RetrogeneDB ID:

retro_ecab_910

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:6:61538559..61539005(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFA12
Ensembl ID:ENSECAG00000015836
Aliases:None
Description:NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 [Source:HGNC Symbol;Acc:23987]


Retrocopy-Parental alignment summary:






>retro_ecab_910
CTGAAGGACATGACTGAGTTCCCATGGGTCCTGAAGAATGGTCTGCAGCAGGTCAGTAGCCACGGTGGCCTCTGAGCCTA
TCTACAAATTTTCTTCGGTGCAAATGATATGAGGATTGGTACATTAGAGGAGGGAGGCAAATATGGAGACAAATACTATG
AAGACAACAAGTAGTTTTTTGGCTGTCACCGATGGGTTATATATACTCCTGACAGGAATGACAGAAACACATTCTGGGAT
GTAGATGGAAGCATGGTGCCCCATGAATGGCATCTTTGGCTTCATTGTATGACCAATGATTCTCCAACAGCAAAACCACC
TATTGCTCATAAATTCATTTGGACAAACCATAAATTCAATGGAGTGGCACTCCAGAACAATATGCAGCTTATTCTACCAC
TAGAAAGAAGATTCGGGAGTGGGTCCCACCTTCAATACCTTACAAG

ORF - retro_ecab_910 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.33 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLRSKMEFLQVLRRGLQRISGHGGR-GYLRVFFRANDARVGTLVGEDKYGNKYYEDNKQFFGRHRWVIYTT
L....EF..VL..GLQ..S.HGG...YL..FF.AND.R.GTL....KYG.KYYEDNK.FFG.HRWVIYT.
RetrocopyLKDMTEFPWVLKNGLQQVSSHGGL*AYLQIFFGANDMRIGTLEEGGKYGDKYYEDNK*FFGCHRWVIYTP
ParentalEMNGKNTYWDVDGSMVPPEWHRWLHSMTDDPPTTKPPTARKFIWTNHKFN-VSGTPEQYVPYSTTRKKIQ
..N..NT.WDVDGSMVP.EWH.WLH.MT.D.PT.KPP.A.KFIWTNHKFN..SGTPEQY..YSTTRKKI.
RetrocopyDRNDRNTFWDVDGSMVPHEWHLWLHCMTNDSPTAKPPIAHKFIWTNHKFN<WSGTPEQYAAYSTTRKKIR
ParentalEWVPPSTPYK
EWVPPS.PYK
RetrocopyEWVPPSIPYK

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 6 .02 RPM
SRP021940_cerebellum 0 .00 RPM 28 .51 RPM
SRP021940_embryo 0 .00 RPM 23 .19 RPM
SRP021940_placental_villous 0 .00 RPM 16 .98 RPM
SRP021940_synovial_membrane 0 .00 RPM 9 .50 RPM
SRP021940_testis 0 .00 RPM 35 .42 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_910 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_910 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_910 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_1377
Parental genes homology:
Parental genes homology involve 28 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000022942 retrocopies
retro_amel_1069, retro_amel_1414,
Bos taurus ENSBTAG000000146694 retrocopies
retro_btau_1294, retro_btau_1377, retro_btau_1449, retro_btau_869,
Choloepus hoffmanni ENSCHOG000000071342 retrocopies
retro_chof_2234, retro_chof_2322,
Callithrix jacchus ENSCJAG000000028462 retrocopies
retro_cjac_1796, retro_cjac_1862,
Cavia porcellus ENSCPOG000000101542 retrocopies
retro_cpor_1326, retro_cpor_650,
Dasypus novemcinctus ENSDNOG000000091921 retrocopy
retro_dnov_1859,
Equus caballus ENSECAG00000015836 1 retrocopy
retro_ecab_910 ,
Echinops telfairi ENSETEG000000101182 retrocopies
retro_etel_1401, retro_etel_787,
Felis catus ENSFCAG000000230503 retrocopies
retro_fcat_1283, retro_fcat_1483, retro_fcat_362,
Homo sapiens ENSG000001847523 retrocopies
retro_hsap_1293, retro_hsap_3199, retro_hsap_3312,
Gorilla gorilla ENSGGOG000000128801 retrocopy
retro_ggor_1015,
Loxodonta africana ENSLAFG000000308871 retrocopy
retro_lafr_671,
Microcebus murinus ENSMICG000000086343 retrocopies
retro_mmur_1630, retro_mmur_224, retro_mmur_544,
Myotis lucifugus ENSMLUG000000271311 retrocopy
retro_mluc_908,
Macaca mulatta ENSMMUG000000188971 retrocopy
retro_mmul_1321,
Mustela putorius furoENSMPUG000000073541 retrocopy
retro_mputfur_1257,
Mus musculus ENSMUSG000000200221 retrocopy
retro_mmus_2605,
Nomascus leucogenys ENSNLEG000000057662 retrocopies
retro_nleu_2105, retro_nleu_2756,
Otolemur garnettii ENSOGAG000000108535 retrocopies
retro_ogar_1158, retro_ogar_1310, retro_ogar_2943, retro_ogar_455, retro_ogar_896,
Pongo abelii ENSPPYG000000048392 retrocopies
retro_pabe_1071, retro_pabe_2652,
Pan troglodytes ENSPTRG000000053062 retrocopies
retro_ptro_2159, retro_ptro_885,
Pteropus vampyrus ENSPVAG000000075645 retrocopies
retro_pvam_1141, retro_pvam_1457, retro_pvam_33, retro_pvam_375, retro_pvam_661,
Rattus norvegicus ENSRNOG000000074071 retrocopy
retro_rnor_874,
Sorex araneus ENSSARG000000132201 retrocopy
retro_sara_442,
Sus scrofa ENSSSCG000000009051 retrocopy
retro_sscr_802,
Tupaia belangeri ENSTBEG000000137248 retrocopies
retro_tbel_1707, retro_tbel_2577, retro_tbel_2822, retro_tbel_2888, retro_tbel_3320, retro_tbel_3566, retro_tbel_4553, retro_tbel_4577,
Tursiops truncatus ENSTTRG000000157202 retrocopies
retro_ttru_1607, retro_ttru_1880,
Vicugna pacos ENSVPAG000000085081 retrocopy
retro_vpac_332,


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