RetrogeneDB ID: retro_opri_824

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_34754:402..1271(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000004902
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YBX2
• Ensembl ID: ENSOPRG00000013773
• Aliases: None
• Description: Y box binding protein 2 [Source:HGNC Symbol;Acc:17948]

Sequence

>retro_opri_824
CCGGCGACGGCAGCCTCGGGGACCCCCGCGCCCCCGGCCCGGAGTCAGGCGGACAAGCCGGTGCTGGCAATTCAGGTCCT
GGGTACCGTCAAATGGTTCAACGTCCGGAATGGTTATGGATTCATCAACAGGAATGACACCAAGGAGGATGTCTTTGTTC
ACCAGACAGCTATCAAGAGAAACAACCCCAGGAAGTTTCTGCGCAGCGTTGGAGACGGGGAGACGGTGGAGTTTGATGTC
GTGGAAGGAGAGAAGGGTGCTGAAGCTGCTAATGTAACTGGGCCTGGGGGTGTGCCAGTGAAGGGCAGCCGCTATGCCCC
CAATCGACGCCGGTTCCGTCGATTCATCCCCCGGCCTCGCCCAGCTGCCCCACCACCCATGGTGGCAGAGGCGCCCACCA
GTGGGGCAGAACCTGGCAGTGAAGGGGAGCGGGCTGAAGACTCAGGGCAGCGGCCCCGGCGCCGGCGCCCGCCGCCTTTT
TCTACCGCCGGCGGTTTGTGCGAGGCCCACGGCCCCCCAACCAGCAGCAGTCCATAGAGGCTATTGACGGGGTGGAGCCC
AAAGACACAGCCCCACTGGAGGGAGACCAACAGCAGGGAGATGAGCGGGTCCCCCCACCAAGATTCCGGCCCAGGTATCG
CAGGCCTTTCCGCCCAAGGCCACCCCAGCAGCCAACCACAGAAGGTGGAGATGGTGAGACCAAGCCCAGCCAAGGCCCCA
CTGACGGCTCCCGGCCCGAGCCCCAGCGCCCACGAAACCGCCCCTACTTCCAGCGGCGCCGGCAACAGCCCCCCGGCCCT
CGGCAGCCCACAGTGCCAGAGACCTCAGCCCCCATCAACAGTGGGGACACCCCCCCTACCATGCTGGAG

Alignment

ORF - retro_opri_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.47 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PATAASGTPAPPARSQADKPVLAIQVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNPRKFLRSV
          PATAASGTPAPPARSQADKPVLAIQVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNPRKFLRSV
Retrocopy PATAASGTPAPPARSQADKPVLAIQVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNPRKFLRSV

Parental  GDGETVEFDVVEGEKGAEAANVTGPGGVSVKGSRYALNRRSFRRFILRPRSAASSLMVTEASSVGQNLGS
          GDGETVEFDVVEGEKGAEAANVTGPGGV.VKGSRYA.NRR.FRRFI.RPR.AA...MV.EA...G...GS
Retrocopy GDGETVEFDVVEGEKGAEAANVTGPGGVPVKGSRYAPNRRRFRRFIPRPRPAAPPPMVAEAPTSGAEPGS

Parental  EGERAEDSGQR-LRRRPPPF-FYRRRFVRGPRPPNQQQSIEATDGVEPKDTAPLEGDQQQGDERVPPPRF
          EGERAEDSGQR..RRRPPPF.FYRRRFVRGPRPPNQQQSIEA.DGVEPKDTAPLEGDQQQGDERVPPPRF
Retrocopy EGERAEDSGQRPRRRRPPPF<FYRRRFVRGPRPPNQQQSIEAIDGVEPKDTAPLEGDQQQGDERVPPPRF

Parental  RPRYRRPFRPRPPQQPTTEGGDGETKPSQGPTDGSRPEPQRPRNRPYFQRRRQQPPGPRQPTVPETSAPI
          RPRYRRPFRPRPPQQPTTEGGDGETKPSQGPTDGSRPEPQRPRNRPYFQRRRQQPPGPRQPTVPETSAPI
Retrocopy RPRYRRPFRPRPPQQPTTEGGDGETKPSQGPTDGSRPEPQRPRNRPYFQRRRQQPPGPRQPTVPETSAPI

Parental  NSGDTPPTMLE
          NSGDTPPTMLE
Retrocopy NSGDTPPTMLE

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_824 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000014006	1 retrocopy	retro_lafr_803,
Ochotona princeps	ENSOPRG00000008050	11 retrocopies	retro_opri_1097, retro_opri_1114, retro_opri_115, retro_opri_1196, retro_opri_340, retro_opri_367, retro_opri_626, retro_opri_781, retro_opri_896, retro_opri_910, retro_opri_984,
Ochotona princeps	ENSOPRG00000013773	5 retrocopies	retro_opri_326, retro_opri_327, retro_opri_534, retro_opri_760, retro_opri_824 ,