RetrogeneDB ID:

retro_ecab_225

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:10:1076119..1076641(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:G3PDH
Ensembl ID:ENSECAG00000022051
Aliases:GAPDH, G3PDH
Description:glyceraldehyde-3-phosphate dehydrogenase [Source:RefSeq peptide;Acc:NP_001157328]


Retrocopy-Parental alignment summary:






>retro_ecab_225
GCTAACGTCATCCTTGACAACTTTGGCATCGTGGAGGGACACATGGCCACAGTCTATGCCATCACTGCCACACAGAAGAC
CATGAACAGTCCCTCTGGGAAGCTGTGGCATGATGCCTGAGGGGCTGCCCACAACATCATCCCTGCTTCTACTGGTGCTG
CCAAGGCTGTGGGCTAGGTCATCCCTGAGCTGAATGGAAAGCTTCCTGGCATGGCCTTCTGTGTCCCCAGCCCTGATGAG
TTGGCCATGCATCTGACCTGCCATCTACAAAAAGCTGTAAAATATGATGACATCAAGAAGGTGGTGAAGTGGGCATCAGA
AGGCCTCCTAAAGGGCATCCTGGGCTATGCTGAGGACAGGTTATCTCCTGTGACTTTAACAGTGACACCCACTCTTCCAC
CTTCGGTCCTGGGGCTGGCATTACCCTCAGCAACCACTTGGTGAAGGTCTTTTCCTGGTATGACAGTGAATTTGACTATA
GCAACGGGGTGGTAGCTGTTAATGGTCCACATGGCCTCCAAG

ORF - retro_ecab_225 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.3 %
Parental protein coverage: 52.25 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGKMWRDGRGAAQNIIPASTGAAKAVGKVIPELNGKLTG
A.VI.D.FGIVEG.M.TV.AITATQKT...PSGK.W.D..GAA.NIIPASTGAAKAVG.VIPELNGKL.G
RetrocopyANVILDNFGIVEGHMATVYAITATQKTMNSPSGKLWHDA*GAAHNIIPASTGAAKAVG*VIPELNGKLPG
ParentalMAFRVPTPNVSVVDLTCRLEKAAKYDEIKKVVKQASEGPLKGILGYTED-QVVSCDFNSDTHSSTFDAGA
MAF.VP.P......LTC.L.KA.KYD.IKKVVK.ASEG.LKGILGY.ED.QV.SCDFNSDTHSSTF..GA
RetrocopyMAFCVPSPDELAMHLTCHLQKAVKYDDIKKVVKWASEGLLKGILGYAED<QVISCDFNSDTHSSTFGPGA
ParentalGIALNDHFVKLISWYDNEFGYSNRVVD-LMAHMASK
GI.L..H.VK..SWYD.EF.YSN.VV..LM.HMASK
RetrocopyGITLSNHLVKVFSWYDSEFDYSNGVVA>LMVHMASK

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 .18 RPM 81 .99 RPM
SRP021940_cerebellum 0 .21 RPM 152 .42 RPM
SRP021940_embryo 0 .20 RPM 128 .63 RPM
SRP021940_placental_villous 0 .14 RPM 79 .05 RPM
SRP021940_synovial_membrane 0 .16 RPM 93 .47 RPM
SRP021940_testis 0 .06 RPM 46 .23 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_225 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_225 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_225 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 390 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Canis familiaris ENSCAFG000000150774 retrocopies
Callithrix jacchus ENSCJAG000000082341 retrocopy
Cavia porcellus ENSCPOG000000263501 retrocopy
Equus caballus ENSECAG00000022051 11 retrocopies
Felis catus ENSFCAG0000000687417 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG000000027803 retrocopies
Myotis lucifugus ENSMLUG0000001432018 retrocopies
Macaca mulatta ENSMMUG0000001867933 retrocopies
Monodelphis domestica ENSMODG0000001806641 retrocopies
Mustela putorius furoENSMPUG0000001689128 retrocopies
Mus musculus ENSMUSG00000057666109 retrocopies
retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Ornithorhynchus anatinus ENSOANG000000044921 retrocopy
Ochotona princeps ENSOPRG0000001251410 retrocopies
Procavia capensis ENSPCAG000000069289 retrocopies
Pteropus vampyrus ENSPVAG0000001257014 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000075389 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



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