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. %
Number of stop codons detected: 2
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalGGDGDDSLYPIAV-LIDELRNEDVQLRLNSIKKLSTIALALGVERTRTE-LLPFLTDTIYDEDEVLLALA
G.DGD.SLY.IAV.LIDELRNEDVQ.RLNSIKKLSTIALALGVERTRT..LLPFLTDTIYDEDE..LA.A
RetrocopyGRDGDESLYLIAV<LIDELRNEDVQPRLNSIKKLSTIALALGVERTRTN<LLPFLTDTIYDEDEAPLAVA
ParentalEQLGNFTGLVGGPDFAHCLLPPLESLATVEETVVRDKAVESLRQISQEHTPVALEAHFVPLVKRL-ASGD
EQLGNFTGL.GGPDFAHCLLPPLESLATVEETV.RDKAVES.R.ISQEHTPVALEA.F.PLVKRL.ASG.
RetrocopyEQLGNFTGLLGGPDFAHCLLPPLESLATVEETVFRDKAVESPR*ISQEHTPVALEARFAPLVKRL>ASGY
ParentalWFTSRTSACGLFSVCYPRASNALKAEIRQCFRSLCT-DDTPMVRRAAA-SKLGEFAKVLELDSVKSEIVP
WFTS.TSACGLFSVCYPRASNALKAEIRQ.F...C...D.....R.AA.SKLGEFAKVLELDSVKSEIVP
RetrocopyWFTSCTSACGLFSVCYPRASNALKAEIRQYFFIPCA<SDDTPMVRRAAASKLGEFAKVLELDSVKSEIVP
ParentalLFTNLASDEQDSVRLLAVEACVSIAQLLSQDDLEALVMPTLRQAAEDKSWRVRYMVADKFSELQKAVGPK
L.T.LASDEQDSVRLLAVEACVSIAQLLSQDDLEAL.MPTL.QAAEDKSWRVRYMVADKFSELQKAVGPK
RetrocopyLLTRLASDEQDSVRLLAVEACVSIAQLLSQDDLEALGMPTL*QAAEDKSWRVRYMVADKFSELQKAVGPK
ParentalITLSDLIPAFQNLLKDCEAEVRAAAAHKVKELCENLPIEGGQGMHGTDMLIYDIELVSDTNQHVKSALAS
IT..DLIPAFQNLL.DCEAEVRAAAAHKV.ELCENLPIEG.........L.Y..ELV.DTNQ.VKSALAS
RetrocopyITVNDLIPAFQNLLQDCEAEVRAAAAHKVRELCENLPIEGRETIITNQILPYRKELVCDTNQDVKSALAS
ParentalVIMGLSTILGKENTIEHLLP-LFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAK
VIMGLSTILGKENTIEHLLP....AQLKDECPEV.LNIISNLDCVNEVIG.RQLSQSLLPAIVELAEDAK
RetrocopyVIMGLSTILGKENTIEHLLP>XXXAQLKDECPEVCLNIISNLDCVNEVIGNRQLSQSLLPAIVELAEDAK
ParentalWRVRLAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLMKLVQKFGTEWAQNTIVPKV
WRVRLAIIEYMPLL.GQLG.EFF.EKLNSLCMAWL.DHVYAIREAATSNLMKLVQKFGTEWAQNTIVPKV
RetrocopyWRVRLAIIEYMPLLVGQLGMEFFEEKLNSLCMAWLMDHVYAIREAATSNLMKLVQKFGTEWAQNTIVPKV
ParentalLVMA-NDPNYLHRMTTLFCINALSEACGQEITTKQMLPIVLKMAGDQVANVRFNV-AKSLQKIGPILDTE
LVMA.NDPNYLHRMTTLFCINALSEA.G.EITTKQML.IVLK.AGDQVANVRFNV.AKSLQKIG.ILDTE
RetrocopyLVMA>NDPNYLHRMTTLFCINALSEAYGREITTKQMLRIVLKTAGDQVANVRFNV<AKSLQKIGTILDTE
ParentalALQEEVKPVLQKLGQDEDMDVKYFAQEAISVLALA
ALQEEVKPVLQKLGQDEDMDVKYF.QEAIS.LALA
RetrocopyALQEEVKPVLQKLGQDEDMDVKYFIQEAISALALA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_233 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

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 ,


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