RetrogeneDB ID: retro_opri_578

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_18067:78769..79174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT2
• Ensembl ID: ENSOPRG00000003291
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 2 [Source:HGNC Symbol;Acc:325]

Sequence

>retro_opri_578
ATCATCAGTTGGTTTGTGCGGACCTTCAAGTACGTGTATAGCCTCCGCTTTGAGGTCAGGGGCTGGCCCAAGCTGGACAT
CGACTAGCCCTGCGTCATCATCTCCAACCGCCAGAGTATCCTGGACATGATGGGCCTCATGGAGGTCCTGCCATGGCGCT
GCGTGCAGGTAGCCAAGTGGGAGCTCCTGTTCCTGGGCTCCATGAGACTCATCATGTACCTGAGTGGCGTCTTCTTCAAG
AGTCGACAGCAGTCCAGCACCGCCATGAGTGTTCTGGCCAGCCTGAGCGAGCGCATGGTCCTGGAGAACCTCAAAGTGTG
GATCTACCCTGAGGGCACGTGCAACACCAATGGTGACCTACTGCCCTGCAGGAAAGGTGGTTTAAGGATGGCATTCATTG
AACAG

Alignment

ORF - retro_opri_578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IISWFVRTFKYMYGLRFEVRGQPKLDVDQPCVIISNHQSILDMMGLMEVLPRRCVQVAKRELLFLGPVGL
          IISWFVRTFKY.Y.LRFEVRG.PKLD.D.PCVIISN.QSILDMMGLMEVLP.RCVQVAK.ELLFLG...L
Retrocopy IISWFVRTFKYVYSLRFEVRGWPKLDID*PCVIISNRQSILDMMGLMEVLPWRCVQVAKWELLFLGSMRL

Parental  IMYLGGVFFINRQQSSTAMSVMADLSERMVRENLKVWIYPEGTRNTNGDLLPFKKGAFYLAIQAQ
          IMYL.GVFF..RQQSSTAMSV.A.LSERMV.ENLKVWIYPEGT.NTNGDLLP..KG....A...Q
Retrocopy IMYLSGVFFKSRQQSSTAMSVLASLSERMVLENLKVWIYPEGTCNTNGDLLPCRKGGLRMAFIEQ

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_578 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003965	1 retrocopy	retro_amel_982,
Canis familiaris	ENSCAFG00000019569	1 retrocopy	retro_cfam_1838,
Equus caballus	ENSECAG00000010932	1 retrocopy	retro_ecab_825,
Felis catus	ENSFCAG00000011607	1 retrocopy	retro_fcat_1778,
Myotis lucifugus	ENSMLUG00000007348	2 retrocopies	retro_mluc_1291, retro_mluc_968,
Mustela putorius furo	ENSMPUG00000011249	1 retrocopy	retro_mputfur_1160,
Ochotona princeps	ENSOPRG00000003291	1 retrocopy	retro_opri_578 ,
Ictidomys tridecemlineatus	ENSSTOG00000023422	1 retrocopy	retro_itri_5,