RetrogeneDB ID:

retro_opri_292

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_4766:204168..204716(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FTH1
Ensembl ID:ENSOPRG00000010734
Aliases:None
Description:ferritin, heavy polypeptide 1 [Source:HGNC Symbol;Acc:3976]


Retrocopy-Parental alignment summary:






>retro_opri_292
ATGACGACCCCTTCCCCCTTGCAGGTGCGCCAGAACTACTGCCAGGACTGGAGACTGCCATCAACCGCCAGATCAACCTG
GAGCCGTACGCCTCCTATGTCTACCTGTCGGTGTCTTACTACTTTGACCCTGATGATGTGGCTTTGAAGAACTTCGCCAA
ATACTTCCTCCACCGGTCTCATGAAGGAGCGGGAACATGCAGAGAAACTGATGCAGCTGCAGAACCAGAGCGGTGGCCGG
AGCTTTCTTCAGGACATCTAGAAACCAGATCGTGATGACTGGGAGAATGGGCTGAAGGCACTGGAGTGCGCATTGCACCT
GGAACAAAGTGTCAGTCAGTCACTACTGGAACTGTACAAGCTGGCCCCTGACAAGAATGATCCCTCCTTGTGTGACTTCA
TCGGGGCTCATTTACTGGATGAGCAGGTGAAAGCTGTCAAGGAACTGGGCAGCCATGTAACCAACTTGCTCAGGATGGGA
GGCCTACAGCTGGCATGGCAGTGTATTTCTTCGCCCAGTACATCCTCGGACACTGTTATAACCAGACC

ORF - retro_opri_292 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.57 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMTTASPSQVRQNYHQD-SEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHE-EREHAE
MTT.SP.QVRQNY.QD..E.AINRQINLE.YASYVYLS.SYYFD.DDVALKNFAKYFLH.SHE.EREHAE
RetrocopyMTTPSPLQVRQNYCQD<LETAINRQINLEPYASYVYLSVSYYFDPDDVALKNFAKYFLHRSHE>EREHAE
ParentalKLMKLQNQRGGRIFLQDIKKPDRDDWENGLNAMECALHLEQSVNQSLLELHKLATDKNDPHLCDFIETHY
KLM.LQNQ.GGR.FLQDI.KPDRDDWENGL.A.ECALHLEQSV.QSLLEL.KLA.DKNDP.LCDFI..H.
RetrocopyKLMQLQNQSGGRSFLQDI*KPDRDDWENGLKALECALHLEQSVSQSLLELYKLAPDKNDPSLCDFIGAHL
ParentalLDEQVKAIKELGDHVTNLRRMGA-PTAGMAEYLFDKHTLGHSDNQS
LDEQVKA.KELG.HVTNL.RMG..PTAGMA.Y.F....LGH..NQ.
RetrocopyLDEQVKAVKELGSHVTNLLRMGG<PTAGMAVYFFAQYILGHCYNQT

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_292 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 18 parental genes, and 203 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000168311 retrocopy
Bos taurus ENSBTAG0000001118410 retrocopies
Canis familiaris ENSCAFG000000159011 retrocopy
Callithrix jacchus ENSCJAG0000001908916 retrocopies
Cavia porcellus ENSCPOG000000265863 retrocopies
Dasypus novemcinctus ENSDNOG0000001712883 retrocopies
Felis catus ENSFCAG000000073821 retrocopy
Gorilla gorilla ENSGGOG000000277227 retrocopies
Latimeria chalumnae ENSLACG000000174261 retrocopy
Loxodonta africana ENSLAFG0000000482412 retrocopies
Myotis lucifugus ENSMLUG0000002572616 retrocopies
Monodelphis domestica ENSMODG000000075829 retrocopies
Oryctolagus cuniculus ENSOCUG000000141084 retrocopies
Ochotona princeps ENSOPRG0000000249210 retrocopies
Ochotona princeps ENSOPRG00000010734 7 retrocopies
Pongo abelii ENSPPYG0000000317312 retrocopies
Sus scrofa ENSSSCG000000145409 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000145211 retrocopy



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