RetrogeneDB ID: retro_opri_508

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_144615:109..519(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS4
• Ensembl ID: ENSOPRG00000013784
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7711]

Sequence

>retro_opri_508
ATGGCGGTGGTATCAGTGTTAGTGGCACTGAGGCAGGTGTTGTTGGGCAGAAGGGCAGTGGCAGTGGCTGCCCTTTCTGT
TTCCAAGGTTCCAATCAGGTGGTTGAGTATTTCCACATGGAGGTTGGAACAGGACCAAACTCGAGACATGCAACTCTTAA
CAGTGGATGAGAAATTGGATATCACTACTTTAACTGGTGTTTCAGGAGAACATATCAAAACCTGAAAAGTCTGGATTTTG
TTCCTGCTCACAATAACATGCAGTCTCGAATAAACAACATGAAGAAATGGAAGATGGAATCTGGTACCAGGGAAATATGG
GAAAATCCTTCGATGGGCTGGGCATCAACGGTCGATCCCTTGTCTAATATGGTGCTAACCTTCAGTACTAAAGAAGATGC
AGGTGCATTT

Alignment

ORF - retro_opri_508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.16 %
• Parental protein coverage: 78.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVSMSVALRQALLGRRAVAAAALSVAKVPTRLLSTSTWRLAQDQTRDMQLITVDEKLDITTLTGVPEE
          MA.VS..VALRQ.LLGRRAVA.AALSV.KVP.R.LS.STWRL.QDQTRDMQL.TVDEKLDITTLTGV..E
Retrocopy MAVVSVLVALRQVLLGRRAVAVAALSVSKVPIRWLSISTWRLEQDQTRDMQLLTVDEKLDITTLTGVSGE

Parental  HIKTRKVRI-FVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADPLSNMVLTFSTKEDAVAF
          HIKT.KV.I.FVPA.NNMQS..NN.KKWKME..TRE.WENP.MGWAST.DPLSNMVLTFSTKEDA.AF
Retrocopy HIKT*KVWI<FVPAHNNMQSRINNMKKWKMESGTREIWENPSMGWASTVDPLSNMVLTFSTKEDAGAF

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_508 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005452	1 retrocopy	retro_cpor_1111,
Erinaceus europaeus	ENSEEUG00000015851	3 retrocopies	retro_eeur_133, retro_eeur_30, retro_eeur_347,
Macropus eugenii	ENSMEUG00000001362	1 retrocopy	retro_meug_651,
Monodelphis domestica	ENSMODG00000019465	1 retrocopy	retro_mdom_1227,
Mus musculus	ENSMUSG00000021764	1 retrocopy	retro_mmus_3372,
Ochotona princeps	ENSOPRG00000013784	1 retrocopy	retro_opri_508 ,
Procavia capensis	ENSPCAG00000013496	1 retrocopy	retro_pcap_268,
Pongo abelii	ENSPPYG00000015455	1 retrocopy	retro_pabe_193,
Sus scrofa	ENSSSCG00000016893	1 retrocopy	retro_sscr_999,