RetrogeneDB ID:

retro_ecab_1092

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:X:116291333..116292647(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000020943
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ELL2
Ensembl ID:ENSECAG00000022933
Aliases:None
Description:elongation factor, RNA polymerase II, 2 [Source:HGNC Symbol;Acc:17064]


Retrocopy-Parental alignment summary:






>retro_ecab_1092
ATCAAAATCCCCCCAAACAATTCACCAACTGATGTATCCAACTTTAACTTTCAATTGTCAAATGTGAGTAAAGACAACCA
TCAAGACCATACTCAACAAACTGTCTCAGGCTATAGTCCCTCACAGCTCAGTTGGCTGCACTTGAGGCGAGATAAAATGA
CGCAGTGTAGAACAACCAATGCTTCTCAGATAACACCAGTAAGAACCCAGGCAGAAGAGGAATCCTGCAACAAATGGAAA
AAAATTGGAAAGCCATGTGGAAAGAAAAGAATGCCAATTCGGAAAGCACCTCAAGCCATTCCAGATCCAGTGCCTGAGAG
AAAAAGAACAGCGCCCCTTAACCCTGCATACACAATTCGAAAATCACGAGTTCCCAACAGTGTCCGCTTGCGGCCATATA
GGGACAGGGTGATTCACTTACTGGCATTGAAGGACTACAAGAAAACAGAACTGCTTTTTCGACTTCGGAAAGATGGTGTG
GAACAAAATGACGAGAACTCCCTTGAAAATATCCTAAACCAAGTAGCCAATCTGAATACTCAGGATTTTTCATATACCTT
AAAGGATTATGTATTTAAAGAACTCCAAAGAGACTGGCCTGGATACAGTGAACTGGACAAGCAGTCATTGGAGTTGGTGC
TTTCCCAAAGAGTAGATCCATTTCAGAATGCTACTGACATTAATCACTCAGAATCTTCTATAGGTTCTAGTACAAATGAA
ACATCATCTCCTCAGAAATGGCTTTTCAATTCTGCTGTTATTGATCCTTTAAAGAAAAAGAAAGTCAGAATATCTCACCT
GACAACTACAGTACAGTCAACATCAAACGGTCGTTTGAATAACACCAGTGAAAAATCTGCTGTTGGTCTCCCACCACTCT
CTGAAGCTCCTGCCAACCCCATCCCTCCACCATTGCCCACAGCCCGTCTTCCTGTTTCACATGCTCCTCGGCGTGTACGT
TCCAACCGCAGTTCTCGCAGCACTGCAGAAGGACCTGGAACCCCAGATCCAGATGGTGACAGTTTTAGTCAAAACAGTAG
AATCTTCGAGAGCCAGCAGGGTAAACATACTTTGAAAATGATAGCCTCGATAACAATTCCAATTAAGTATTCGAAGCTCA
TGGGGAAAAATTATTTGATGCCTGATAAGTTCAAATATGAAATTGTGAAATGCAAAGCAAAGAGCCAAGAGTACAGTATT
GAGATCACCGAGAAACAGAAAACAGATCCTGAAAGATGCGGTAAAGGTGCAAAGCTGAATTCCGGGGAAGAAGTTGAAAA
GCTTTGCACTGCCTCTGGGAAGACTTGTTCAACA

ORF - retro_ecab_1092 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.54 %
Parental protein coverage: 78.47 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalIKIPKNDPPNEVHTFNFYLSNVGKDNPQGSFDCIQQTFSSSGASQLNCLGFIQDKITVCATNDSYQMTRE
IKIP.N..P..V..FNF.LSNV.KDN.Q...D..QQT.S....SQL..L....DK.T.C.T....Q.T..
RetrocopyIKIPPNNSPTDVSNFNFQLSNVSKDNHQ---DHTQQTVSGYSPSQLSWLHLRRDKMTQCRTTNASQITPV
ParentalRMTQAEEESRNRSTKVIKPGGPYVGKRVQIRKAPQAVSDAVPERKRSTPMNPANTIRKTHGSSSVSQRPY
R.TQAEEES.N...K..KP.G....KR..IRKAPQA..D.VPERKR..P.NPA.TIRK.....SV..RPY
RetrocopyR-TQAEEESCNKWKKIGKPCGK---KRMPIRKAPQAIPDPVPERKRTAPLNPAYTIRKSRVPNSVRLRPY
ParentalRDRVIHLLALKAYKKPELLARLQKDGVNQKDKNSLGAILQQVANLNPKDLSYTLKDYVFKELQRDWPGYN
RDRVIHLLALK.YKK.ELL.RL.KDGV.Q.D.NSL..IL.QVANLN..D.SYTLKDYVFKELQRDWPGY.
RetrocopyRDRVIHLLALKDYKKTELLFRLRKDGVEQNDENSLENILNQVANLNTQDFSYTLKDYVFKELQRDWPGYS
ParentalEIDRRSLESVLSRKLNPSQNAASTSRSESPVCSSRDTASSPQKRLLDSDFIDPLMNKKARISHLTNRVPP
E.D..SLE.VLS....P.QNA.....SES...SS....SSPQK.L..S..IDPL..KK.RISHLT..V..
RetrocopyELDKQSLELVLSQRVDPFQNATDINHSESSIGSSTNETSSPQKWLFNSAVIDPLKKKKVRISHLTTTVQS
ParentalTLNGHLNPTSEKSATGLPPPPAAAAISTPPPPPSAHLPVSNPPQTVNSNSNSPSTPEGRGTQDLPVDSFS
T.NG.LN.TSEKSA.GLPP...A.A...PPP.P.A.LPVS..P..V.SN..S.ST.EG.GT.D...DSFS
RetrocopyTSNGRLNNTSEKSAVGLPPLSEAPANPIPPPLPTARLPVSHAPRRVRSNRSSRSTAEGPGTPDPDGDSFS
ParentalQNGSVYEDQQDKYTSRTSLETLPPGSVLLKCPKPMEENHSMSHKKSKKKSKKHREKDQIKKHDIEMIEEK
QN....E.QQ.K.T....L..........K..K.M..N..M...K.K....K...K.Q.....IE..E..
RetrocopyQNSRIFESQQGKHT----LKMIASITIPIKYSKLMGKNYLMP-DKFKYEIVKCKAKSQ--EYSIEITEKQ
ParentalEEDLKREEEIAKLNDSSPDSNEGVKEGCTAST
..D..R....AKLN............G.T.ST
RetrocopyKTDPERCGKGAKLNSGEEVEKLCTASGKTCST

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 .00 RPM 35 .48 RPM
SRP021940_cerebellum 0 .00 RPM 6 .18 RPM
SRP021940_embryo 0 .00 RPM 4 .19 RPM
SRP021940_placental_villous 0 .00 RPM 13 .18 RPM
SRP021940_synovial_membrane 0 .00 RPM 12 .88 RPM
SRP021940_testis 2 .88 RPM 17 .39 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1092 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1092 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_1092 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000106071 retrocopy
Dasypus novemcinctus ENSDNOG000000051031 retrocopy
Equus caballus ENSECAG00000022933 1 retrocopy
retro_ecab_1092 ,
Homo sapiens ENSG000001189851 retrocopy
Nomascus leucogenys ENSNLEG000000141921 retrocopy
Pongo abelii ENSPPYG000000156471 retrocopy
Pan troglodytes ENSPTRG000000170901 retrocopy



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