RetrogeneDB ID:

retro_ecab_1061

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:X:41972115..41973614(+)
Located in intron of:ENSECAG00000006020
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSECAG00000017673
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ecab_1061
CCACCTAGGCCGTGCTGGCCCCCAGCCAGCAGCCCGAGGTCTTCTACAACCAGATCTTCATAAACAAGGAGTGGCATGAC
GCCATCAGCAAGAAAACATTCCCTACCGTCAATCCGTCCACTGGGGAGGTCATCTGTTGGGTAGCTACAGGTGACAAGGA
AGATGTGGACAGGGCAGTGAAGGCTGCCCGGGCCACCTTTCAGCTTGGCTTGCCCTGGCACTGCATGGATGCGTCCAACA
GGGGTCGGCTGCTAAACCACCTGGCCGATCTGATTGAGTGGGACCAGACCTACCTGGCAGCCTTGGAGACCCTGGATAAT
GGCAAGCCGTACGTTATCTCTTACCTGGTGGATTTGGACATGGTCCTCAAATGTCTCCGTTATTATGCCAGCTGGGCCGA
GTAGTACCATGGGAAAACCATTCTCATCGATGGGGACTTCTTCAGCTACACCCTGCATGAACCTGTGGGGGTGTGCAGGC
AGATCATTCCATGGAACTTCCCTCTCTTCATGCAAGCATGGAAACTGGGCCCAGGCCTTGGCAACTGGAAACGTGGTTGT
AATGAAGGTGGCTGAGCAGACTCCACTCACTGCCCTCTATGTGGCCAACTTGATTAAGGAGGCTGGCTTTCCCCCTGGTG
TGGTCAATATTGTTCTTGGATTTGGCCCCATGGGTGGGGCTACCATTGCCTCCCATGAGGATGTGGACAAAGTGACTTTC
ACAGGCTCCACTGAGGTTAGCCACCTAATCTAGGTTGCTGTGGGGAGAGGTAACCTCAAGAAAGTCACCCTGGAGCTTGG
AGGGAAAAGCCCCAATATCCATAATGTCAGATGCTGATATGGACTGGGTGGTGGAGCAGACCCACTTTGCCCTGTTCTTC
AGCCAGGGCCAGTGCTGCTGTGGGGGCTCCCGGACCTTTGTGCAGGAGGATGTTTACACTGAGTTTGTGGAGCACAGCGT
TGCCCAGGCCCGGTCTCGGTCTGGTGTGGTCAGGAACCCCTTTGACAGCCAGACCAAGCAGGGGCCACAGGTGGATGAAA
CTCAGTTTAAGAAGGTCCTGGGCAATATCAAATCTGGGAAGGAAGAGGGGGGCGAAGCTGCTGTGTGGTGGAGGGACAGC
TGCTGACCATGGCTACTTCATCCAGCCCACCGTGTTTGGAGATGTGCAAGATGGCATGATAGTCGCAAAGGAGCAGATCT
TTGGGCCAGTGATGCAGATCCTGAAGTTGAAGACCATAGAGGAAGTCGTTGGGAGAGCCAACAATTCCAAGTATAAGCTG
GCCGTAGCTGTCTTCATGAAGGACTTGGACAAGGCCAAGTATCTGTCCCAAGCCCTCTAGGCTGGCACTGTGTGGATCAA
CTGCTATGACGTGTTTAGGGCCCAGTCACTATTTGGTAGCTACAAGATGTCTGGGAATGGCCAGGAGCTGGGAGAGTATG
GCCTGCAGGCATATACCAAAGTGAGAACTGTCACAATCAGAGTTCCTCAGAAGAACTCA

ORF - retro_ecab_1061 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.28 %
Parental protein coverage: 99.6 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalPPRAC-RLPNQQPEVFYNQIFINNEWHDAVSKKTFPTVNPSTGEVICQVAAGDKEDVDRAVKAARAAFQL
PPR.C...P.QQPEVFYNQIFIN.EWHDA.SKKTFPTVNPSTGEVIC.VA.GDKEDVDRAVKAARA.FQL
RetrocopyPPRPC<LAPSQQPEVFYNQIFINKEWHDAISKKTFPTVNPSTGEVICWVATGDKEDVDRAVKAARATFQL
ParentalGSPWRRMDASDRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK
G.PW..MDAS.RGRLLN.LADLIE.D.TYLAALETLDNGKPYVISYLVDLDMVLKCLRYYA.WA..YHGK
RetrocopyGLPWHCMDASNRGRLLNHLADLIEWDQTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYASWAE*YHGK
ParentalTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGP-ALATGNVVVMKVAEQTPLTALYVANLTKEA
TI.IDGDFFSYT.HEPVGVC.QIIPWNFPL.MQAWKLGP.ALATGNVVVMKVAEQTPLTALYVANL.KEA
RetrocopyTILIDGDFFSYTLHEPVGVCRQIIPWNFPLFMQAWKLGP>ALATGNVVVMKVAEQTPLTALYVANLIKEA
ParentalGFPPGVVNVVPGFGPTAGAAIASHEDVDKVAFTGSTEVGHLIQVAAGRSNLKKVTLELGGKSPNI-IMSD
GFPPGVVN.V.GFGP..GA.IASHEDVDKV.FTGSTEV.HLI.VA.GR.NLKKVTLELGGKSPNI.IMSD
RetrocopyGFPPGVVNIVLGFGPMGGATIASHEDVDKVTFTGSTEVSHLI*VAVGRGNLKKVTLELGGKSPNI>IMSD
ParentalADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDVYAEFVERSVARARSR--VVGNPFDSQTEQGPQVDET
ADMDW.VEQ.HFALFF.QGQCCC.GSRTFVQEDVY.EFVE.SVA.ARSR..VV.NPFDSQT.QGPQVDET
RetrocopyADMDWVVEQTHFALFFSQGQCCCGGSRTFVQEDVYTEFVEHSVAQARSRSGVVRNPFDSQTKQGPQVDET
ParentalQFNKVLGYIKSGKEE-GAKLLCGGGAAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVV
QF.KVLG.IKSGKEE.GAKLLCGGG.AAD.GYFIQPTVFGDVQDGM..AKE.IFGPVMQILK.KTIEEVV
RetrocopyQFKKVLGNIKSGKEE>GAKLLCGGGTAADHGYFIQPTVFGDVQDGMIVAKEQIFGPVMQILKLKTIEEVV
ParentalGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWINCYDVFGAQSPFGGYKMSGNGRELGEYGLQAYTE
GRANNSKY.LA.AVF.KDLDKA.YLSQAL.AGTVWINCYDVF.AQS.FG.YKMSGNG.ELGEYGLQAYT.
RetrocopyGRANNSKYKLAVAVFMKDLDKAKYLSQAL*AGTVWINCYDVFRAQSLFGSYKMSGNGQELGEYGLQAYTK
ParentalVKTVTIKVPQKNS
V.TVTI.VPQKNS
RetrocopyVRTVTIRVPQKNS

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 .24 RPM 300 .46 RPM
SRP021940_cerebellum 0 .26 RPM 217 .39 RPM
SRP021940_embryo 1 .51 RPM 125 .79 RPM
SRP021940_placental_villous 0 .72 RPM 129 .52 RPM
SRP021940_synovial_membrane 1 .18 RPM 191 .67 RPM
SRP021940_testis 1 .79 RPM 302 .77 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_1061 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_1061 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_1061 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136641 retrocopy
retro_amel_51,
Bos taurus ENSBTAG000000087431 retrocopy
retro_btau_48,
Canis familiaris ENSCAFG000000086831 retrocopy
retro_cfam_1493,
Equus caballus ENSECAG00000017673 2 retrocopies
retro_ecab_1054, retro_ecab_1061 ,
Felis catus ENSFCAG000000220001 retrocopy
retro_fcat_1590,
Homo sapiens ENSG000001112751 retrocopy
retro_hsap_19,
Gorilla gorilla ENSGGOG000000071081 retrocopy
retro_ggor_33,
Latimeria chalumnae ENSLACG000000117981 retrocopy
retro_lcha_108,
Microcebus murinus ENSMICG000000034871 retrocopy
retro_mmur_19,
Myotis lucifugus ENSMLUG000000170841 retrocopy
retro_mluc_1918,
Macaca mulatta ENSMMUG000000083361 retrocopy
retro_mmul_247,
Mustela putorius furoENSMPUG000000022821 retrocopy
retro_mputfur_27,
Mus musculus ENSMUSG000000294551 retrocopy
retro_mmus_222,
Nomascus leucogenys ENSNLEG000000000161 retrocopy
retro_nleu_22,
Otolemur garnettii ENSOGAG000000330931 retrocopy
retro_ogar_203,
Pongo abelii ENSPPYG000000049661 retrocopy
retro_pabe_32,
Pteropus vampyrus ENSPVAG000000131891 retrocopy
retro_pvam_163,
Rattus norvegicus ENSRNOG000000013441 retrocopy
retro_rnor_307,
Sus scrofa ENSSSCG000000098891 retrocopy
retro_sscr_9,
Ictidomys tridecemlineatus ENSSTOG000000150091 retrocopy
retro_itri_33,
Xenopus tropicalis ENSXETG000000209301 retrocopy
retro_xtro_12,


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