RetrogeneDB ID:

retro_ecab_397

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:17:35126825..35127160(+)
Located in intron of:ENSECAG00000019161
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL31
Ensembl ID:ENSECAG00000024079
Aliases:None
Description:ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]


Retrocopy-Parental alignment summary:






>retro_ecab_397
AGAAGGGTGGCGAGAAGGCCTGCCATCAACGAGATGGGGACCAGAGAATACATCATCAACATGCACAAGCTCAGCCATGG
AGTGGGCTTCAAAAAGCATGCCCCATAGGCTTTCAAAGAAATTGGAAATTTGCCATGAAGAAGACAGGAACTCCAGAAGT
ATGCATTGACACCAGGCTCAACAAAGCTGCCTGGGCCAAAGGAATAAGGAATGCCCCATACCATATCCATGTGTGGTTGT
CCAGAAAATGTAATGACGATGAAGATTCACCAAACAGACTCTATATGTTGGTTACCTATGTACCTGTCACCACCTTCAAA
AATCTACAGTCAATG

ORF - retro_ecab_397 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.14 %
Parental protein coverage: 92.74 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRRVARRRRAAAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIR-KFAMKEMGTPDVRIDTRLNKAVWA
RRVARR....AINE..TREY.IN.HK..HGVGFKK.AP.A.KEI..KFAMK..GTP.V.IDTRLNKA.WA
RetrocopyRRVARR---PAINEMGTREYIINMHKLSHGVGFKKHAP*AFKEIG<KFAMKKTGTPEVCIDTRLNKAAWA
ParentalKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTV
KGIRN.PY.I.V.LSRK.N.DEDSPN.LY.LVTYVPVTTFKNLQ..
RetrocopyKGIRNAPYHIHVWLSRKCNDDEDSPNRLYMLVTYVPVTTFKNLQSM

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 .00 RPM 327 .91 RPM
SRP021940_cerebellum 0 .00 RPM 157 .98 RPM
SRP021940_embryo 0 .13 RPM 312 .70 RPM
SRP021940_placental_villous 0 .00 RPM 177 .00 RPM
SRP021940_synovial_membrane 0 .05 RPM 274 .11 RPM
SRP021940_testis 0 .13 RPM 148 .80 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_397 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_397 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_397 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 86 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000210315 retrocopies
Equus caballus ENSECAG00000024079 13 retrocopies
Latimeria chalumnae ENSLACG000000136031 retrocopy
Loxodonta africana ENSLAFG0000002787312 retrocopies
Macropus eugenii ENSMEUG000000009638 retrocopies
Myotis lucifugus ENSMLUG0000000250721 retrocopies
Mustela putorius furoENSMPUG000000121972 retrocopies
Otolemur garnettii ENSOGAG0000001449410 retrocopies
Pongo abelii ENSPPYG000000258704 retrocopies
Sus scrofa ENSSSCG000000081704 retrocopies
Sus scrofa ENSSSCG000000251806 retrocopies



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