RetrogeneDB ID:

retro_ecab_32

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:11:28877674..28879693(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000002842
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSECAG00000019810
Aliases:None
Description:kinesin heavy chain member 2A [Source:HGNC Symbol;Acc:6318]


Retrocopy-Parental alignment summary:






>retro_ecab_32
ATGGCCAGCCAGTTATGCTTCCCTGTCGCTCCCCACCTCTCGTCCTCAAAACCCTTGAAGCCACACTTCGGAGTTCAACT
GGGCCTCTGTGTGGCGATCCAGCGCAGCGACGGACGGATCCACCACGCTGTGGTGACCGAGATCAAAAGAGAAAATGCTT
GGGTCGCCGTAGAGTGGGTTGAAAAAGGAGTCAAAAAAGGCAAGAAGGTTGATCTAGAGACCATATTCCTACTGAATCCA
GCTCTGGTTTCTGTTGAACAGCCCCCACCGTCCAGGTCATTGCCCTCCTTGTCTCTAGGGCCCTCTTCGGCCATCGGGGA
CCAGCGCAAAGCCACGCGGTGGATTGCAACAATCCCCCAGAAAAACGAAACGCCCTCAGGGGACAGCCTGACTGTGAGAG
TCCCCAGCAATCCTTGCCTGATGAAGCAGAAAAAGTCTCCCTGCCTTCGGGAAGTTGAGAAACTGCAAAAGCAGCGGGAG
AAGCGCAGGCAGCTGCAGATGGAGATCAGAGCCCAACGTGCCCTCAGAGTCAACACGGGAAACCCCAACTACGAGATGTT
GCGCATGATCGAAGAGTACCGCAGGCACCTGGACCTCAGCAAGGTGTCCCTCCTGGAACCGCGGGAAGACCATCGCATCT
GCGTCTGCGTGAGAAAGCGGCCTCTCAGCCAGCAAGAGACCACCATGAAGGACCTGGATATCATCACCATCCCCTCCAAC
AACGTGGTCATGGTACACGAGTCCAAGCAAAAGGTGGACCTCACTCGCTACCTGGAGAACCAGATCTTTTGCTTCGATCA
TGCCTTCGATGACACCGCCTCCAACGAGTTAGTGTACCAGTTCACTGCCCAGCCACTGGTGGAGTCCATCTTCCGTAAGG
GCATGGCCACCTGCTTTGCCTATGGGCAGACGGGCAGTGGGAAAACGCATACGATGGGCGGAACTTTTTCTGGAAGGGAC
CAAGATTGTTCTAAAGGCATTTATGCCCTGGTGGCGCAGGATGTCTTCTTCCTACTCAAAACCTTGACTTATGAGAAGCT
AGACCTCAAAGTCTATGGGAGCTTTTTTGAGATTTACGGGGGCAAGGTGTATGATTTGTTGAACTGGAAGAAGAAGTTGC
AAGTCCTTGAGGATGGCAATCAGCAAATCCAGGTGGTCGGGCTACAGGAACAGGAGGTATGTTGTGTGGAGGACGTGCTG
CACCTCGTGGAACTAGGGAACAGCTGCCGGACTTCAGGACAGACCTCTGTCAACGCCCACTCTTCCAGGAGCCACGCCAT
CTTCCAGATCATTCTAAAGTCGCGAGGGAAACTGCACGGCAAGTTTTCCCTCGTTGACTTAGCTGGGAACGAAAGGGGAG
CAGACACTGCCAAGGCCAACCGGAAAAGGCAGCTGGAAGGGGCGGAGATCAATAAGAGTCTCCTGGCTCTCAAAGAATGC
ATTCGGGCTTTGGGTCAGCACAAGTCCCATACCCCATTCAGAGCCAGCAAACTCACACAGGTGCTCCGGGACTCCTTCAT
AGGCCAGAACTCCTCCACTTGCATGATTGCTACTATTTCTCCAGGGATGACCTCTTGCGAAAACACCCTCAACACTTTAA
GATATGCAAATAGAGTAAAAGAATTAACTCTTGATTTAAGGCCCCACCATCGTTGTCTCTATCCAGTTGGACAGGAGGTG
CCTAAGATGTTGGAAAAACACATTAGAAATTCAGAAATGTCCTTTCAGAGGGATAAATTTATTGAAAGACCTTGTATACA
GACTGAGGAGGAGGAAGAGACTAAAGAAATGAAACCAGTAGCCACTCCATTAATGGAGGATACAACGAGTTCTGGGAGGA
AATCAAGCCAATGGCCAGGGACCAACATCCAGGACACAGCCGATGCGGTAAACTATGATGTTGATCTTTGCATTGCCCAG
TTATTGTCCATTTTGGAGCAGAAAGTAGATATTCTGGCTGAGATTCAAAAGAAACTGAAATTATTACGAGCTGACTTCCA
AAAGAAGAGCAAGTCTAGT

ORF - retro_ecab_32 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.44 %
Parental protein coverage: 59.35 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHR
..KS.C..EVEKLQ..REKRR..Q.E.R..RA..V...NPNYE...MI...R..LD........P...HR
RetrocopyQKKSPCLREVEKLQKQREKRRQLQMEIRAQRALRVNTGNPNYEMLRMIEEYRRHLDLSKVSLLEPREDHR
ParentalICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFT
ICVCVRKRPL...ET.MKDLD.ITIPS..VVMVHE.KQKVDLTRYLENQ.F.FD.AFDD.A.NE.VY.FT
RetrocopyICVCVRKRPLSQQETTMKDLDIITIPSNNVVMVHESKQKVDLTRYLENQIFCFDHAFDDTASNELVYQFT
ParentalARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVY
A.PLVE.IF..GMATCFAYGQTGSGKTHTMGG.FSG..QDCSKGIYAL.A.DVF..LK...Y.KL.L.VY
RetrocopyAQPLVESIFRKGMATCFAYGQTGSGKTHTMGGTFSGRDQDCSKGIYALVAQDVFFLLKTLTYEKLDLKVY
ParentalATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSS
..FFEIY.GKV.DLLN.K.KL.VLEDG.QQ.QVVGLQE.EV.CVEDVL.L...GNSCRTSGQTS.NAHSS
RetrocopyGSFFEIYGGKVYDLLNWKKKLQVLEDGNQQIQVVGLQEQEVCCVEDVLHLVELGNSCRTSGQTSVNAHSS
ParentalRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTP
RSHA.FQIIL...GKLHGKFSL.DLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG..K.HTP
RetrocopyRSHAIFQIILKSRGKLHGKFSLVDLAGNERGADTAKANRKRQLEGAEINKSLLALKECIRALGQHKSHTP
ParentalFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKELTVD
FRASKLTQVLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYANRVKELT.D
RetrocopyFRASKLTQVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKELTLD

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 .00 RPM 7 .91 RPM
SRP021940_cerebellum 0 .00 RPM 20 .36 RPM
SRP021940_embryo 0 .00 RPM 56 .49 RPM
SRP021940_placental_villous 0 .24 RPM 17 .37 RPM
SRP021940_synovial_membrane 0 .00 RPM 11 .42 RPM
SRP021940_testis 352 .01 RPM 45 .59 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_32 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_32 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_32 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_69
Pongo abelii retro_pabe_88
Parental genes homology:
Parental genes homology involve 24 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000095191 retrocopy
retro_apla_3,
Bos taurus ENSBTAG000000150221 retrocopy
retro_btau_180,
Choloepus hoffmanni ENSCHOG000000078881 retrocopy
retro_chof_1348,
Cavia porcellus ENSCPOG000000093931 retrocopy
retro_cpor_72,
Dipodomys ordii ENSDORG000000063351 retrocopy
retro_dord_763,
Equus caballus ENSECAG00000019810 1 retrocopy
retro_ecab_32 ,
Homo sapiens ENSG000000687961 retrocopy
retro_hsap_69,
Gorilla gorilla ENSGGOG000000047741 retrocopy
retro_ggor_68,
Macaca mulatta ENSMMUG000000003991 retrocopy
retro_mmul_145,
Monodelphis domestica ENSMODG000000196051 retrocopy
retro_mdom_242,
Mus musculus ENSMUSG000000216931 retrocopy
retro_mmus_68,
Nomascus leucogenys ENSNLEG000000028651 retrocopy
retro_nleu_2329,
Oryctolagus cuniculus ENSOCUG000000104661 retrocopy
retro_ocun_156,
Otolemur garnettii ENSOGAG000000005275 retrocopies
retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps ENSOPRG000000117681 retrocopy
retro_opri_815,
Procavia capensis ENSPCAG000000050891 retrocopy
retro_pcap_22,
Rattus norvegicus ENSRNOG000000140002 retrocopies
retro_rnor_1284, retro_rnor_47,
Sorex araneus ENSSARG000000077681 retrocopy
retro_sara_457,
Sarcophilus harrisii ENSSHAG000000019501 retrocopy
retro_shar_30,
Ictidomys tridecemlineatus ENSSTOG000000127101 retrocopy
retro_itri_40,
Tupaia belangeri ENSTBEG000000093961 retrocopy
retro_tbel_761,
Tarsius syrichta ENSTSYG000000021151 retrocopy
retro_tsyr_1791,
Vicugna pacos ENSVPAG000000088641 retrocopy
retro_vpac_572,
Drosophila melanogaster FBgn00302682 retrocopies
retro_dmel_1, retro_dmel_2,


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