RetrogeneDB ID: retro_opri_1065

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_64759:4771..5395(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGA
• Ensembl ID: ENSOPRG00000015381
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class A [Source:HGNC Symbol;Acc:8957]

Sequence

>retro_opri_1065
AGATACCAGCTACATGACAGGGTGCATCTTTTGGGAGCTTTAGAACACAAGGACGTTAGAAACGTCTTAGTGCAAGGACA
TATTTTTCTGAATACCTCTCTCACGGAAGCATTCTGCATGGCGATTGTGGAAGCAGCCAGTTGCGGTTTACAGGTTGTGA
GTACCAGGGTTGGTGGAATCCCTGAGGTCCTTCCCAAAGATCTCATTATTGTATGTGAGCCTTCAGTAAAATCTTTGTGT
GATGGATTAGAAAAAGCTATTCTCCGATTCAAGTCAGGGTTACTGCGAGCTCCAGAAGAGATCCACAACCTAGGAAAGAC
GTTCTAACCCTGGAGGGATGTTGCAGAGAGAACTGAAAGGGTTTATGACCGGGTGGCTGGGGAAGCTGTGTTGCCCATCG
TCAAACGGCTGGACAGGCTCATCTCTTGCTGCGCCCCAGTAACAGGCTACATTTTGGCCTTATTGGCTGTGTTCAGCCTT
CTCTTCCTCATTCTCCTGAGATGGATAACTCCAGATTCCGTCACTGATGTTGCAGTAGATGCCACGGGGCCAAAGAGCTC
GTGGACTCTGCAGCACCCTCGCAGAGCAAAACTGGATGAAGATGATGGCAAGTCTGAAACCAGG

Alignment

ORF - retro_opri_1065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.19 %
• Parental protein coverage: 84.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYQLHDRVHLLGALEHKDVRNVLVQGHIFLNTSLTEAFCMAIVEAASCGLQVVSTRVGGIPEVLPEDLII
          RYQLHDRVHLLGALEHKDVRNVLVQGHIFLNTSLTEAFCMAIVEAASCGLQVVSTRVGGIPEVLP.DLII
Retrocopy RYQLHDRVHLLGALEHKDVRNVLVQGHIFLNTSLTEAFCMAIVEAASCGLQVVSTRVGGIPEVLPKDLII

Parental  LCEPSVKSLCDGLEKAILQFKSGLLRAPEEIHNLVKTFYTWRDVAERTERVYDRVAGEAVLPIDKRLDRL
          .CEPSVKSLCDGLEKAIL.FKSGLLRAPEEIHNL.KTF..WRDVAERTERVYDRVAGEAVLPI.KRLDRL
Retrocopy VCEPSVKSLCDGLEKAILRFKSGLLRAPEEIHNLGKTF*PWRDVAERTERVYDRVAGEAVLPIVKRLDRL

Parental  ISCCGPVTGYIFALLAVFSLLFLILLRWITPDSVIDVAVDATGPKSSWTLQHPRRAKLDEDDGKSETR
          ISCC.PVTGYI.ALLAVFSLLFLILLRWITPDSV.DVAVDATGPKSSWTLQHPRRAKLDEDDGKSETR
Retrocopy ISCCAPVTGYILALLAVFSLLFLILLRWITPDSVTDVAVDATGPKSSWTLQHPRRAKLDEDDGKSETR

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_1065 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006415	1 retrocopy	retro_chof_2311,
Homo sapiens	ENSG00000165195	1 retrocopy	retro_hsap_1050,
Gorilla gorilla	ENSGGOG00000007293	1 retrocopy	retro_ggor_828,
Nomascus leucogenys	ENSNLEG00000009352	1 retrocopy	retro_nleu_2070,
Ochotona princeps	ENSOPRG00000015381	1 retrocopy	retro_opri_1065 ,
Pongo abelii	ENSPPYG00000020142	1 retrocopy	retro_pabe_876,
Pan troglodytes	ENSPTRG00000021684	1 retrocopy	retro_ptro_716,
Rattus norvegicus	ENSRNOG00000003554	1 retrocopy	retro_rnor_2566,