RetrogeneDB ID: | retro_ecab_233 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 10:19935032..19936795(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP2R1B | ||
| Ensembl ID: | ENSECAG00000012108 | ||
| Aliases: | None | ||
| Description: | protein phosphatase 2, regulatory subunit A, beta [Source:HGNC Symbol;Acc:9303] |
Retrocopy-Parental alignment summary:
>retro_ecab_233
GGCCGAGATGGAGACGAGTCGCTATATCTGATCGCGGTTTAATCGACGAGCTGCGCAATGAGGACGTGCAGCCCCGTCTC
AACAGTATTAAGAAGTTATCCACAATTGCTCTAGCACTTGGAGTAGAAAGGACGCGAACTAACTGCTGCCATTCCTTACA
GACACAATTTATGATGAAGATGAGGCACCGTTAGCTGTTGCAGAGCAGCTGGGAAATTTCACCGGCCTGCTGGGAGGTCC
TGACTTTGCCCACTGTTTGCTGCCTCCTTTGGAAAGCCTGGCGACGGTGGAAGAGACTGTGTTTCGCGACAAGGCGGTGG
AGTCCCCGAGGTAGATCTCCCAGGAGCATACTCCTGTGGCTCTGGAAGCTCGTTTTGCACCTCTGGTGAAACGCCTGGGC
GAGTGGCTATTGGTTCACTTCTTGCACATCTGCCTGTGGTTTGTTCAGCGTTTGCTATCCCAGGGCTTCAAATGCTCTCA
AAGCAGAAATTAGACAATACTTTTTCATTCCTTGTGCTCAGATGACACACCAATGGTACGACGTGCTGCTGCTTCCAAGT
TGGGTGAATTTGCAAAAGTTTTGGAATTAGACAGTGTGAAAAGTGAAATTGTTCCGTTGTTGACTCGTCTAGCTTCAGAT
GAACAGGATTCGGTGCGCCTCCTAGCTGTGGAAGCTTGTGTCAGTATTGCCCAGTTACTGTCTCAGGACGACCTTGAGGC
TTTGGGGATGCCCACCCTTTGACAAGCAGCGGAAGATAAATCCTGGCGAGTTCGCTATATGGTAGCTGACAAATTTTCAG
AGCTCCAGAAAGCTGTGGGTCCTAAAATCACCGTAAATGACCTCATCCCCGCCTTTCAGAACCTACTTCAAGACTGCGAA
GCTGAGGTCCGAGCAGCTGCTGCCCACAAAGTCAGAGAACTTTGTGAGAACTTGCCCATTGAAGGCAGAGAGACCATCAT
TACGAATCAAATTCTGCCCTATAGAAAGGAATTAGTGTGTGATACAAATCAAGATGTCAAATCAGCTCTAGCTTCTGTAA
TTATGGGATTGTCTACAATTTTGGGCAAAGAGAATACCATTGAACATCTTTTACCTCTTTTTTTTAGCTCAGTTAAAGGA
TGAGTGTCCTGAAGTTTGTTTGAATATCATCTCCAATTTAGACTGTGTAAATGAAGTGATTGGCAACCGTCAGCTCTCTC
AGTCTCTCCTTCCTGCCATCGTGGAGCTGGCTGAAGATGCCAAGTGGAGGGTCCGGCTGGCCATCATTGAGTACATGCCT
CTGCTGGTGGGCCAGCTGGGCATGGAATTCTTTGAGGAAAAGCTGAATTCTTTATGTATGGCCTGGCTTATGGACCATGT
ATATGCCATCCGTGAAGCCGCCACCAGCAACCTCATGAAACTAGTTCAGAAGTTTGGTACAGAGTGGGCCCAAAATACCA
TTGTTCCCAAAGTGTTAGTAATGGCAAAATGATCCTAATTACTTACATAGAATGACTACTTTATTCTGCATTAACGCACT
GTCCGAAGCCTATGGTCGAGAAATAACCACTAAACAGATGCTGCGCATCGTATTGAAAACAGCAGGAGACCAAGTAGCGA
ATGTCCGTTTCAATGTGCCAAATCTCTACAGAAAATTGGAACAATTCTAGATACCGAGGCTTTGCAGGAGGAAGTTAAGC
CGGTGCTACAGAAGTTAGGCCAAGATGAAGACATGGATGTCAAATACTTCATACAGGAAGCAATAAGTGCGCTTGCGTTG
GCA
ORF - retro_ecab_233 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.56 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | GGDGDDSLYPIAV-LIDELRNEDVQLRLNSIKKLSTIALALGVERTRTE-LLPFLTDTIYDEDEVLLALA |
| G.DGD.SLY.IAV.LIDELRNEDVQ.RLNSIKKLSTIALALGVERTRT..LLPFLTDTIYDEDE..LA.A | |
| Retrocopy | GRDGDESLYLIAV<LIDELRNEDVQPRLNSIKKLSTIALALGVERTRTN<LLPFLTDTIYDEDEAPLAVA |
| Parental | EQLGNFTGLVGGPDFAHCLLPPLESLATVEETVVRDKAVESLRQISQEHTPVALEAHFVPLVKRL-ASGD |
| EQLGNFTGL.GGPDFAHCLLPPLESLATVEETV.RDKAVES.R.ISQEHTPVALEA.F.PLVKRL.ASG. | |
| Retrocopy | EQLGNFTGLLGGPDFAHCLLPPLESLATVEETVFRDKAVESPR*ISQEHTPVALEARFAPLVKRL>ASGY |
| Parental | WFTSRTSACGLFSVCYPRASNALKAEIRQCFRSLCT-DDTPMVRRAAA-SKLGEFAKVLELDSVKSEIVP |
| WFTS.TSACGLFSVCYPRASNALKAEIRQ.F...C...D.....R.AA.SKLGEFAKVLELDSVKSEIVP | |
| Retrocopy | WFTSCTSACGLFSVCYPRASNALKAEIRQYFFIPCA<SDDTPMVRRAAASKLGEFAKVLELDSVKSEIVP |
| Parental | LFTNLASDEQDSVRLLAVEACVSIAQLLSQDDLEALVMPTLRQAAEDKSWRVRYMVADKFSELQKAVGPK |
| L.T.LASDEQDSVRLLAVEACVSIAQLLSQDDLEAL.MPTL.QAAEDKSWRVRYMVADKFSELQKAVGPK | |
| Retrocopy | LLTRLASDEQDSVRLLAVEACVSIAQLLSQDDLEALGMPTL*QAAEDKSWRVRYMVADKFSELQKAVGPK |
| Parental | ITLSDLIPAFQNLLKDCEAEVRAAAAHKVKELCENLPIEGGQGMHGTDMLIYDIELVSDTNQHVKSALAS |
| IT..DLIPAFQNLL.DCEAEVRAAAAHKV.ELCENLPIEG.........L.Y..ELV.DTNQ.VKSALAS | |
| Retrocopy | ITVNDLIPAFQNLLQDCEAEVRAAAAHKVRELCENLPIEGRETIITNQILPYRKELVCDTNQDVKSALAS |
| Parental | VIMGLSTILGKENTIEHLLP-LFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAK |
| VIMGLSTILGKENTIEHLLP....AQLKDECPEV.LNIISNLDCVNEVIG.RQLSQSLLPAIVELAEDAK | |
| Retrocopy | VIMGLSTILGKENTIEHLLP>XXXAQLKDECPEVCLNIISNLDCVNEVIGNRQLSQSLLPAIVELAEDAK |
| Parental | WRVRLAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLMKLVQKFGTEWAQNTIVPKV |
| WRVRLAIIEYMPLL.GQLG.EFF.EKLNSLCMAWL.DHVYAIREAATSNLMKLVQKFGTEWAQNTIVPKV | |
| Retrocopy | WRVRLAIIEYMPLLVGQLGMEFFEEKLNSLCMAWLMDHVYAIREAATSNLMKLVQKFGTEWAQNTIVPKV |
| Parental | LVMA-NDPNYLHRMTTLFCINALSEACGQEITTKQMLPIVLKMAGDQVANVRFNV-AKSLQKIGPILDTE |
| LVMA.NDPNYLHRMTTLFCINALSEA.G.EITTKQML.IVLK.AGDQVANVRFNV.AKSLQKIG.ILDTE | |
| Retrocopy | LVMA>NDPNYLHRMTTLFCINALSEAYGREITTKQMLRIVLKTAGDQVANVRFNV<AKSLQKIGTILDTE |
| Parental | ALQEEVKPVLQKLGQDEDMDVKYFAQEAISVLALA |
| ALQEEVKPVLQKLGQDEDMDVKYF.QEAIS.LALA | |
| Retrocopy | ALQEEVKPVLQKLGQDEDMDVKYFIQEAISALALA |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .06 RPM | 4 .19 RPM |
| SRP021940_cerebellum | 0 .21 RPM | 14 .33 RPM |
| SRP021940_embryo | 0 .13 RPM | 25 .85 RPM |
| SRP021940_placental_villous | 0 .10 RPM | 21 .27 RPM |
| SRP021940_synovial_membrane | 0 .14 RPM | 14 .82 RPM |
| SRP021940_testis | 0 .51 RPM | 130 .70 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_233 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_233 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_233 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000012108 | 1 retrocopy |
retro_ecab_233 ,
|