RetrogeneDB ID: retro_opri_761

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2897:140028..140501(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf58
• Ensembl ID: ENSOPRG00000000154
• Aliases: None
• Description: chromosome 11 open reading frame 58 [Source:HGNC Symbol;Acc:16990]

Sequence

>retro_opri_761
TCTAGCAATTGGGAGGCAAGAGATGTGGGTAAGGAAGAGAGATAACAAAAGCTCTTGAGATTTATGGATGCAGGCAAGAA
AGAACATGTCGTCTGTCTTGTTACAGAAGTTCACAAATCAACATCTGACTTTGCAACAGGAGAAGACAAGAAAATTAATG
AATTGGAGTCTCAGTATCAATAAAGGATGAATAGTGAATTATCAGAACGATACAGGTGACACTGTGGACTTGGCTTCAGT
GAGTAGAAGATCAAGATGGAGAAGGAGATGGGGCTGGAGATGATGATGATGATGAAGATAATTTACTTGAAGGGAAAGAT
CCAGATGACTCTGAAAGTAACTCAGAGTCAGTAAAAGAGGAACCTGTAGAAGAATTTCAAACTACTGAGTCCTCTGGCAA
AGTAGAAGGTTTCCAAAATAAAAACGATGCAAAAAGCAATTATAAAACGGTGTTTGTTCAATCCAGTGGATCA

Alignment

ORF - retro_opri_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.46 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSNWETADLGNEERKQKFLRLMGAGKKEHTGRLVIGDHKSTSHFRTGEEDKKINEELESQYQQSMDSKLS
          SSNWE..D.G.EER.QK.LR.M.AGKKEH...LV...HKSTS.F.TGE.DKKINE.LESQYQ..M.S.LS
Retrocopy SSNWEARDVGKEER*QKLLRFMDAGKKEHVVCLVTEVHKSTSDFATGE-DKKINE-LESQYQ*RMNSELS

Parental  GRYRRHCGLGFSE-VEDQDGDGDVAGEDDDDDDDSPDPESPDDSESDSESDKEESAEELQAAEHPDEVED
          .RYR.HCGLGFSE.VEDQDG.GD.AG.DDDD.D.......PDDSES.SES.KEE..EE.Q..E....VE.
Retrocopy ERYR*HCGLGFSE<VEDQDGEGDGAGDDDDDEDNLLEGKDPDDSESNSESVKEEPVEEFQTTESSGKVEG

Parental  PKNKKDAKSNYKMMFVKSSGS
          ..NK.DAKSNYK..FV.SSGS
Retrocopy FQNKNDAKSNYKTVFVQSSGS

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_761 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 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160, retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190, retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761 ,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622,