RetrogeneDB ID: retro_opri_1000

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5492:64160..64443(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DENR
• Ensembl ID: ENSOPRG00000015974
• Aliases: None
• Description: density-regulated protein [Source:HGNC Symbol;Acc:2769]

Sequence

>retro_opri_1000
TGCAAAGAAGGCCCCAGGCACAGTGCCTAGCTAGACGCCAATTACCCACTTTGAGTCCCTTTATTGTGGAGTCTGTTCAT
TACCAACAGAGTGCTGTAAATCTATGCCTGGTATTGCTAAATAGAGCCAAGTGTCAGGGAAGAATTTTCCAAATGAACTT
GCAAAATTTACCATAGAAAATCCACCCAAACAACAAGATGGAATCACTGAGGGTTAAGGAACCAGGGGAGGAAGGGAAGA
AAAAGCAAAAGAGGTAGAAGGGGTCAGATAAAGCAAAAAACAA

Alignment

ORF - retro_opri_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.08 %
• Parental protein coverage: 68.84 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CRGDPRNNAKPDGDYPLRV-LYCGGKCXXXXXYCEYMPDVAKCRQWLEKNFPNEFAKLTVENSPKQEAGI
          C...PR..A..D..YPL.V.LYCG..C......C..MP..AK..Q...KNFPNE.AK.T.EN.PKQ..GI
Retrocopy CKEGPRHSA*LDANYPL*V>LYCG-VCSLPTECCKSMPGIAK*SQVSGKNFPNELAKFTIENPPKQQDGI

Parental  TEGQGTAGEEEEKKKQKRGGRGQIKQ
          TEG.GT.G..EEK.K...G.R...KQ
Retrocopy TEG*GTRGGREEKAKEVEGVR*SKKQ

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_1000 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 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016012	1 retrocopy	retro_acar_71,
Bos taurus	ENSBTAG00000032433	1 retrocopy	retro_btau_110,
Callithrix jacchus	ENSCJAG00000020488	4 retrocopies	retro_cjac_1665, retro_cjac_2303, retro_cjac_2377, retro_cjac_2627,
Homo sapiens	ENSG00000139726	4 retrocopies	retro_hsap_1028, retro_hsap_1854, retro_hsap_2471, retro_hsap_4313,
Gorilla gorilla	ENSGGOG00000005562	3 retrocopies	retro_ggor_2156, retro_ggor_2883, retro_ggor_813,
Nomascus leucogenys	ENSNLEG00000002186	3 retrocopies	retro_nleu_1465, retro_nleu_2136, retro_nleu_906,
Oryctolagus cuniculus	ENSOCUG00000008150	2 retrocopies	retro_ocun_1325, retro_ocun_1524,
Ochotona princeps	ENSOPRG00000015974	5 retrocopies	retro_opri_1000 , retro_opri_1139, retro_opri_1147, retro_opri_133, retro_opri_183,
Pongo abelii	ENSPPYG00000005073	3 retrocopies	retro_pabe_1821, retro_pabe_3509, retro_pabe_861,
Pan troglodytes	ENSPTRG00000005584	4 retrocopies	retro_ptro_1236, retro_ptro_2921, retro_ptro_2955, retro_ptro_703,