RetrogeneDB ID: | retro_btau_1779 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:125008985..125010749(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP2R1A | ||
| Ensembl ID: | ENSBTAG00000019851 | ||
| Aliases: | None | ||
| Description: | serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform [Source:RefSeq peptide;Acc:NP_001032554] |
Retrocopy-Parental alignment summary:
>retro_btau_1779
ATGGCGGCGGCTGACGGCGATAACTCGCTCGACCCCATGTCGATCCTCATAGACGAGCTCCAGAATGAGGACATTCAGCT
TCGCATCAACAGCATCAATAAGCTGTCCACCATCGCGTTGGCCCTTGGAGTCGAAAAGACCCGCAGTGAGCTTCTGCCCC
TCATTATAGACATTATGTACGACGAGGACGAGGTCCTCTTGGCCCTAGCGGAGCAGCTGGGCACCTTCACCCCTCTGGTC
GGAGGTCCTGAGTATGTTCACCACCTGCTTCCACCCCTAGAGTTGCTGGCTGTGGAGGAGGAGGCCATAGTGCGGGAGAA
GGCGGTGCAGTCCCTGAGGGCCATCTCGCATGAGCACTCACCCTCCCATCTCGAGGACTACTTTGTGCCACTCGTGAAGC
GGCTGGTGGGCGGCAACTTGGTCAACTCCCGCATCTCAGCCTGCAGCCTTTTCTCCGTCTGCTACCCTGGCGTGTCCATT
GCCATCAAGGCAGAACTTCTACAGTGCTTCCGGGATCTGTGCTCAGACAACAGCCTCGTGGTGCGGAGTGCAGCAGCCTC
CAACCTGGGGGATTTCACCAAGGTGCTTGAGATTGACGACATGAAGAGTGAGATCATCCCCATATTCTCCAACCTGGCCT
CTGACGAGCAGGATTCAGTGCGGCTGCTAATGGTGGAAGTGTGCGTGAACATCGCCCAGCTCCTGCCCCAGGACATCCTA
GAGGCCCTGGTGATGATTACTCTGTGCCAGGCTGCTGAGGACACATCCTGGCGCGTCCGTTACATGGTGGCCGAGAAGTT
CACAGAGCTCCAGACAGCAGTGAGGCCTGAGATCACCAAAACGGGCCTGGTCCCTGCCTTCCAGAACCTGATGCAAGACC
ATGAGCCTGAGGTGAGGGCCGCTGCCTCCTACAAGCTCAAAGAATTCTGTGAAAATCTCTCCGCTGACTATCGGGAGAAT
GTGATCCTGACCGAGATCTTGCCTTTCAGCCAGGAGCTGGTCTCAGATACCAACCAGCATGTCAGGTCAGCCCTGGCCTC
CGTCATCCTAGGCCTCTGCCCCATCCTGGGCAAAGATAACACCATCGAGCACATCATGCCCCTCTTCCTGGCTCTGCTGA
GGGATGAGTGCTCTGATGTGCGGCTGAACGTCATCTCTAACCTCCATTACATGAAAGAGGTGATCGGCATCCAGGATCTG
TCCCATTTCCTGCTCCCCACCATCATGGAGCTTGCAGAGGATGCCAACTGGCGGGTGCGTCTGGTCATCATTGAGTACAT
GCCTCTTCTGGCTGGACAGTTTGGGCTGGAGTTCTTTGATGCACAGCTCCACTCCTTGTGCATGTCCTGGCTTGTGGATC
ATGTCTATGCCATCCGCGAGGCGGCCACCAACAACCTGAAGAAGCTGGTGGAGCAGTTTGGGAAGGAGTGGGCCCTTGCC
GCTGTCATCCCGAGGGTCCTCACCCTGTCTGAGGAACCCAACTACCTGCACCGCATGACTACACTCTTCTGCATCAATGT
GCTGTCTGAGGTCTGTGGGCAGGATATCACCACCAAGCACATGCTGCCCACAGTGCTGTATATGGCTGGGGACCCTGTCG
CCAATGTCCGCTTCAATGTGGCCAAGTCCCTACAGAAGATTGGGTCCATCCTGGAAAACAGCACACTGCAGACTGAGGTC
AAGCCCATCCTGGAGAAGCTGACCCAGGACCGAGATGTGGATGTCAAGTACTTTGCCCAGGAGGCTCTGACTGTCCTGTC
TCTT
ORF - retro_btau_1779 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.59 % |
| Parental protein coverage: | 99.83 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAADGDDSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEVLLALA |
| MAAADGD.SL.P...LIDEL.NED.QLR.NSI.KLSTIALALGVE.TRSELLP...D..YDEDEVLLALA | |
| Retrocopy | MAAADGDNSLDPMSILIDELQNEDIQLRINSINKLSTIALALGVEKTRSELLPLIIDIMYDEDEVLLALA |
| Parental | EQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLEAHFVPLVKRLAGGDW |
| EQLGTFT.LVGGPEYVH.LLPPLE.LA..EE..VR.KAV.SLRAISHEHSPS.LE..FVPLVKRL.GG.. | |
| Retrocopy | EQLGTFTPLVGGPEYVHHLLPPLELLAVEEEAIVREKAVQSLRAISHEHSPSHLEDYFVPLVKRLVGGNL |
| Parental | FTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAAASKLGEFAKVLELDNVKSEIIPMFS |
| ..SR.SAC.LFSVCYP.VS.A.KAEL.Q.FR.LCSD....VR.AAAS.LG.F.KVLE.D..KSEIIP.FS | |
| Retrocopy | VNSRISACSLFSVCYPGVSIAIKAELLQCFRDLCSDNSLVVRSAAASNLGDFTKVLEIDDMKSEIIPIFS |
| Parental | NLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVMPTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITK |
| NLASDEQDSVRLL.VE.CVNIAQLLPQ..LEALVM.TL.QAAED.SWRVRYMVA.KFTELQ.AV.PEITK | |
| Retrocopy | NLASDEQDSVRLLMVEVCVNIAQLLPQDILEALVMITLCQAAEDTSWRVRYMVAEKFTELQTAVRPEITK |
| Parental | TDLVPAFQNLMKDCEAEVRAAASHKVKEFCENLSADCRENVIMTQILPCIKELVSDANQHVKSALASVIM |
| T.LVPAFQNLM.D.E.EVRAAAS.K.KEFCENLSAD.RENVI.T.ILP...ELVSD.NQHV.SALASVI. | |
| Retrocopy | TGLVPAFQNLMQDHEPEVRAAASYKLKEFCENLSADYRENVILTEILPFSQELVSDTNQHVRSALASVIL |
| Parental | GLSPILGKDSTIEHLLPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVR |
| GL.PILGKD.TIEH..PLFLA.L.DEC..VRLN.ISNL....EVIGI..LS..LLP.I.ELAEDA.WRVR | |
| Retrocopy | GLCPILGKDNTIEHIMPLFLALLRDECSDVRLNVISNLHYMKEVIGIQDLSHFLLPTIMELAEDANWRVR |
| Parental | LAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPKVLAMS |
| L.IIEYMPLLAGQ.G.EFFD..L.SLCM.WLVDHVYAIREAAT.NLKKLVE.FGKEWA.A..IP.VL..S | |
| Retrocopy | LVIIEYMPLLAGQFGLEFFDAQLHSLCMSWLVDHVYAIREAATNNLKKLVEQFGKEWALAAVIPRVLTLS |
| Parental | GDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQKIGPILDNSTLQSEV |
| ..PNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVL.MAGDPVANVRFNVAKSLQKIG.IL.NSTLQ.EV | |
| Retrocopy | EEPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLYMAGDPVANVRFNVAKSLQKIGSILENSTLQTEV |
| Parental | KPVLEKLTQDQDVDVKYFAQEALTVLSL |
| KP.LEKLTQD.DVDVKYFAQEALTVLSL | |
| Retrocopy | KPILEKLTQDRDVDVKYFAQEALTVLSL |
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 | 17 .09 RPM |
| ERP005899_muscle | 0 .00 RPM | 155 .89 RPM |
| SRP017611_brain | 0 .00 RPM | 398 .87 RPM |
| SRP017611_kidney | 0 .00 RPM | 110 .78 RPM |
| SRP017611_liver | 0 .00 RPM | 58 .97 RPM |
| SRP030211_testis | 6 .77 RPM | 151 .90 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1779 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1779 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1779 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000019851 | 2 retrocopies |
retro_btau_1778, retro_btau_1779 ,
|
| Cavia porcellus | ENSCPOG00000008583 | 1 retrocopy |