RetrogeneDB ID: retro_opri_52

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1414:244814..245333(+)
• Located in intron of: ENSOPRG00000013718

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANP32E
• Ensembl ID: ENSOPRG00000010058
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member E [Source:HGNC Symbol;Acc:16673]

Sequence

>retro_opri_52
GAATGAAGGTGAACAGCCCCTGAGGAGGTGATGGAGCTGGTCCTTGATAATTGCCTGTGTTTCAATGGGGGAATTGAAGG
CCCGAATGACACTGTTAAAGAACTGGAGTTTCTGAGTACGGCTAATGTGGAACTCAGTTCCTTGGCTCAGCTGCCCAGCT
TAAATAAACTTCAGAAGTTGGAACTCAGCGACAATTTAATTTCTGGAGGCCTGGAGATTCTGGTGGAGAAATGCCCAAAT
CTGACCTACCGTAATTTGAGTGGAAACAAAACCAAAGATCTCAGTACAGTTGAAGCTCTGCAAAATCCTAAAAATTTGAA
AAGTCTGGACTTGTTTAACTGTAAGATCACAAACTTGAAAGATTACAGAGGAAGTATTTTTGAACTGCTGCAGCAAATCA
CATAATTGGATCGATTTGATCAGGAGGATAATGAGGCCCTGGACTCTGAAGAGGACAGTGACGAGGATGGTGATGAAGAT
GATGAGGAAGAAGATAAAGCTGGTCCCCCTGAGGGATTT

Alignment

ORF - retro_opri_52 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 72.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELRNRAPEEVTELVLDNCLCVNGEIEGLNDTFKELEFLSMANVELSSLAQLPSLNKLRKLELSDNIISGG
          E.R..APEEV.ELVLDNCLC.NG.IEG.NDT.KELEFLS.ANVELSSLAQLPSLNKL.KLELSDN.ISGG
Retrocopy E*R*TAPEEVMELVLDNCLCFNGGIEGPNDTVKELEFLSTANVELSSLAQLPSLNKLQKLELSDNLISGG

Parental  LEVLAEKCPNLTYLNLSGNKIKDLSTVEALQNLKNLKSLDLFNCEITNLEDYRGSIFELLQQITYLDGFD
          LE.L.EKCPNLTY.NLSGNK.KDLSTVEALQN.KNLKSLDLFNC.ITNL.DYRGSIFELLQQIT.LD.FD
Retrocopy LEILVEKCPNLTYRNLSGNKTKDLSTVEALQNPKNLKSLDLFNCKITNLKDYRGSIFELLQQIT*LDRFD

Parental  QEDNEAPDSEEDDDEDGDEDDDEEEDEAGPPEGF
          QEDNEA.DSEED.DEDGDE.DDEEED.AGPPEGF
Retrocopy QEDNEALDSEEDSDEDGDE-DDEEEDKAGPPEGF

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_52 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009710	1 retrocopy	retro_cjac_2926,
Dipodomys ordii	ENSDORG00000011690	4 retrocopies	retro_dord_311, retro_dord_358, retro_dord_495, retro_dord_777,
Loxodonta africana	ENSLAFG00000026778	1 retrocopy	retro_lafr_580,
Microcebus murinus	ENSMICG00000015265	1 retrocopy	retro_mmur_115,
Monodelphis domestica	ENSMODG00000027412	2 retrocopies	retro_mdom_1802, retro_mdom_569,
Ochotona princeps	ENSOPRG00000010058	3 retrocopies	retro_opri_1223, retro_opri_52 , retro_opri_774,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302, retro_opri_563,