RetrogeneDB ID:

retro_ecab_82

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:19:37029252..37030245(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000005033
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:WDR5
Ensembl ID:ENSECAG00000017389
Aliases:None
Description:WD repeat domain 5 [Source:HGNC Symbol;Acc:12757]


Retrocopy-Parental alignment summary:






>retro_ecab_82
ATGGCGGCGAAGGAGTCGGGCGATGCAGGAGCGGAGTCGGCCCTCTGCCCATCAGCCAATCCGAGCCAGCAAGCCTCTGA
AAAACCAAACTATGCCCTCAAGTGTACTCTCGTGGGACACACGGAAGCCGTATCATCAGTTAAGTTTAGTCCTAGTGGAG
AATGGCTAGCAAGTTCTTCTGCTGATAAAGTAATTATTATTTGGGGAGCCTATGATGGAAAATATGAGAAAACACTTTAT
GGTCACAGTCTGGAAATATCAGACGTTGCGTGGTCATCAGATTCCAGTCGTCTTGTTTCTGCCTCAGATGATAAAACTCT
AAAGATTTGGGATGTGAGATCTGGAAAATGTTTGAAAACGCTGAAGGGGCACAGTAATTATGTTTTTTGCTGTAATTTCA
ATCCACCATCCAACCTCATCATTTCAGGATCTTTTGATGAGAGCGTGAAAATATGGGAGGTGAAAACAGGAAAGTGCCTC
AAGACTTTGTCTGCTCATTCTGACCCAGTTTCTGCTGTTCATTTTAATTGTAGCGGCTCCTTGATAGTGTCAGGTAGCTA
TGATGGTGTCTGTAGAATCTGGGATGCTGCATCAGGTCAGTGTTTAAAAATGCTTGTTGATGATGATAATCCTCCAGTCT
CTTTTGTAAAATTTTCTCCGAATGGTAAATATCTGCTCATTGCAACTTTGGACAATACTCTCAAACTATGGGATTATAGC
AGAGGCAGATGCCTGAAGACATACACGGGTCATAAGAATGAGAAATACTGCATATTTGCCAATTTTTCAGTTACTGGTGG
AAAGTGGATTGTGTCTGGTTCAGAGGATAACCTGGTTTACATTTGGAACCTCCAGACTAAAGAGATTGTACAGACATTAC
AAGGTCATACAGATGTCGTAATCTCAGCAGCTTGTCATCCTACAGAAAACATCATTGCATCAGCAGCATTAGGAAATGAC
AGAACAATTAAACTGTGGACGAGTAACTACTAA

ORF - retro_ecab_82 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.69 %
Parental protein coverage: 97.31 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGK
E...A.A......SA..S.....KPNYALK.TL.GHT.AVSSVKFSP.GEWLASSSADK.I.IWGAYDGK
RetrocopyESGDAGAESALCPSANPSQQASEKPNYALKCTLVGHTEAVSSVKFSPSGEWLASSSADKVIIIWGAYDGK
ParentalFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGS
.EKT..GH.L.ISDVAWSSDS..LVSASDDKTLKIWDV.SGKCLKTLKGHSNYVFCCNFNP.SNLI.SGS
RetrocopyYEKTLYGHSLEISDVAWSSDSSRLVSASDDKTLKIWDVRSGKCLKTLKGHSNYVFCCNFNPPSNLIISGS
ParentalFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVS
FDESV.IW.VKTGKCLKTL.AHSDPVSAVHFN..GSLIVS.SYDG.CRIWD.ASGQCLK.L.DDDNPPVS
RetrocopyFDESVKIWEVKTGKCLKTLSAHSDPVSAVHFNCSGSLIVSGSYDGVCRIWDAASGQCLKMLVDDDNPPVS
ParentalFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
FVKFSPNGKY.L.ATLDNTLKLWDYS.G.CLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
RetrocopyFVKFSPNGKYLLIATLDNTLKLWDYSRGRCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
ParentalQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSD
QTKEIVQ.LQGHTDVVIS.ACHPTENIIASAAL.ND.TIKLW.S.
RetrocopyQTKEIVQTLQGHTDVVISAACHPTENIIASAALGNDRTIKLWTSN

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 2 .66 RPM 6 .49 RPM
SRP021940_cerebellum 1 .87 RPM 16 .15 RPM
SRP021940_embryo 3 .45 RPM 34 .22 RPM
SRP021940_placental_villous 2 .21 RPM 17 .32 RPM
SRP021940_synovial_membrane 2 .20 RPM 20 .97 RPM
SRP021940_testis 2 .05 RPM 75 .90 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_82 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_82 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_82 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_11
Pan troglodytes retro_ptro_18
Gorilla gorilla retro_ggor_171
Macaca mulatta retro_mmul_190
Callithrix jacchus retro_cjac_1
Mus musculus retro_mmus_132
Rattus norvegicus retro_rnor_258
Bos taurus retro_btau_299
Sus scrofa retro_sscr_1
Canis familiaris retro_cfam_128
Parental genes homology:
Parental genes homology involve 26 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000111791 retrocopy
retro_amel_29,
Bos taurus ENSBTAG000000470311 retrocopy
retro_btau_299,
Canis familiaris ENSCAFG000000198301 retrocopy
retro_cfam_128,
Callithrix jacchus ENSCJAG000000101231 retrocopy
retro_cjac_1,
Cavia porcellus ENSCPOG000000147901 retrocopy
retro_cpor_12,
Dipodomys ordii ENSDORG000000150101 retrocopy
retro_dord_7,
Equus caballus ENSECAG00000017389 1 retrocopy
retro_ecab_82 ,
Echinops telfairi ENSETEG000000157311 retrocopy
retro_etel_15,
Felis catus ENSFCAG000000057121 retrocopy
retro_fcat_119,
Homo sapiens ENSG000001963631 retrocopy
retro_hsap_11,
Gorilla gorilla ENSGGOG000000049972 retrocopies
retro_ggor_171, retro_ggor_2023,
Loxodonta africana ENSLAFG000000111921 retrocopy
retro_lafr_55,
Microcebus murinus ENSMICG000000080851 retrocopy
retro_mmur_34,
Myotis lucifugus ENSMLUG000000022361 retrocopy
retro_mluc_11,
Macaca mulatta ENSMMUG000000141591 retrocopy
retro_mmul_190,
Mustela putorius furoENSMPUG000000121841 retrocopy
retro_mputfur_2,
Mus musculus ENSMUSG000000269171 retrocopy
retro_mmus_132,
Nomascus leucogenys ENSNLEG000000134721 retrocopy
retro_nleu_63,
Otolemur garnettii ENSOGAG000000089601 retrocopy
retro_ogar_86,
Procavia capensis ENSPCAG000000134761 retrocopy
retro_pcap_43,
Pan troglodytes ENSPTRG000000236532 retrocopies
retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus ENSPVAG000000016661 retrocopy
retro_pvam_112,
Rattus norvegicus ENSRNOG000000082121 retrocopy
retro_rnor_258,
Sus scrofa ENSSSCG000000249121 retrocopy
retro_sscr_1,
Ictidomys tridecemlineatus ENSSTOG000000158991 retrocopy
retro_itri_117,
Drosophila melanogaster FBgn00400661 retrocopy
retro_dmel_69,




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