RetrogeneDB ID: retro_opri_985

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5289:94897..95769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSOPRG00000008591
• Aliases: None
• Description: eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]

Sequence

>retro_opri_985
CTTGCATTTAAGATCCAAATGGTAATTCCAGCACTTGGAGACTATATGGGAGTAACTTGCCATGCCTGCATTGGAGGAAC
AAACGTTAGAAATGAAATGCAAAAGTTGCAGGCTGAGGTACCACATATTTTTGTTGGTACACCAGGCAGAGTGTTTGATA
TGTTAAATAGAAGATACCTTTCTCCAAAATGGATCAAAATGTTTGTTTTGAATGAAGCAGATGAAATGCTGAGCCAGGGG
GTTAAGGATCAAATTTATGAAATTTTCCAAAAACTAAATGCTAGTATTCAGGTTGTGTTGCTGTCTGCCACGATGCCAAC
TGATGTCTTAGAAGTGACCAAAAATTTCATGAGAAATCCAATTCGAATACTGGTGAAAAAGGAGGACTTGACCCTTGAAG
GAATCAGTTGTACATCATTGTTGAATGAGAGGAATGGAAGTTGGATACACTTTGTGACTTGTAGGAAACATTGACCATTA
CGCAGGCTGTTACTTTTCTCAATACAAGGTGCAAAGTGGACTGGCTCACTGAGAAAATGTATGCCATGGACTTCACAATT
TCTGCTCTGCATGGTGACAGGACCAGAAGGAAAGAGGTGTCATGATGAGAGAATTCCAGTCAGGCTCAAGCTGTGTTCCG
ATCACTACCACTTGTGCTCGTGGGATGATGTACAGCAGTATCTTGTCATAACTATAATCTACGGACCAATCATGAAAACT
ACATTCACAGAATTGGCAGAGAGGGTCGATTTGGGAGGAAGGGTGTGGCTATAAACTTCGTTACTGAAGAAGACAAGAGG
ATTCTTTGTGACATTGAAATTTTCTGCAGTACTACAGTGGAGGAGATGCCCATGAATGTGGCTGACCTTATT

Alignment

ORF - retro_opri_985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.17 %
• Parental protein coverage: 72.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LAQQIQKVVMALGDYMGASCHACIG-TNVRAEVQKLQMEAPIIV--TP-RVFDMLNRRYLSPKYIKMFVL
          LA..IQ.V..ALGDYMG..CHACIG.TNVR.E.QKLQ.E.P.I...TP.RVFDMLNRRYLSPK.IKMFVL
Retrocopy LAFKIQMVIPALGDYMGVTCHACIGGTNVRNEMQKLQAEVPHIFVGTPGRVFDMLNRRYLSPKWIKMFVL

Parental  DEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE-IRQFYI
          .EADEMLS.G.KDQIY.IFQKLN...QVVLLSATMP.DVLEVTK.FMR.PIRILVKKE.LTLE...Q.YI
Retrocopy NEADEMLSQGVKDQIYEIFQKLNASIQVVLLSATMPTDVLEVTKNFMRNPIRILVKKEDLTLE<RNQLYI

Parental  NVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGD-MDQKERDVIMREFRS
          .VE.EEWKLDTLCDL.ETLTITQAV.F.NTR.KVDWLTEKM.A.DFT.SA.HGD..DQKER.V.MREF.S
Retrocopy IVE*EEWKLDTLCDL*ETLTITQAVTFLNTRCKVDWLTEKMYAMDFTISALHGD<QDQKERGVMMREFQS

Parental  GSSRVLITTDLLARGI-DVQQVSLVI-NYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIE
          GSS.V.ITT...ARG..DVQQ..LVI.NY.L.TN.ENYIHRIGR.GRFGRKGVAIN.VTEEDKR.L.DIE
Retrocopy GSSCVPITT-TCARGM<DVQQY-LVI<NYNLRTNHENYIHRIGREGRFGRKGVAINFVTEEDKRILCDIE

Parental  TFYNTSIEEMPLNVADLI
          .F..T..EEMP.NVADLI
Retrocopy IFCSTTVEEMPMNVADLI

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_985 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 12 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000004170	1 retrocopy	retro_opri_498,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985 ,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,