RetrogeneDB ID:

retro_ecab_862

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:5:69095771..69097401(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPSS1
Ensembl ID:ENSECAG00000021678
Aliases:None
Description:3'-phosphoadenosine 5'-phosphosulfate synthase 1 [Source:HGNC Symbol;Acc:8603]


Retrocopy-Parental alignment summary:






>retro_ecab_862
ATGGTTTGCCTTGCTATTCCATGCTGCACTTTGGATGGTGACAACATTCATCAAGGTCTCAATAAAAATCTTGGCTTTAG
TCCTGAAGACAGAGAAGAGAATTTCAATGCATTACAGGGGTTGCTAAACTATTTGCAGATGTGGGCTTAGTGTGCATCGC
AAGTTTTATATCGCTTTATACTCAGGATCACAGCAATGCAAGGCAAATTCATGAGGGTGCAAATTTACCTTTTTCTAAAC
TATTTGTTGATGCTCCTAAGCATGTTTGTGGACAGAGAGATGTCAAAGAACTCTACAGACAAGCATGGGCTGGAGAAATT
AAAGATTTCACTGGGATTGATTCTGAATGTGAAAAACCAAGACCCCTGAATTAGTGTTGAAAATAGACTCCTGTGATATA
AATGACTGCATCCAGCAAATTGTGAAACTTCTACAGGAATGGGATATCATACTCATGAATACCTCTTATGAAGTAAAAGA
ACTGTATGTGCCAGAAAATAAACTACATTTGTCAAAAACAGATGCAGAAACATTACTGGCACTGAAAATTAGTAAGTGGA
TATGCAGTGGGTACAGATTTTGTGGAAGGTTGGGAAACCCCACTGAATGACTTTATGAGAGAGAAAGAGTACTTACAATG
CCATCATTTCGATTGTCTTCTGGATGGGGGTGTCATGAACTTGCCAGTGCCTATAGTTCTGATAGCTATTCATGAAGATA
AAGAGAGGCTAGATGGTCAAACAGCATTTGCTCTGATGTAGGAGGGCTGCTATCTGGCTATTTTTCACAGTTCAAAGTTC
TTTGAGCACAGGATGGAAGAGTGCTGTGCCAGACAGTGGGGAACAACGTGCAAGAACCAACCCTACATCAAGATGGTTAT
GGAACAAGGAGGTTGGCTGATTGGAAGAGATCTTCAAGTCTGGGACCAAGTTCATTGGAATGATGGTCTTGGTTAGTATT
GTTTTACTCCGCCCGAGCTAAAGCAGATGTTTAAAGGTATGAATGCTGATGCTATCTTTGCATTTCAATTACATAAGCCA
TTGCTCAACAGACATGCTCTATTAATGCAGGATACCCATTAGCAATTTCTAGAGAGGGGCTACTGGCACCTTGTCCTTTT
CAATCACTTTCTTGATGGCTAGACAAAGGATGATGATGTTCCTTTGGTGTAGTTCTTGAAGCAGCATGCTGCAGTGCTGA
AGGGAGGAGTTCTGAATCCTGAAACAACAGTGATGCCATTTTCCTATCTCCCATGGTGTATGCTGGATCACCTGATGTCC
AGTGGCATTGCAGAGCACGGATGGTTGCAGGAATCAATTTTTACATTATAGGGTGAGACCCTGAGGGTGTGCCTCGTCCA
GAAGCAGGGAAGGATCTTTATGAACCAATTCATGACACCAAAGTGCCGACAATTGCCCCTGGCCTAATCATCTTGGAAAT
GATTGCAACTTAAAACAAGCAAAAGAAGCATATGGACTACTATGACTCTGAACACCATGAAGACTTTGAATTTATTTCAA
GAACACATATGTGCAAACTTAGCTGAGAAGGCCAGAAGTTTCCTGAAGTTTTTGTGACTCCCAAGGCCTAGGCTGTGCTG
ATGGAATACTAGAAATACTTGGAGAAAGCT

ORF - retro_ecab_862 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.1 %
Parental protein coverage: 90.89 %
Number of stop codons detected: 10
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRR-IAEVAKLFADAGLVCITSFISPYTQDRNNARQ
.VC..IPC.TLDGDNI.QGLNKNLGFSPEDREEN....I..VAKLFAD.GLVCI.SFIS.YTQD..NARQ
RetrocopyMVCLAIPCCTLDGDNIHQGLNKNLGFSPEDREENFNA<ITGVAKLFADVGLVCIASFISLYTQDHSNARQ
ParentalIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAGEIKGFTGIDSEYEKP-EAPELVLKTDSCDVNDCV
IHEGA.LPF...FVDAP.HVC.QRDVK.LY..A.AGEIK.FTGIDSE.EKP...PELVLK.DSCD.NDC.
RetrocopyIHEGANLPFSKLFVDAPKHVCGQRDVKELYRQAWAGEIKDFTGIDSECEKP<KTPELVLKIDSCDINDCI
ParentalQQVVELLQERDIVPVDASYEVKELYVPENKLHLAKTDAETLPALKINK-VDMQWVQVL-AEGWATPLNGF
QQ.V.LLQE.DI.....SYEVKELYVPENKLHL.KTDAETL.ALKI.K.VDMQWVQ.L..EGW.TPLN.F
RetrocopyQQIVKLLQEWDIILMNTSYEVKELYVPENKLHLSKTDAETLLALKISK<VDMQWVQIL<VEGWETPLNDF
ParentalMREREYLQCLHFDCLLDGGVINLSVPIVLTATHEDKERLDGCTAFALMYEGRRVAILRNPEFFEHRKEER
MRE.EYLQC.HFDCLLDGGV.NL.VPIVL.A.HEDKERLDG.TAFALM.EG...AI.....FFEHR.EE.
RetrocopyMREKEYLQCHHFDCLLDGGVMNLPVPIVLIAIHEDKERLDGQTAFALM*EGCYLAIFHSSKFFEHRMEEC
ParentalCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRIYWNDGLDQYRFTPTELKQKFKDMNADAVFAFQLR
CARQWGTTCKN.PYIKMVMEQG.WLIG.DLQV.D...WNDGL..Y.FTP.ELKQ.FK.MNADA.FAFQL.
RetrocopyCARQWGTTCKNQPYIKMVMEQGGWLIGRDLQVWDQVHWNDGLG*YCFTPPELKQMFKGMNADAIFAFQLH
ParentalNPVHNGHALLMQDTHQQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLDEGVLNPATTVV-AI
.P..N.HALLMQDTH.Q.LERGY...VL..H.L.G.TKDDDVPL....KQHAAVL..GVLNP.TTV..AI
RetrocopyKPLLNRHALLMQDTH*QFLERGYWHLVLFNHFLDG*TKDDDVPLV*FLKQHAAVLKGGVLNPETTVM<AI
ParentalFPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGLPHPETGKDLYEPTHGAKVLTMAPGLITLEIVPF
F.SPM.YAG...VQWHCRARMVAG.NFYI.G.DP.G.P.PE.GKDLYEP.H..KV.T.APGLI.LE....
RetrocopyFLSPMVYAGSPDVQWHCRARMVAGINFYIIG*DPEGVPRPEAGKDLYEPIHDTKVPTIAPGLIILEMI--
ParentalRVAAYNKKKKQMDYYDSEHNEDFEFISGTRMRKLAREGQKPPEGFMAPKAWTVLMEYYKSLEKA
..A..NK.KK.MDYYDSEH.EDFEFIS.T.M.KL..EGQK.PE.F..PKA..VLMEY.K.LEKA
Retrocopy--AT*NKQKKHMDYYDSEHHEDFEFISRTHMCKLS*EGQKFPEVFVTPKA*AVLMEY*KYLEKA

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 177 .68 RPM
SRP021940_cerebellum 0 .05 RPM 157 .77 RPM
SRP021940_embryo 0 .03 RPM 152 .16 RPM
SRP021940_placental_villous 0 .00 RPM 92 .04 RPM
SRP021940_synovial_membrane 0 .00 RPM 100 .69 RPM
SRP021940_testis 0 .00 RPM 33 .51 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_862 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_862 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_862 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000159051 retrocopy
retro_cjac_1756,
Equus caballus ENSECAG00000021678 1 retrocopy
retro_ecab_862 ,


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