RetrogeneDB ID: retro_opri_343

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5452:4111..4633(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT5
• Ensembl ID: ENSOPRG00000014343
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 5 [Source:HGNC Symbol;Acc:20886]

Sequence

>retro_opri_343
ATAATCCCATATGGAGATTTGCCAAAAAATAAAGAAAATATAATATATTTAGCAAATCATCGAAGCACAGTCGACTGGAT
CATTGCTGATATGTTGGCCATCAGGCAGAATGCTCTTGGACATGTGTGGTATGTGCTCAAAGATGGCTTAAAATGGCTTC
CTCTGTATGGGTGCTACTTGTCTCAGCATGGAGGAATCTATGTAAAGCGAAGTGCCAAATTCAACGAGAAAGAGATGAGA
AGCAAGCTGCAGAGCCACGTGGCCGCAGGAACTCCAATGTATCTTGTGATATTTCCAGAGGGAACAAGATATAATCCAGA
ACAAAGTGAAGTCCTTTTGGCTAGTCAAACATTTGCTGCTCAGCAAGGTCTCCCAGTATTAAAGCATGTGCTAACACCAA
GAATAAAGGCAACTTGCATCGCTTTTGATTCTCTGAAGAATTACTTAGATGCAATTTATGATGTTACAGTGGTTTATGAG
GGCAAGACTGATAAAGGGCAGCGGAAAGAATCGCCCTCCATG

Alignment

ORF - retro_opri_343 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.7 %
• Parental protein coverage: 59.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IILYGDLPKNKENIIYLANHRSTVDWIIADMLAIRQNALGHVRYVLKDGLKWLPLYGCYLSQHGGIYVKR
          II.YGDLPKNKENIIYLANHRSTVDWIIADMLAIRQNALGHV.YVLKDGLKWLPLYGCYLSQHGGIYVKR
Retrocopy IIPYGDLPKNKENIIYLANHRSTVDWIIADMLAIRQNALGHVWYVLKDGLKWLPLYGCYLSQHGGIYVKR

Parental  SAKFNEKEMRSKLQSHVAAGTPMYLVIFPEGTRYNPEQSEVLLASQTFAAQQGLPALKHVLTPRIKATHI
          SAKFNEKEMRSKLQSHVAAGTPMYLVIFPEGTRYNPEQSEVLLASQTFAAQQGLP.LKHVLTPRIKAT.I
Retrocopy SAKFNEKEMRSKLQSHVAAGTPMYLVIFPEGTRYNPEQSEVLLASQTFAAQQGLPVLKHVLTPRIKATCI

Parental  AFDSLKNYLDAIYDVTVVYEGKTDKGQRKESPSM
          AFDSLKNYLDAIYDVTVVYEGKTDKGQRKESPSM
Retrocopy AFDSLKNYLDAIYDVTVVYEGKTDKGQRKESPSM

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_343 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005142	1 retrocopy	retro_chof_376,
Dasypus novemcinctus	ENSDNOG00000004979	1 retrocopy	retro_dnov_823,
Dipodomys ordii	ENSDORG00000008708	1 retrocopy	retro_dord_523,
Ochotona princeps	ENSOPRG00000014343	3 retrocopies	retro_opri_343 , retro_opri_829, retro_opri_935,
Sarcophilus harrisii	ENSSHAG00000000051	1 retrocopy	retro_shar_687,
Tupaia belangeri	ENSTBEG00000013084	1 retrocopy	retro_tbel_2948,