RetrogeneDB ID: retro_opri_301

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4885:56503..56940(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP2
• Ensembl ID: ENSOPRG00000006045
• Aliases: None
• Description: WW domain binding protein 2 [Source:HGNC Symbol;Acc:12738]

Sequence

>retro_opri_301
ATGGCGCTCAACAAGAATCATTCGGAGGGCGGCGGAGTGATCGTTAACAACACGGAGAGCATCCCATGTCCTATGATCAT
GTGGAGCTTACATTCGCCATGAAGAACATGGCCGAGGCCTTCAAAGGCACCAACAAAGGCACCATCTATCTTACCCCCTA
CCGGGTCATCTTCCTGTCCAAAGGGAAGGACGCCATGCAGTCCTTCATGATGCCCTTTTACCTGATGAAGGACTGCGAGA
TCAAGCAGCCCGTGTTTGGGGCCAACTACATCAAGGGGATGGTGAAGGCCAAAGTCGGAGGTGGCTGGGAGGGTGCTGCA
TCCTACAAGTTGACCTTCACAGCGGGGGGCGCCATTGAGTATGGACGGCGCAAGCTCCAGGTGGCATCTCAAGAGTTCTA
TCCAGGACCTCCCATGATGGATGGGGCCATGGGATAC

Alignment

ORF - retro_opri_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.03 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALNKNHSEGGGVIVNNTESIL-MSYDHVELTFDMKNMPEAFKGTKKGTVYLTPYRVIFLSKGKDAMQSF
          MALNKNHSEGGGVIVNNTESI..MSYDHVELTF.MKNM.EAFKGT.KGT.YLTPYRVIFLSKGKDAMQSF
Retrocopy MALNKNHSEGGGVIVNNTESIP<MSYDHVELTFAMKNMAEAFKGTNKGTIYLTPYRVIFLSKGKDAMQSF

Parental  MMPFYLMKDCEIKQPVFGANYIKGMVKAEAGGGWEGATSYKLTFTAGGAIEFGQRMLQVASQASRGEAP-
          MMPFYLMKDCEIKQPVFGANYIKGMVKA..GGGWEGA.SYKLTFTAGGAIE.G.R.LQVASQ......P.
Retrocopy MMPFYLMKDCEIKQPVFGANYIKGMVKAKVGGGWEGAASYKLTFTAGGAIEYGRRKLQVASQEFYPGPPM

Parental  -SGAYGY
          ..GA.GY
Retrocopy MDGAMGY

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_301 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004946	1 retrocopy	retro_cfam_1038,
Callithrix jacchus	ENSCJAG00000037619	1 retrocopy	retro_cjac_575,
Felis catus	ENSFCAG00000005760	1 retrocopy	retro_fcat_1454,
Homo sapiens	ENSG00000132471	1 retrocopy	retro_hsap_1926,
Gorilla gorilla	ENSGGOG00000009241	2 retrocopies	retro_ggor_1404, retro_ggor_698,
Macropus eugenii	ENSMEUG00000000070	1 retrocopy	retro_meug_579,
Macaca mulatta	ENSMMUG00000009381	2 retrocopies	retro_mmul_1062, retro_mmul_854,
Monodelphis domestica	ENSMODG00000007725	3 retrocopies	retro_mdom_1410, retro_mdom_1847, retro_mdom_375,
Mustela putorius furo	ENSMPUG00000013775	1 retrocopy	retro_mputfur_645,
Nomascus leucogenys	ENSNLEG00000001625	1 retrocopy	retro_nleu_1214,
Ochotona princeps	ENSOPRG00000006045	2 retrocopies	retro_opri_301 , retro_opri_851,
Pongo abelii	ENSPPYG00000008640	3 retrocopies	retro_pabe_693, retro_pabe_75, retro_pabe_913,
Pan troglodytes	ENSPTRG00000009660	1 retrocopy	retro_ptro_15,
Ictidomys tridecemlineatus	ENSSTOG00000021421	2 retrocopies	retro_itri_1585, retro_itri_660,