RetrogeneDB ID: retro_opri_381

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_10437:33451..34001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG3
• Ensembl ID: ENSOPRG00000012837
• Aliases: None
• Description: BTG family, member 3 [Source:HGNC Symbol;Acc:1132]

Sequence

>retro_opri_381
AATAAATTTTAGAGAGTTGGCCCTGGTGTCCTGAAGGCCTGTGAGAATAGCTGTGTCTTGCGCAGTGACCAGGGCTTGCC
AAAGGAGCTCACTCCCTGGGTGGACCCACGTGAGGTATGCTAGCGGTGTGAGAAAAACAGTGCATTCACTGTCAGGATGA
GAATAAGGATGAGATCTCCAGGAAAGTTACCAGGGCTCTTGGTGCAGTTACCTCTGGCTATCGTTTGGGATCGTCTTCAT
CAGATGAAGAAACGAGTAAGGAAGTGGAAGTGAAACCCAGCTCTGTGCCTGCAGCTCCAAGCCCTGTGTACCAGACATCA
GGACTGATATCACCACCCCTTACAATATGGCATCCTTTGCCCAGACAAAAGCCTGGAATATAGTGAGGGAATGGTCATCA
GAATCGCTGTCCTCCTCCCGTTCCATCTGGTTACCCAAATCAGGGAAGGAAGAATAAACCGTACCACCCAATTCCAGTGA
CACGGGTGCCCCCTCCTGGAATGCACTGCGACCAGAATCACTGGTTAATCCTCACATGTTGGCATCTCAC

Alignment

ORF - retro_opri_381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.2 %
• Parental protein coverage: 75.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKFQRVDPDVLKACENSCILYSDLGLPKELTLWVDPCEVCCRNGEKNHADIV-PNFENDENKEKISKKVT
          NKF.RV.P.VLKACENSC.L.SD.GLPKELT.WVDP.EVC.R..EKN.A..V......DE...K......
Retrocopy NKF*RVGPGVLKACENSCVLRSDQGLPKELTPWVDPREVC*R-CEKNSAFTV<QDENKDEISRKVTR---

Parental  RALDKVTSDYHSGSSSSDEETSKEVEVKPSSVPAAPSPVYQISELILPPLPMWHPLPRKKPGMYRGNGHQ
          .AL..VTS.Y..GSSSSDEETSKEVEVKPSSVPAAPSPVYQ.S.LI.PPL..WHPLPR.KPG...GNGHQ
Retrocopy -ALGAVTSGYRLGSSSSDEETSKEVEVKPSSVPAAPSPVYQTSGLISPPLTIWHPLPRQKPGI**GNGHQ

Parental  HHYPPPVPFGYPNQGRKNKPFRPIPVTWVPPPGMHCDRNHW-INPHMLAPH
          ...PPPVP.GYPNQGRKNKP..PIPVT.VPPPGMHCD.NHW..NPHMLA.H
Retrocopy NRCPPPVPSGYPNQGRKNKPYHPIPVTRVPPPGMHCDQNHW<VNPHMLASH

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_381 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003406	1 retrocopy	retro_cjac_4118,
Dasypus novemcinctus	ENSDNOG00000012987	2 retrocopies	retro_dnov_1703, retro_dnov_2682,
Macaca mulatta	ENSMMUG00000002116	1 retrocopy	retro_mmul_2534,
Mustela putorius furo	ENSMPUG00000010746	1 retrocopy	retro_mputfur_849,
Mus musculus	ENSMUSG00000022863	1 retrocopy	retro_mmus_225,
Otolemur garnettii	ENSOGAG00000013303	8 retrocopies	retro_ogar_1693, retro_ogar_1755, retro_ogar_2575, retro_ogar_2769, retro_ogar_2795, retro_ogar_3346, retro_ogar_524, retro_ogar_551,
Ochotona princeps	ENSOPRG00000012837	1 retrocopy	retro_opri_381 ,
Ictidomys tridecemlineatus	ENSSTOG00000010285	1 retrocopy	retro_itri_617,
Tarsius syrichta	ENSTSYG00000006151	5 retrocopies	retro_tsyr_1172, retro_tsyr_1406, retro_tsyr_1753, retro_tsyr_231, retro_tsyr_495,