGTTATGGCTCATCT
CTTTTTGCCCAATGTGAAGCAGTGGAAAATGCATGTCAGCAGGTTCTGTGGCTCTATGGAGAAGATAATCAAATAACTGA
AGTTGGAACTATGACTCTTTTTCTTTATTGGATAAATGAAGATGGAGAAGAAGAACTGGCAACTCCTCCGCTAGATGGCA
TCATTCTTCCAGGAGTGACGAGGCAGAGCATCCTGGACTTGGCACACCTGTGGGGTGAATTTAAGGTATCAGAGAGACAC
CTAACCATGGATGACTTGACCACAGCTGTGGAGGAGAACCGGGTGAGGGAGATGTTTGGTTCAGGCACCGCCTGTGTTGT
TTGCCCTGTTTCGACTACACTGTACAAGGATGAGACTATACACATTGCAACTATGGAGAATGGTCCTAAGCTTGCAAGCC
GCATCTTAGAAAAACTGACTGATATTCAGTACGGAAGAGAAGACAGCGACTGGACAATCACTGTA
ORF - retro_btau_679 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.65 % |
| Parental protein coverage: | 94.4 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GSRRYASSSFKAADLQLEMTQEPHKKPDPSQPLLFGKTFTDHMLMVEWNQEKGWGQPRIQPFQNLTLHPA |
| G....A...FKA.DL..........KPD.S.P..FG..FTDHML.VEW..E.GW..PRI.P.QNL.LHP. | |
| Retrocopy | GGSKEAVETFKAEDLIITRATVLKEKPDSSTPV-FGTVFTDHMLTVEWSLELGWEKPRIKPLQNLSLHPG |
| Parental | CSALHYSLQLFEGMKAFKGGDQRVRLFRPWLNMERMLRSALRLCLPSFDKIELLECIRRLVEVDQDWVPG |
| ..A.HY...LFEG.KAF.G.D...RLF.P.LNM.RM.RSA.R..LP.FDK.ELLECI..LV..D..WVP. | |
| Retrocopy | SPAFHYAVELFEGLKAFRGVDNKIRLFWPNLNMDRMYRSAMRATLPAFDKKELLECIQQLVKLDEEWVPY |
| Parental | SMGTSLYVRPVLIGNEPSLGVGHPTRALLFVILSPVGAY-FPGDALKPVSLLADPSFIRAWVGGVGNYKL |
| S...SLY.RP..IG.E.SLG...PT.ALLFVILSPVG.Y.FP..AL........P...RAW.GG.G..K. | |
| Retrocopy | STFASLYIRPTFIGTESSLGIKKPTKALLFVILSPVGPY>FPLEAL--ILCPCGPKYVRAWKGGTGDCKM |
| Parental | GGNYGPTVLVQQEAQKKGCEQVLWLYGPDHELTEVGTMNIFVFWTYEDGVLELVTPPLDGIILPGIVRQS |
| GG.YG.....Q.EA....C.QVLWLYG.D...TEVGTM..F..W..EDG..EL.TPPLDGIILPG..RQS | |
| Retrocopy | GGSYGSSLFAQCEAVENACQQVLWLYGEDNQITEVGTMTLFLYWINEDGEEELATPPLDGIILPGVTRQS |
| Parental | LLDLARTWGEFRVVERKITMKEFLRALKDGRVREVFGSGTACQVCPVHQILYQGKHFHIPTMENGPQLIL |
| .LDLA..WGEF.V.ER..TM.....A....RVRE.FGSGTAC.VCPV...LY.....HI.TMENGP.L.. | |
| Retrocopy | ILDLAHLWGEFKVSERHLTMDDLTTAVEENRVREMFGSGTACVVCPVSTTLYKDETIHIATMENGPKLAS |
| Parental | RFHKELKAIQYGSKAHEWMLPV |
| R....L..IQYG.....W...V | |
| Retrocopy | RILEKLTDIQYGREDSDWTITV |
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 .66 RPM |
| ERP005899_muscle | 0 .00 RPM | 4 .49 RPM |
| SRP017611_brain | 0 .09 RPM | 9 .41 RPM |
| SRP017611_kidney | 0 .00 RPM | 9 .78 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .87 RPM |
| SRP030211_testis | 0 .19 RPM | 29 .43 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_679 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_679 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_679 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009172 | 1 retrocopy |
retro_btau_679 ,
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