RetrogeneDB ID: retro_opri_3

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_33177:16902..17259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000001028
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSOPRG00000007411
• Aliases: None
• Description: ADP-ribosylation factor 3 [Source:HGNC Symbol;Acc:654]

Sequence

>retro_opri_3
ATGGGTTTGCTGAATTCTAAGAACCTGAAGGTCAGGCACGCCCAGATTCTGCTTCTGGGACTTGACTCTGCCGGGAAGTC
CACTCTTCTTTACAAACTAAAGCTTGCTAATGACATCACCACCATCCCAACCATAGGTTTTAACGTGGAGATGATCGAAT
TCGAGAAGAGCTTCTCGTTGACAGTGTGGGACGTTGGAGGACAGGAGAAGATGAGAACCACCTGGAGTGACTTCTGCGAG
AACACCGATGGGCTGGTGTACGTGGTGGACAGTTCCGACAAACTGCGCCTGGAGAAGTCCCGGAGAGAGTTTGAGCGCAT
TCTGAAGAATGAACACATTAAACATGTGCCTGTTGTC

Alignment

ORF - retro_opri_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.43 %
• Parental protein coverage: 56.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEY-KNISFTVWDVGGQDKIRPLWRHYFQN
          ....IL..GLD.AGK.T.LYKLKL....TTIPTIGFNVE..E..K..S.TVWDVGGQ.K.R..W.....N
Retrocopy RHAQILLLGLDSAGKSTLLYKLKLANDITTIPTIGFNVEMIEFEKSFSLTVWDVGGQEKMRTTWSDFCEN

Parental  TQGLIFVVDSNDRERVNEAREELMRMLAEDELR
          T.GL..VVDS.D..R....R.E..R.L......
Retrocopy TDGLVYVVDSSDKLRLEKSRREFERILKNEHIK

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_3 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007042	2 retrocopies	retro_amel_28, retro_amel_70,
Canis familiaris	ENSCAFG00000008767	1 retrocopy	retro_cfam_119,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000000088	2 retrocopies	retro_fcat_2, retro_fcat_59,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Myotis lucifugus	ENSMLUG00000029846	1 retrocopy	retro_mluc_119,
Macaca mulatta	ENSMMUG00000006968	1 retrocopy	retro_mmul_174,
Mustela putorius furo	ENSMPUG00000014730	1 retrocopy	retro_mputfur_86,
Ochotona princeps	ENSOPRG00000007411	2 retrocopies	retro_opri_13, retro_opri_3 ,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317, retro_opri_759,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Pongo abelii	ENSPPYG00000004473	1 retrocopy	retro_pabe_126,
Pteropus vampyrus	ENSPVAG00000004626	1 retrocopy	retro_pvam_7,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,