RetrogeneDB ID:

retro_ecab_52

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:28:15584077..15585814(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000002702
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSECAG00000016546
Aliases:None
Description:UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) [Source:HGNC Symbol;Acc:19877]


Retrocopy-Parental alignment summary:






>retro_ecab_52
ATGGCCGTGAGGTGGACCTGGGCTGGCAAAAGCTGCCTGCTGCTGGCGCTTTTAACGGTGGCCTATATCCTGGTGGAAGT
CTCGGTCTCCACTTTCCATGCCTCCCCGGGAACCGGCCTGGCCAGGGATTGGGGATCAAGACAGATCTCCGACCCTGGGG
ACAAGGCAGAGGATTTGTCTCGACCGCTTTATGAGAAGCCCCCTGCGGATTCCCATGCACTTGGGGAGTGGGGGAAAGCC
AGCAAACTCCAGCTCAACGAGGGGGAACTGAAGCAGCAAGAAGAACTCATTGAGAGATATGCCATTAATATTTACCTCAG
TGACAGGATCTCCCTCCACCGCCACATAGAGGATAAAAGAATGTATGAGTGTAAATCCCAGAAGTTCAACTATAGGAAAC
TTCCCACCACGTCTGTTGTTATTGCTTTTTATAATGAAGCCTGGTCGACTCTGCTCCGCACCATCCACAGTGTTCTAGAA
ACTTCTCCTGCAGTCCTTTTGAAGGAGATCATCTTAGTCGATGACTTGAGTGACAGAGTTTATTTGAAGACACAACTTGA
AACTTATATCAGCAATCTTGATAGAGTCCGCTTGATTAGAACAAATAAGCGAGAGGGGCTGGTCAGGGCCCGTCTGATTG
GGGCCACTTTTGCCACTGGGGATGTCCTCACTTTCTTGGATTGTCACTGTGAGTGTAATTCTGGTTGGTTGGAACCACTT
TTGGAAAGGATCAGTAAAGATGAAACGGCAGTTGTGTGTCCTGTCATAGACACCATTGATTGGAATACTTTTGAATTCTA
TATGCAGACTGGGGAGCCCATGATTGGTGGTTTTGACTGGCGTTTAACGTTCCAGTGGCATTCTGTCCCCAAACATGAAA
GGGACAGGCGGAAATCGAGAATTGACCCAATCAGTTCACCCACCATGGCTGGAGGACTGTTTGCTGTCAGCAAGAAGTAT
TTTGAGTACCTTGGAACATATGACACTGGAATGGAAGTGTGGGGAGGTGAAAACCTCGAGCTGTCTTTTAGGGTGTGGCA
GTGTGGAGGTAAATTGGAGATCCACCCCTGTTCCCACGTGGGCCATGTATTCCCGAAACGGGCACCGTATGCTCGGCCCA
ATTTCCTCCAGAATACTGCCCGGGCAGCAGAAGTGTGGATGGACGAGTACAAAGAGCATTTCTACAATCGGAACCCTCCA
GCACGGAAAGAAGCTTATGGTGATATTTCTGAAAGAAAATTACTACGAAAACGACTGAAGTGCAAGAGCTTTGACTGGTA
TTTGAAAAATGTGTTTTCTAATTTGCACGTTCCGGAGGATAGGCCAGGCTGGCACGGAGCTATTCGCAGTATGGGGATCC
CTTCTGAATGTTTAGATTATAATGCTCCTGACAACAACCCTACAGGTGCTAACCTTTCACTGTTTGGATGCCATGGTCAA
GGCGGCAATCAATTCTTTGAATATACTTCAAAGAAAGAAATAAGGTTTAATTCTGTGACGGAGTTATGTGCAGAGGTTCC
TGAGCAAAAAAACCATGTAGGAATGCAAAATTGTCCAAAAGATGGGTTCTCTATTCCAGCAAACATTATTTGGCATTTTA
AAGAAGATGGAACCATTTTTCATCCACACTCAGGACAGTGCCTTAGCGCTTATTGGACACCTGAGGGCCGACCGAATGTT
GAAATGAGAACTTGTCGTGCTCTAGCTAAAAATCAAATCTGGAAGTTTGAGAAATAG

ORF - retro_ecab_52 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.39 %
Parental protein coverage: 99.34 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalCKKKTYDYERLPTTSVVIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDREHLKERLASELSRL
CK.....Y..LPTTSVVIAFYNEAWSTLLRT..SVLETSP..LL.E.ILVDD.SDR..LK..L....S.L
RetrocopyCKSQKFNYRKLPTTSVVIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVYLKTQLETYISNL
ParentalPKVRLIRANKREGLVRARLLGASAAKGDVLTFLDCHCECHEGWLEPLLQRIHEEESAVVCPVIDVIDWNT
..VRLIR.NKREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLL.RI...E.AVVCPVID.IDWNT
RetrocopyDRVRLIRTNKREGLVRARLIGATFATGDVLTFLDCHCECNSGWLEPLLERISKDETAVVCPVIDTIDWNT
ParentalFEYLGNSGEPQIGGFDWRLVFTWHVVPERERLRMRSPTDVIRSPTMAGGLFAVSKKYFEYLGSYDTGMEV
FE.....GEP.IGGFDWRL.F.WH.VP..ER.R..S..D.I.SPTMAGGLFAVSKKYFEYLG.YDTGMEV
RetrocopyFEFYMQTGEPMIGGFDWRLTFQWHSVPKHERDRRKSRIDPISSPTMAGGLFAVSKKYFEYLGTYDTGMEV
ParentalWGGENLEFSFRIWQCGGTLETHPCSHVGHVFPKQAPYSRSKALANSVRAAEVWMDGYKELYYHRNPHARL
WGGENLE.SFR.WQCGG.LE.HPCSHVGHVFPK.APY.R...L.N..RAAEVWMD.YKE..Y.RNP.AR.
RetrocopyWGGENLELSFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYKEHFYNRNPPARK
ParentalEPFGDVTERKQLREKLRCKDFRWFLENVYPELHVPEDRPGCFGMLQNKGLKDYCFDYNPPNENQITGHQV
E..GD..ERK.LR..L.CK.F.W.L.NV...LHVPEDRPG..G.....G....C.DYN.P..N..TG...
RetrocopyEAYGDISERKLLRKRLKCKSFDWYLKNVFSNLHVPEDRPGWHGAIRSMGIPSECLDYNAPDNNP-TGANL
ParentalTLYLCHGMGQNQFFEYTSRNEIRYNTRQPEGCVAVDAGTDILTMHLCKE---VAPENQKFILQDDGSLFH
.L..CHG.G.NQFFEYTS..EIR.N....E.C..V........M..C.......P.N.......DG..FH
RetrocopySLFGCHGQGGNQFFEYTSKKEIRFNS-VTELCAEVPEQKNHVGMQNCPKDGFSIPANIIWHFKEDGTIFH
ParentalIQSKKCVQAERKASGDSFVPLLRDCTDSDHQRWFFKE
..S..C..A.....G...V...........Q.W.F..
RetrocopyPHSGQCLSAYWTPEGRPNVEMRTCRALAKNQIWKFEK

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 .13 RPM 11 .39 RPM
SRP021940_cerebellum 0 .57 RPM 0 .36 RPM
SRP021940_embryo 3 .04 RPM 8 .67 RPM
SRP021940_placental_villous 10 .97 RPM 29 .68 RPM
SRP021940_synovial_membrane 7 .25 RPM 7 .03 RPM
SRP021940_testis 3 .84 RPM 17 .01 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_52 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_52 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_52 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_777
Gorilla gorilla retro_ggor_890
Pongo abelii retro_pabe_949
Macaca mulatta retro_mmul_888
Mus musculus retro_mmus_183
Rattus norvegicus retro_rnor_2453
Oryctolagus cuniculus retro_ocun_1260
Bos taurus retro_btau_1410
Parental genes homology:
Parental genes homology involve 33 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
retro_acar_54,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG000000090371 retrocopy
retro_btau_1410,
Canis familiaris ENSCAFG000000024941 retrocopy
retro_cfam_683,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG00000016546 1 retrocopy
retro_ecab_52 ,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG000000220111 retrocopy
retro_lafr_536,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG000000195611 retrocopy
retro_mmul_888,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
retro_pvam_1347,
Rattus norvegicus ENSRNOG000000080993 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,


Copyright © RetrogeneDB 2014-2017