RetrogeneDB ID:

retro_ecab_398

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:17:46660896..46661282(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000013210
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS24
Ensembl ID:ENSECAG00000016939
Aliases:None
Description:ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]


Retrocopy-Parental alignment summary:






>retro_ecab_398
AACGACACAGTAACTATCTGGACCCGGAAGTTCATGACCAACCGACTACTTCAGCAGAAACAATGGTCATAGATGTCCTT
CACCCTGGGAAGGCAACAGTGCCTAAGACAGAAATTCGGGAAAAACTAGCCAAAATGTACAAGACCACACCAGATGTCAT
CTTTGTATTTGGATTCAGAACCCATTTTGGTGGTGGGAAGACAACTGGCTCTGGCATGATTTATGATTCCTGGGATCACA
CAAAGAAAAATGAACCAAAACATAGACTTGCAAGACGTGGCCTGTATGAGAAGAAAAACACCTCAAGAAAACAACGGAAG
GAACGCAAGAACAGAAGGAAGAGAGTCAGGGGGCCTGCAAAGGCCAATGTCAGCGCTGGCAAAAAG

ORF - retro_ecab_398 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90. %
Parental protein coverage: 98.47 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalNDTVTIRTRKFMTNRLLQRKQ-MVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
NDTVTI.TRKFMTNRLLQ.KQ.MVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
RetrocopyNDTVTIWTRKFMTNRLLQQKQ<MVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
ParentalGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKK
G.GMIYDS.D..KKNEPKHRLAR.GLYEKK.TSRKQRKERKNR.K.VRG.AKANV.AGKK
RetrocopyGSGMIYDSWDHTKKNEPKHRLARRGLYEKKNTSRKQRKERKNRRKRVRGPAKANVSAGKK

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 .41 RPM 363 .39 RPM
SRP021940_cerebellum 0 .62 RPM 178 .44 RPM
SRP021940_embryo 0 .41 RPM 346 .31 RPM
SRP021940_placental_villous 0 .38 RPM 206 .78 RPM
SRP021940_synovial_membrane 0 .55 RPM 221 .32 RPM
SRP021940_testis 0 .26 RPM 165 .93 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_398 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_398 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_398 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 7 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG00000016939 5 retrocopies
Gadus morhua ENSGMOG000000125951 retrocopy
Microcebus murinus ENSMICG000000059517 retrocopies
Monodelphis domestica ENSMODG000000250913 retrocopies
Ornithorhynchus anatinus ENSOANG000000063291 retrocopy
Sarcophilus harrisii ENSSHAG000000080903 retrocopies
Sus scrofa ENSSSCG000000103288 retrocopies



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