RetrogeneDB ID: retro_opri_262

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4352:274883..275213(-)
• Located in intron of: ENSOPRG00000017282

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDAP1
• Ensembl ID: ENSOPRG00000013615
• Aliases: None
• Description: PDGFA associated protein 1 [Source:HGNC Symbol;Acc:14634]

Sequence

>retro_opri_262
CAAAAGCGCAAAGGCGTGGAAGGGCTCATCGACATTGAGAACCCCAACCGAGTGGCACAGACAACCAAAAAGGTCACACA
ACTGGATCTGGATGGGCCAAAAGAACTTTCCAGGAGAGAACGAGAAGAAATTGAAAAGCAGAAAGCAAAAGAGCGTTACA
TGAAAATGCATTTGGCTGGGAAGACAGAGCAAGCCAAGGCTGACCTTGCCCGACTGGCAATTATCCGGAAGCAGCGGGAA
GAGGCAGCAAGAAAGAAAGAGGAAGAGAGGAAAGCAAAAGATGACGCGACCTTGTCAGGAAAACGAATGCAGTCGCTGTC
CCTGAACAAG

Alignment

ORF - retro_opri_262 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 61.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKRKGVEGLIDIENPNRVAQTTKKVTQLDLDGPKELSRREREEIEKQKAKERYMKMHLAGKTEQAKADLA
          QKRKGVEGLIDIENPNRVAQTTKKVTQLDLDGPKELSRREREEIEKQKAKERYMKMHLAGKTEQAKADLA
Retrocopy QKRKGVEGLIDIENPNRVAQTTKKVTQLDLDGPKELSRREREEIEKQKAKERYMKMHLAGKTEQAKADLA

Parental  RLAIIRKQREEAARKKEEERKAKDDATLSGKRMQSLSLNK
          RLAIIRKQREEAARKKEEERKAKDDATLSGKRMQSLSLNK
Retrocopy RLAIIRKQREEAARKKEEERKAKDDATLSGKRMQSLSLNK

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_262 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 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015838	2 retrocopies	retro_cjac_2676, retro_cjac_2725,
Equus caballus	ENSECAG00000024426	1 retrocopy	retro_ecab_449,
Echinops telfairi	ENSETEG00000009926	1 retrocopy	retro_etel_900,
Felis catus	ENSFCAG00000015067	1 retrocopy	retro_fcat_1227,
Homo sapiens	ENSG00000106244	3 retrocopies	retro_hsap_1061, retro_hsap_3210, retro_hsap_3506,
Gorilla gorilla	ENSGGOG00000025196	5 retrocopies	retro_ggor_1776, retro_ggor_1778, retro_ggor_2179, retro_ggor_2371, retro_ggor_837,
Macaca mulatta	ENSMMUG00000001460	2 retrocopies	retro_mmul_1865, retro_mmul_943,
Mus musculus	ENSMUSG00000029623	1 retrocopy	retro_mmus_2581,
Nomascus leucogenys	ENSNLEG00000011017	1 retrocopy	retro_nleu_1158,
Otolemur garnettii	ENSOGAG00000010874	2 retrocopies	retro_ogar_2199, retro_ogar_789,
Ochotona princeps	ENSOPRG00000013615	2 retrocopies	retro_opri_262 , retro_opri_512,
Pongo abelii	ENSPPYG00000017375	4 retrocopies	retro_pabe_2659, retro_pabe_2806, retro_pabe_2901, retro_pabe_884,
Pan troglodytes	ENSPTRG00000041711	4 retrocopies	retro_ptro_1711, retro_ptro_2240, retro_ptro_2378, retro_ptro_722,
Ictidomys tridecemlineatus	ENSSTOG00000001679	1 retrocopy	retro_itri_765,
Tupaia belangeri	ENSTBEG00000010152	5 retrocopies	retro_tbel_1365, retro_tbel_3543, retro_tbel_4066, retro_tbel_766, retro_tbel_975,
Tursiops truncatus	ENSTTRG00000003004	1 retrocopy	retro_ttru_1343,