RetrogeneDB ID: retro_opri_1148

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_80213:3460..4180(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000001057
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ETFA
• Ensembl ID: ENSOPRG00000000755
• Aliases: None
• Description: electron-transfer-flavoprotein, alpha polypeptide [Source:HGNC Symbol;Acc:3481]

Sequence

>retro_opri_1148
TTAGCCCCCATCACTCTAAACACCATCACGGCAGCCAAGCGCCTGGAAGGAGACGTGTCCTGCCTAGTGGCTGGAATCAA
ATGTGACGAGGTGGCACAAGAGCTGTGTAAAGTGGAAAGTGTGGCAAAAGTCCTAGCGGTTCAACACGATGGGTACAAGG
GCCTGCTTCCAGAGGAGCTGACACCATTGATCCAAGCAACGCAGAAGCAGTTCAATTGCATGCACATTTGTGCCGGAGCA
TCTGCCTTTGGAAAGAACCTTTTGCCTAGAGTAACGGCCAAGCTTGATGCTGCCCGCATTTCTCACCTCATTGCCATCAA
GTCTCCCGACACGTTTCTGAGGACTATTTATGCAGGAAATGCTTTGCGCACAGTGAAGTGTGATGAGACAGTGAAGGTGT
TTTCTGTCCGAGGAACAGCTTTCGAAGCTGCGGCAACAAGTGGAGGTGGTGCCAGATCAGAAAACGCTTTCAGTACCTCT
CCGGTGGGAGTGTCAGAGTGGCTCGGCCAGAAACTAACCAAGAGCGACCGGCTTGAGCCGACAGGTGCCAAAGTGGTGGT
CTCTGTGCGCCGGGGCTTGAAGAGCAGAGAGAACGTTAAGCTGCTGTATGACCTGGCAGATCAGCTGCATGCCGAGGTTG
GTGCTTCTCCAGCTGCTGTTGATGCTGGCCTTGTTCCCAATGACATGCAAGTTGGACAGACAGGAAAAATCGCAGCACCT

Alignment

ORF - retro_opri_1148 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 74.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAPITLNAITAAKRLGGDVSCLVAGTKCDKVAQELCKVEGVAKVLVAQHDAYKGLLPEELTPLILATQKQ
          LAPITLN.ITAAKRL.GDVSCLVAG.KCD.VAQELCKVE.VAKVL..QHD.YKGLLPEELTPLI.ATQKQ
Retrocopy LAPITLNTITAAKRLEGDVSCLVAGIKCDEVAQELCKVESVAKVLAVQHDGYKGLLPEELTPLIQATQKQ

Parental  FNYTHICAGASAFGKNLLPRVAAKLDVAPISDIIAIKSPDTFVRTIYAGNALCTVKCDEQVKVFSVRGTA
          FN..HICAGASAFGKNLLPRV.AKLD.A.IS..IAIKSPDTF.RTIYAGNAL.TVKCDE.VKVFSVRGTA
Retrocopy FNCMHICAGASAFGKNLLPRVTAKLDAARISHLIAIKSPDTFLRTIYAGNALRTVKCDETVKVFSVRGTA

Parental  FEAAATSGGSASSENASSTSPVGVSECLDK--LQSDRPELTGXXXXXXXXRGLKSGENFKLLYDLADQLH
          FEAAATSGG.A.SENA.STSPVGVSE.L......SDR.E.TG........RGLKS.EN.KLLYDLADQLH
Retrocopy FEAAATSGGGARSENAFSTSPVGVSEWLGQKLTKSDRLEPTGAKVVVSVRRGLKSRENVKLLYDLADQLH

Parental  AAVGASRAAVDAGFVPNDMQVGQTGKIVAP
          A.VGAS.AAVDAG.VPNDMQVGQTGKI.AP
Retrocopy AEVGASPAAVDAGLVPNDMQVGQTGKIAAP

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_1148 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011967	1 retrocopy	retro_mdom_4,
Ochotona princeps	ENSOPRG00000000755	1 retrocopy	retro_opri_1148 ,
Xenopus tropicalis	ENSXETG00000015322	1 retrocopy	retro_xtro_65,