RetrogeneDB ID: retro_opri_595

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1852:149650..150091(+)
• Located in intron of: ENSOPRG00000008238

Retrocopy information

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

Parental gene information

• Parental gene symbol: NADK2
• Ensembl ID: ENSOPRG00000009281
• Aliases: None
• Description: NAD kinase 2, mitochondrial [Source:HGNC Symbol;Acc:26404]

Sequence

>retro_opri_595
CAGAAGCCTTGCAGAAATTATGTCATGGTGGCTATGGAGGCAGTGAATCTGCCTGTACTTTGAAGGGACTGGTATAAATC
CTGTACCCATGAATCTTCATGAGCAGAAACTAAGCTTGAAATAACACAGTAGCACTTTCAACATCGATAGAATTGATGAC
AAAGAGGCTTCAGGACCCCAACTTTTGCCAGTAAGAGCATTAAATGACATCTTCATCAGGGACAGTCTTTCTTTGAGCAT
CTCTTACTATGAGACTTCAGTTGATGACGGTCCATTGGAAAACAGTAGAGTTCAGGGCTCAATTTGTGTGCCGGCACAGA
ATCAAAGGCCTTGTCATTCAGTATTAATAGGGTTGCAACTCAGACTGTGGAAGATGTGTTAAATATTGCAAAATGAGAAG
GAAATTTGGATCTTCTATTGAACAAAGAATTGGTTAGAGAA

Alignment

ORF - retro_opri_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.85 %
• Parental protein coverage: 53.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKFCRGEFR-WLWRQRIRLYLEGTGINPVPVDLHEQQLSLNQHSRAFNIERIDDERSEASGPQLLPVRAL
          QK.CR.....WLWRQ.I.LY.EGTGINPVP..LHEQ.LSL..HS..FNI.RIDD...EASGPQLLPVRAL
Retrocopy QKPCRNYVM>WLWRQ*ICLYFEGTGINPVPMNLHEQKLSLK*HSSTFNIDRIDDK--EASGPQLLPVRAL

Parental  NEVFIGESLSSRASYYEISVDDGPWE-KQKSSGLNLCTGTGSKAWSFNINRVATQAVEDVLNIAKRQGNL
          N..FI..SLS...SYYE.SVDDGP.E.KQ.SSGLNLC.GT.SKA.SF.INRVATQ.VEDVLNIAK..GNL
Retrocopy NDIFIRDSLSLSISYYETSVDDGPLE<KQ*SSGLNLCAGTESKALSFSINRVATQTVEDVLNIAK*EGNL

Parental  DLPLNKELVEK
          DL.LNKELV..
Retrocopy DLLLNKELVRE

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_595 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000016064	1 retrocopy	retro_nleu_3046,
Ochotona princeps	ENSOPRG00000009281	1 retrocopy	retro_opri_595 ,
Pongo abelii	ENSPPYG00000015401	1 retrocopy	retro_pabe_3323,
Rattus norvegicus	ENSRNOG00000016691	1 retrocopy	retro_rnor_2925,