RetrogeneDB ID:

retro_ecab_291

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:14:1979931..1981872(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSECAG00000013510
Aliases:None
Description:Heat shock cognate 71 kDa protein [Source:UniProtKB/Swiss-Prot;Acc:A2Q0Z1]


Retrocopy-Parental alignment summary:






>retro_ecab_291
ACCATGTCTGAGGGACCTGCAGTTGGCATTGATCTTGGCACCACCTACTCGTGTGTGGGTGTTTTCCAGCATGGAAAAGT
GGAAATAATAGCCAATGATCAAGGAAACCGAACCACCCCAAGCTATGTCGCTTTTACTGACACGGAACGATTGATCGGTG
ATGCTGCAAAGAACCAAGTTGCAACGAACCCGACCAACACGGTTTTTGATGCCAAACGTCTGATTGGACGTAGATTTGAT
GATGCTGTTGTCCAGTCTGATATGAAGCATTGGCCCTTCATGGTGGTGAATGATGCAGGCAGGCCCAAGGTCCAAGTAGA
ATACAAGGGAGAGACAAAAAGTTTCTATCCAGAGGAGGTGTCTTCTATGGTTTTGACAAAGATGAAGGAAATCACAGAAG
CCTACCTTGGGAAGACTGTTACCAATGCTGTTGTCACAGTACCTGCTTACTTTAATGACTCTCAGCGTCAGGCTACCAAA
GATGCTGGAACTATTGCTGGTCTCAATGTACTTAGAATCATCAATGAGCCAACTGCTGCTGCTATTGCTTACGGTTTAGA
CAAAAAGGTTGGAGCTGAGAGAAACGTACTGACCTTTGACTTAGGAGGTGGCACTTTCGATGTGTCAATCCTCTCTATTG
AAGATGGAATCTTTGAGGTCAAATCTACAGCTGGAGACACCCACTTAAGTGGAGAAGACTTTGACAACTGAATGGTCAAC
CATTTTATCGCAGAATTCAAGCGCAAGCATAAGAAGGACATCAGTGAGAACAAGAGGGCCGTCCGACGCCTGCGCACTTC
TTGTGAACGTGCTAAGCGTACTCTCTCTTCTAGCACCCAGGCCAGTATTGAGATTGATTCACTCTATGAAGGAATCGACT
TCTATACCTCTATTACCCGTGCCCGATTTGAAGAATTGAATGCTGACCTGTTCCGTGGCACCCTGGACCCTGTAGAGAAA
GCCCTTCGGGATGCCAAGCTGGACAAGACCCAGATTCATGATATTGTCCTAGTGGGTGGTTCTACCTGCATCCCCAAGAT
TCAGAAACTTCTACAGGACTTCTTCAATGGAAAAGAACTGAATAAGAGCATCAACCCTGATGAGGCTGTTGCTTATGGTG
CAGCTGTCCAGGCAGCCATCCTATCTGGAGACAAATCTGAAAATGTTCAAGATTTGCTGCTGTTGGATGTCACTCCTCTT
TCCCTTGGCATGGAAACTGCTGGTGGAGTCATGACTGTGCTCATAAAGTGCAACACTACGATTCCTACCAAGCAGACACA
AACCTTCACTACCTACTCTGACAACCAGCCTGGTGTGCTCATTCAGGTTTATGAAGGTGAGCATGCCATGACCAAGGATA
ACAATCTGCTTGGCAAGTTTGAACTCACAGGCATACCTCCAGCCCCTCGTGGTGTTCCTCAGATTGAAGTCACTTTTGAT
ATTGATGCCAATGGCATTCTCAATGTCTCTGCTGTGGACAAGAGTACAGGGAAAGAAAACAAGATCACCATCACTAACGA
CAAGGGTCGTTTGAGCAAGGAAGACATAGAGTGCATGGTCCAGGAAGCTGAGAAGTACAAGGCTAAAGATGAAAAGCAGC
AGGACAAGGTGTCTTCTAAGAATTCACTTGAGTCCTATGCATTCAACATGAAAGCAACTGTTGAAGATGAAAAACTTCAA
GGCAAGATCAATGACGAGGACAAACAGAAGATTCTTGACAAGCGCAATGAAATCATCAACTGGCTTGACAAGAACCAGAC
TGCAGAGAAGGAAGAATTTGAACATCAGCAGAAAGAGCTGGAGAAAGTTTGCAACTCCATCATTACCAAGCTGTACCAGA
GTGCAGGAAGCATGCCAGGAGGAATGCCTGGGGGTTTCCCTGGTGGTGGAGCTCCTCCATCTGGTGGTGCCTCCTCTGGA
CCCACCATTGAAGAGGTGGAT

ORF - retro_ecab_291 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.06 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFD
TMS.GPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVA.NPTNTVFD
RetrocopyTMSEGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVATNPTNTVFD
ParentalAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTV
AKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEI.EAYLGKTV
RetrocopyAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEITEAYLGKTV
ParentalTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSI
TNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVL.FDLGGGTFDVSI
RetrocopyTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLTFDLGGGTFDVSI
ParentalLTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
L.IEDGIFEVKSTAGDTHL.GEDFDN.MVNHFIAEFKRKHKKDISENKRAVRRLRT.CERAKRTLSSSTQ
RetrocopyLSIEDGIFEVKSTAGDTHLSGEDFDN*MVNHFIAEFKRKHKKDISENKRAVRRLRTSCERAKRTLSSSTQ
ParentalASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
ASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDK.QIHDIVLVGGST.IPKIQKL
RetrocopyASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKTQIHDIVLVGGSTCIPKIQKL
ParentalLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
LQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLG.ETAGGVMTVLIK.NTT
RetrocopyLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGMETAGGVMTVLIKCNTT
ParentalIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
IPTKQTQTFTTYSDNQPGVLIQVYEGE.AMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
RetrocopyIPTKQTQTFTTYSDNQPGVLIQVYEGEHAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
ParentalAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
AVDKSTGKENKITITNDKGRLSKEDIE.MVQEAEKYKA.DEKQ.DKVSSKNSLESYAFNMKATVEDEKLQ
RetrocopyAVDKSTGKENKITITNDKGRLSKEDIECMVQEAEKYKAKDEKQQDKVSSKNSLESYAFNMKATVEDEKLQ
ParentalGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGG
GKINDEDKQKILDK.NEIINWLDKNQTAEKEEFEHQQKELEKVCN.IITKLYQSAG.MPGGMPGGFPGGG
RetrocopyGKINDEDKQKILDKRNEIINWLDKNQTAEKEEFEHQQKELEKVCNSIITKLYQSAGSMPGGMPGGFPGGG
ParentalAPPSGGASSGPTIEEVD
APPSGGASSGPTIEEVD
RetrocopyAPPSGGASSGPTIEEVD

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 1 .71 RPM 93 .27 RPM
SRP021940_cerebellum 4 .47 RPM 421 .85 RPM
SRP021940_embryo 4 .71 RPM 381 .14 RPM
SRP021940_placental_villous 2 .50 RPM 399 .85 RPM
SRP021940_synovial_membrane 7 .03 RPM 245 .97 RPM
SRP021940_testis 1 .02 RPM 210 .82 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_291 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_291 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_291 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Equus caballus ENSECAG00000013510 2 retrocopies
retro_ecab_291 , retro_ecab_628,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Nomascus leucogenys ENSNLEG000000074198 retrocopies
retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Ictidomys tridecemlineatus ENSSTOG000000037561 retrocopy
retro_itri_51,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,




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