RetrogeneDB ID: retro_opri_694

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2441:90998..91716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDI1
• Ensembl ID: ENSOPRG00000008692
• Aliases: None
• Description: isopentenyl-diphosphate delta isomerase 1 [Source:HGNC Symbol;Acc:5387]

Sequence

>retro_opri_694
GGAGCCAGGGACCTGGAGGAGAGCAGTACTCCAGGCCAGATCAAATGTTTGGTAATGATGCGTGAAACACATGCTAGACA
TCGCGATAACAGCAAGTTCAATTTCTAGCAAAGATATATTTTCTCATTGGTGAAAATGACAATAAAATTGGGACTGTGAC
TAAGAACTGTCACCTAAATAAAAACATTGAGGAAGGGTTATTGCATTGAGCTTTTAGTGTCTTTCTATTAAATACTGAAA
ATAAGCTCCTGCTATAGCAGTGCCCAGATGCTAAAATTACCTCTCCAGGTGGCTTTCCCAGCGTGTGTTGTTGTTCCCCA
CGAAGTAATCCTCATGAACTTAAAGAAAATGACACCATTGGAGTAACAAGAATGGCACAGAGGCATTTCAAAGCTGAATT
AGGAATTCCTATGGGAAAAGTTCTTCCAGAAGAAATAAATTATCTAACACAAATTCACTACAAAGCTCAGTCTGAAGGCA
TTTGGGGTGAACATGAAATTAATTAATTTGTGTCTGTGAGAAGAGTGTAACTGTGAATCCAGATCCAGATATGAATAAAA
GCAATTGCTATGCGGCAAAAGGATAAACTTCTGAAAAGGTAGCCAGTGTTGAAATTAAGGTAACTCCATAATCTCAAATT
ATTGCAGAGACTTTCAAATGGTGGGATAGTTTAAGTCATTGGAATCGGTTTGTAGAACACGACAATGTACCCAGAATA

Alignment

ORF - retro_opri_694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.29 %
• Parental protein coverage: 92.83 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLRGESRAQTLGQIRSTATMPAIHTDHLDE-QQVQLLAEMCILIDENDNKIGAETKKNCHLNENIEKGLL
          G.R......T.GQI.....M...H..H.D..QQVQ.LA....LI.ENDNKIG..TK.NCHLN.NIE.GLL
Retrocopy GARDLEESSTPGQIKCLVMMRETHARHRDN<QQVQFLAKIYFLIGENDNKIGTVTK-NCHLNKNIEEGLL

Parental  HRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPRELEEDDAIGVRRAAQRRLKAELGIPM
          H.AFSVFL.NTENKLLL.Q..DAKIT.PG.F...CC..P.SNP.EL.E.D.IGV.R.AQR..KAELGIPM
Retrocopy H*AFSVFLLNTENKLLL*QCPDAKITSPGGFPSVCCCSPRSNPHELKENDTIGVTRMAQRHFKAELGIPM

Parental  EEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILFVR-KDVTLNPDPNEIKSYCYVSKEELKELLKQAASG
          ..V.PEEINYLT.IHYKAQS.GIWGEHEI.....VR.K.VT.NPDP...KS.CY..K....E.....AS.
Retrocopy GKVLPEEINYLTQIHYKAQSEGIWGEHEIN*FVSVR<KSVTVNPDPDMNKSNCYAAKG*TSE---KVASV

Parental  EIKITPWFQIIAETFLFKWWDNLSHLNQFVDHEKIHRM
          EIK.TP..QIIAET..FKWWD.LSH.N.FV.H....R.
Retrocopy EIKVTP*SQIIAET--FKWWDSLSHWNRFVEHDNVPRI

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_694 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 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008483	3 retrocopies	retro_cjac_2083, retro_cjac_2591, retro_cjac_2820,
Erinaceus europaeus	ENSEEUG00000012555	3 retrocopies	retro_eeur_188, retro_eeur_198, retro_eeur_61,
Homo sapiens	ENSG00000067064	3 retrocopies	retro_hsap_2161, retro_hsap_2444, retro_hsap_4053,
Gorilla gorilla	ENSGGOG00000000934	3 retrocopies	retro_ggor_1521, retro_ggor_1717, retro_ggor_2722,
Macaca mulatta	ENSMMUG00000017115	3 retrocopies	retro_mmul_2340, retro_mmul_632, retro_mmul_899,
Monodelphis domestica	ENSMODG00000005998	5 retrocopies	retro_mdom_1107, retro_mdom_1692, retro_mdom_1697, retro_mdom_1724, retro_mdom_547,
Mus musculus	ENSMUSG00000058258	4 retrocopies	retro_mmus_2032, retro_mmus_2660, retro_mmus_417, retro_mmus_552,
Nomascus leucogenys	ENSNLEG00000013594	3 retrocopies	retro_nleu_1810, retro_nleu_2777, retro_nleu_2804,
Oryctolagus cuniculus	ENSOCUG00000007493	1 retrocopy	retro_ocun_267,
Ochotona princeps	ENSOPRG00000008692	2 retrocopies	retro_opri_694 , retro_opri_755,
Pongo abelii	ENSPPYG00000002039	2 retrocopies	retro_pabe_1783, retro_pabe_3327,
Pan troglodytes	ENSPTRG00000002239	3 retrocopies	retro_ptro_1412, retro_ptro_1647, retro_ptro_2747,
Ictidomys tridecemlineatus	ENSSTOG00000023260	1 retrocopy	retro_itri_118,
Tursiops truncatus	ENSTTRG00000011174	1 retrocopy	retro_ttru_255,