RetrogeneDB ID: retro_opri_168

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3175:233621..234130(-)
• Located in intron of: ENSOPRG00000002602

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PRTFDC1
• Ensembl ID: ENSOPRG00000016040
• Aliases: None
• Description: phosphoribosyl transferase domain containing 1 [Source:HGNC Symbol;Acc:23333]

Sequence

>retro_opri_168
TTGGAAAGGGTGTTCATTCCTCATGGACTGATTGTGGACAGGACTGAAAGGCTTGCTCGGGATGTGATGAAAGAGATGGC
AGGCCATCACATTGTTGCTCTCTGTGTGCTGAAGGGGGGCTATAAGTTCTTTGCTGACTTGCTGCATTGCATTAAAGCAC
TGAATAGAAATAGTGATAGATCCATTCCTATGACTGTAGACTTTATCAGACTGAAGAGCTACTATAACGACCAGTCAACA
GGGGACATAAAAGTGATTGGTGGAGACGATCTCTCAACCTTAACTGGAAAGAACGTCTTGATTGTTGAAGATATAATTGA
CACTGGCAAAACAATGCAGACCTTGCTTTTGTTGGTCAAGCAGTATAATCCCAAAATGGTCAAGGTTGCAAGCCTGCTGG
TGAAAAGGACCTCTCGAAGTGTTGATACAGGCCAGACTTTGTCGGATTTGAAATTCCAGACAAGTTTGTTGTAGGATATG
CCCTCGACTATAATGAATACTTCAGAGAT

Alignment

ORF - retro_opri_168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.99 %
• Parental protein coverage: 75.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEYVLIPHGIITDRIERLAKDIMKDIGYCDLMVLCVLKGGYKFCADLVDQLKNISRNSDRCVSMKVDFIR
          LE.V.IPHG.I.DR.ERLA.D.MK.........LCVLKGGYKF.ADL....K...RNSDR...M.VDFIR
Retrocopy LERVFIPHGLIVDRTERLARDVMKEMAGHHIVALCVLKGGYKFFADLLHCIKALNRNSDRSIPMTVDFIR

Parental  LKSYRNDQSMEEMQIIGGEDLSTLAGKSVLFAKDVVGTGRTMRALLSSIQKYQPTMIKVASLLVKRTPRS
          LKSY.NDQS......IGG.DLSTL.GK.VL...D...TG.TM..LL.....Y.P.M.KVASLLVKRT.RS
Retrocopy LKSYYNDQSTGDIKVIGGDDLSTLTGKNVLIVEDIIDTGKTMQTLLLLVKQYNPKMVKVASLLVKRTSRS

Parental  DG-FRPHYAGFEIPNLFVVGYALDYNEYFRD
          ....RP...GFEIP..FVVGYALDYNEYFRD
Retrocopy VD<YRPDFVGFEIPDKFVVGYALDYNEYFRD

Legend:

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

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_168 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012241	1 retrocopy	retro_etel_84,
Macropus eugenii	ENSMEUG00000000136	3 retrocopies	retro_meug_1887, retro_meug_2035, retro_meug_295,
Ochotona princeps	ENSOPRG00000016040	2 retrocopies	retro_opri_168 , retro_opri_419,