RetrogeneDB ID: retro_opri_350

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_569:43159..43534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000001789
• Aliases: None
• Description: None

Sequence

>retro_opri_350
ATGCATGGCCCTGGAGCCCTAGAGCCATGCTTCGTGGGAATCCACTTCTCCCAGGAATGTTAACAACATGCTGTACCCCA
AAGAAGAGAAGGAGAATCACTTTCTGCTCAAGGCGTGCTGGAACTACAGCTACCAGCAGGAGGTCGACAACAGGTGTGTG
TTTGTCAAAAAGATCATGCAGAGGTGGACAAGCTGACCCAGATCATCACAGACTTGTTGCAGGACCCCATGCTGCCACAA
CCCAAGGACCACCCGTGCCTTAAGCGAGGCCACAAGGAGGCAGTGTTCTTCCAGTCCCACAATGCTTGGGCCGAGGGCGC
CAAAAGGTCCTACTACAAGTGCACTGCCCCTCACTGTGGCCCCCGCTGGACGCAG

Alignment

ORF - retro_opri_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEADGTYEPGFVGIRFCQEC-NNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH-EVDELTQI
          M...G..EP.FVGI.F.QEC.NNMLYPKE.KEN..LL.AC.N..YQQE.DN.C..V.KI...EVD.LTQI
Retrocopy MHGPGALEPCFVGIHFSQEC>NNMLYPKEEKENHFLLKACWNYSYQQEVDNRCVFVKKIMQ<EVDKLTQI

Parental  IADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE
          I.D..QDP.LP...DHPC.K.GHKEAVFFQSH.A.AE.A.R.YY.CTAPHCG.RWT.
Retrocopy ITDLLQDPMLPQPKDHPCLKRGHKEAVFFQSHNAWAEGAKRSYYKCTAPHCGPRWTQ

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_350 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006601	1 retrocopy	retro_cfam_1400,
Callithrix jacchus	ENSCJAG00000009671	1 retrocopy	retro_cjac_2777,
Dipodomys ordii	ENSDORG00000001852	2 retrocopies	retro_dord_264, retro_dord_555,
Monodelphis domestica	ENSMODG00000014172	1 retrocopy	retro_mdom_1465,
Mus musculus	ENSMUSG00000019738	1 retrocopy	retro_mmus_2287,
Oryctolagus cuniculus	ENSOCUG00000013044	2 retrocopies	retro_ocun_103, retro_ocun_1603,
Otolemur garnettii	ENSOGAG00000024254	1 retrocopy	retro_ogar_386,
Ochotona princeps	ENSOPRG00000001789	2 retrocopies	retro_opri_350 , retro_opri_837,
Tursiops truncatus	ENSTTRG00000003919	1 retrocopy	retro_ttru_223,