RetrogeneDB ID:

retro_opri_871

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_3930:89440..89860(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS27A
Ensembl ID:ENSOPRG00000010469
Aliases:None
Description:ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]


Retrocopy-Parental alignment summary:






>retro_opri_871
CTTACAGGGAAGACTACCACACTTGAGGTTGACCTGTTGGATACAACAAAAAATGTAAGACCCAATATCCAGGAAAAGGA
ACGTATTCTTTCTGATCTGCAAAGACTGATCTTCGCTGGCAAGCCACTGGAGTACGGACAGACTTCATCTGACTACAACA
TTCAAAAGGAGTGTATTCATGTGTTGGGACTTTGTGGTGGTGGTAAGAAAAGCAAGTCTTACACCACTCCTAAGAGGAAT
AAGCACAAGACAAAGATTAAGTCAGGTGTCCTGAAGTACAAGAATGGGAGATTTAGCTGCTTATGTAGCAGTACCCTTCA
GGTGAATGTGGTGTTGGGAGTGTTCACATCAGCCATTCTGACAGACATTACCGTGGGTGAATGCTGTTTGACTTACTGCT
TCCACAAACCAGAAAGCAAG

ORF - retro_opri_871 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.93 %
Parental protein coverage: 96.75 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGA
LTGKT.TLEV...DT..NV...IQ.KE.I..D.QRLIFAGK.LE.G.T.SDYNIQKE...H.VL.L.GG.
RetrocopyLTGKTTTLEVDLLDTTKNVRPNIQEKERILSDLQRLIFAGKPLEYGQTSSDYNIQKE-CIH-VLGLCGGG
ParentalKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKIS-RLRRECPSDECGAGVFMASHFDRHY-CGKCC
K..K.KSYTTPK.NKHK..K.K..VLKY.....NG..S..L....PS.ECG.G....SH.DRHY..G.CC
RetrocopyK--KSKSYTTPKRNKHK-TKIKSGVLKY----KNGRFS<LLM*QYPSGECGVGSVHISHSDRHY>VGECC
ParentalLTYCFNKPEDK
LTYCF.KPE.K
RetrocopyLTYCFHKPESK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_871 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 15 parental genes, and 78 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000040175 retrocopies
Canis familiaris ENSCAFG000000234713 retrocopies
Callithrix jacchus ENSCJAG000000100525 retrocopies
Gorilla gorilla ENSGGOG000000076789 retrocopies
Loxodonta africana ENSLAFG000000231332 retrocopies
Myotis lucifugus ENSMLUG0000001706410 retrocopies
Myotis lucifugus ENSMLUG000000294491 retrocopy
Macaca mulatta ENSMMUG000000155638 retrocopies
Monodelphis domestica ENSMODG000000018193 retrocopies
Oryctolagus cuniculus ENSOCUG0000000361310 retrocopies
Ochotona princeps ENSOPRG00000010469 13 retrocopies
Pongo abelii ENSPPYG000000258711 retrocopy
Pan troglodytes ENSPTRG000000119281 retrocopy
Rattus norvegicus ENSRNOG000000044262 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000095665 retrocopies



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