RetrogeneDB ID: retro_opri_305

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4949:243333..243596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NHP2
• Ensembl ID: ENSOPRG00000007907
• Aliases: None
• Description: NHP2 ribonucleoprotein [Source:HGNC Symbol;Acc:14377]

Sequence

>retro_opri_305
ATGACCGAATTAAAGGTTGATCCCAATGGGCTGCAGGCCCAGGAGGAGGCATGTTGTGGGGAGAGCACTTACCAGGAGCT
GCTGGTCAACCTGAACCCCATCACGCAGCCCCTGGTTTGCCGCCGCCTCGCGGGAAAGCTTTACAAGTACATCAAGAAAG
CCGTGAAGCAGAAGCAGATTCTGCGCGGGTGAAGGAGGTGCACAAGTTTGTCAACAACGGTGAGAAAGGGATCATGGTTT
TGGCAGGAGCCACGCTGCCCGTT

Alignment

ORF - retro_opri_305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.4 %
• Parental protein coverage: 58.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTKIKADADGPEAQGEACCGERTYQELLVNLNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRG-VKEVQK
          MT..K.D..G..AQ.EACCGE.TYQELLVNLNPI.QPL..RRL..KLYK.IKKAVKQKQI.RG.VKEV.K
Retrocopy MTELKVDPNGLQAQEEACCGESTYQELLVNLNPITQPLVCRRLAGKLYKYIKKAVKQKQILRG<VKEVHK

Parental  FVNKGEKGIMVLAGDTLPI
          FVN.GEKGIMVLAG.TLP.
Retrocopy FVNNGEKGIMVLAGATLPV

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_305 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012244	1 retrocopy	retro_cjac_264,
Homo sapiens	ENSG00000145912	2 retrocopies	retro_hsap_3712, retro_hsap_611,
Gorilla gorilla	ENSGGOG00000000015	1 retrocopy	retro_ggor_2509,
Macropus eugenii	ENSMEUG00000003839	2 retrocopies	retro_meug_285, retro_meug_320,
Macaca mulatta	ENSMMUG00000018757	1 retrocopy	retro_mmul_1702,
Monodelphis domestica	ENSMODG00000004231	1 retrocopy	retro_mdom_345,
Mus musculus	ENSMUSG00000001056	1 retrocopy	retro_mmus_565,
Oryctolagus cuniculus	ENSOCUG00000016057	1 retrocopy	retro_ocun_151,
Ochotona princeps	ENSOPRG00000007907	3 retrocopies	retro_opri_305 , retro_opri_421, retro_opri_810,
Pongo abelii	ENSPPYG00000016105	3 retrocopies	retro_pabe_1704, retro_pabe_3143, retro_pabe_481,
Rattus norvegicus	ENSRNOG00000004247	2 retrocopies	retro_rnor_1436, retro_rnor_2198,
Sus scrofa	ENSSSCG00000014032	1 retrocopy	retro_sscr_407,