RetrogeneDB ID: retro_opri_536

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1579:52984..53722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000001014
• Aliases: None
• Description: None

Sequence

>retro_opri_536
TCATTGAAGAAAGCTGGCCAAGATTCTACTGTCTGACTTATCTGTATCACCGTGTTTCTTTCCTGCCTCCCTGAAGCTGG
ACAGTATTCGAGCTGTTTTCTGTATCTCAGGCAGGTCATAGATTTTGGATCTGTGAAAACTGTAGCTTTCATAGCTATGG
TAGGAATTCTTTCTATTGTGGCTCAGACAGTCTTTCTTAGCATCTTGATGAGGTCATTGGGAAACAAGAACACTGTCCTC
CCTCTCCTGGGCTTCCAGATGTTCCAGTTGGCCTGGTACGGGTTTGGATCTCAGGCCTGGATGATATGGGCGGCAGGCAC
TGTGGCCGCCATGTCCAGCGTCACATTCCCTATGATTGGCGCCCTCATCTCTCAGAATGCAGAGCCGGATCAGCGAGGAG
TTGCTCAGGGGATCATAACTGGAATCAGAGGCTTATGCAATGGCCTTGGGCCAGCACTTTATGGCTTAATAGTCTACATG
TTCCATGTGGAGCTCACCGATCTCGGCACGGAATTGAATTTCGACAGTGCCACCCTGCAGGGCGCTGTCATCCCAGGCCC
ACCATTTTTATTTGGAGCATGTATAGTTCTTACATCTTTTCTTGTTGCCTTATTCATCCCTGAGTACAGCAAAGCTGGGA
GCGCTCAAAAACATAGCAGTGACAGTGGCAGCCTGGCCAGCTCCCCTGAAAGGGACACTGGGGAGGACGTTGAGCCACTG
TTGCAAGACAGCAGGATT

Alignment

ORF - retro_opri_536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.46 %
• Parental protein coverage: 52.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLKKVGQDSTVLLICITVFLSYLPEAGQYSSFFLYLRQVIGFGSVKIVAFIAMVGILSIVAQTVFLSILM
          SLKK.GQDSTV.LICITVFLS.LPEAGQYSS.FLYLRQVI.FGSVK.VAFIAMVGILSIVAQTVFLSILM
Retrocopy SLKKAGQDSTV*LICITVFLSCLPEAGQYSSCFLYLRQVIDFGSVKTVAFIAMVGILSIVAQTVFLSILM

Parental  RSLGNKNTVLLGLGFQMFQLAWYGFGSQAWMMWAAGTVAAMSSITFPAISALISRNAEPDQQGVAQGIIT
          RSLGNKNTVL..LGFQMFQLAWYGFGSQAWM.WAAGTVAAMSS.TFP.I.ALIS.NAEPDQ.GVAQGIIT
Retrocopy RSLGNKNTVLPLLGFQMFQLAWYGFGSQAWMIWAAGTVAAMSSVTFPMIGALISQNAEPDQRGVAQGIIT

Parental  GIRGLCNGLGPALYGLIFYMFHVELTDLGTELNSDSATLQSAVIPGPPFLFGACIVLTSFLVALFIPEYS
          GIRGLCNGLGPALYGLI.YMFHVELTDLGTELN.DSATLQ.AVIPGPPFLFGACIVLTSFLVALFIPEYS
Retrocopy GIRGLCNGLGPALYGLIVYMFHVELTDLGTELNFDSATLQGAVIPGPPFLFGACIVLTSFLVALFIPEYS

Parental  KAGGAQKHSSGSGSLASSPERGTGEDVEPLLQDSSI
          KAG.AQKHSS.SGSLASSPER.TGEDVEPLLQDS.I
Retrocopy KAGSAQKHSSDSGSLASSPERDTGEDVEPLLQDSRI

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_536 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
Loxodonta africana	ENSLAFG00000015429	1 retrocopy	retro_lafr_793,
Ochotona princeps	ENSOPRG00000001014	1 retrocopy	retro_opri_536 ,
Drosophila melanogaster	FBgn0035400	1 retrocopy	retro_dmel_13,