RetrogeneDB ID: retro_opri_317

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5144:37928..38309(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSOPRG00000015063
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_opri_317
ATGGGGAACATCTTTGCAGACCTCTTAAAGGGCTTTTTTGGCAAAAGGGAAATGCGCATCCTCATAGTGGGCCTGGATGC
TGCAGGGAAGACGATTTTGTGCAAGCTGAAGCTCAGTGAGATCATGACCACCAATCCCACCATAGGTTTCAATGTGGAGA
CTGCAGAATTCAAGAACATCAGCTTCACAGTGTGGAATGTAGGCTGCCAGGACAAGACTCAGTCACTGTGGTGCCACTAC
TTCCAAAATACCCAAGGCTTGATCTTTGTGGTGGACAGCAATGACAGACAGCATGTGAATGAGGCAAGGAAGGAGCTCAT
GAGGATACTAGCTGAGGATGAGCTGAGGGATGCAGTCCTCCTAGTGTCTGCCAATAAGCGG

Alignment

ORF - retro_opri_317 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 70.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG
          MGNIFA.L.KG.FGK.EMRIL.VGLDAAGKT.IL.KLKL.EI.TT.PTIGFNVET.E.KNISFTVW.VG.
Retrocopy MGNIFADLLKGFFGKREMRILIVGLDAAGKT-ILCKLKLSEIMTTNPTIGFNVETAEFKNISFTVWNVGC

Parental  QDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQ
          QDK...LW.HYFQNTQGLIFVVDSNDR..VNEAR.ELMR.LAEDELRDAVLLV.ANK.
Retrocopy QDKTQSLWCHYFQNTQGLIFVVDSNDRQHVNEARKELMRILAEDELRDAVLLVSANKR

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_317 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 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Ochotona princeps	ENSOPRG00000007411	2 retrocopies	retro_opri_13, retro_opri_3,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317 , retro_opri_759,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pteropus vampyrus	ENSPVAG00000007383	1 retrocopy	retro_pvam_1324,
Rattus norvegicus	ENSRNOG00000030591	3 retrocopies	retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Sus scrofa	ENSSSCG00000013992	2 retrocopies	retro_sscr_429, retro_sscr_82,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,