RetrogeneDB ID: retro_opri_199

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3497:285538..285757(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR5
• Ensembl ID: ENSOPRG00000004283
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 5 [Source:HGNC Symbol;Acc:17955]

Sequence

>retro_opri_199
GTCCTGCAACCGGATTCACAAGGACTTGCCTTGCTCTGAAGGGCCCTGTTGGATGGGCCTCTGGGGGCGATGTGCTTGTC
CGTTCTAGCCCAGCGGGCAGCTAAGCTAACCTCTGCTCCTCCCACCGATATTTCCGTGGCGTGTCTAGAATCAGATAATG
GGAACGTTATGATTCAGAGACACAGTGACATCATGATGACTGAGCACAAAATGGCTACT

Alignment

ORF - retro_opri_199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.9 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLCTDSQGLNLGCRGTLSDEHAGV-ISVLAQQAAKLTS-DPTDIPVVCLESDNGNIMIQKHDGITVAVHK
          VL..DSQGL.L..R..L.........SVLAQ.AAKLTS..PTDI.V.CLESDNGN.MIQ.H..I....HK
Retrocopy VLQPDSQGLALL*RALLDGPLGAMCLSVLAQRAAKLTSAPPTDISVACLESDNGNVMIQRHSDIMMTEHK

Parental  MAS
          MA.
Retrocopy MAT

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_199 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 21 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011504	2 retrocopies	retro_amel_118, retro_amel_974,
Bos taurus	ENSBTAG00000014970	3 retrocopies	retro_btau_1505, retro_btau_1755, retro_btau_71,
Callithrix jacchus	ENSCJAG00000003438	1 retrocopy	retro_cjac_2918,
Dipodomys ordii	ENSDORG00000005672	3 retrocopies	retro_dord_147, retro_dord_642, retro_dord_775,
Equus caballus	ENSECAG00000021821	1 retrocopy	retro_ecab_1026,
Homo sapiens	ENSG00000134248	1 retrocopy	retro_hsap_162,
Gorilla gorilla	ENSGGOG00000016522	1 retrocopy	retro_ggor_247,
Microcebus murinus	ENSMICG00000005264	4 retrocopies	retro_mmur_1114, retro_mmur_152, retro_mmur_422, retro_mmur_454,
Myotis lucifugus	ENSMLUG00000007198	2 retrocopies	retro_mluc_512, retro_mluc_708,
Macaca mulatta	ENSMMUG00000015023	4 retrocopies	retro_mmul_164, retro_mmul_2452, retro_mmul_440, retro_mmul_499,
Mustela putorius furo	ENSMPUG00000003833	5 retrocopies	retro_mputfur_1013, retro_mputfur_1020, retro_mputfur_1187, retro_mputfur_1387, retro_mputfur_921,
Mus musculus	ENSMUSG00000087260	3 retrocopies	retro_mmus_1061, retro_mmus_1901, retro_mmus_3723,
Oryctolagus cuniculus	ENSOCUG00000002449	2 retrocopies	retro_ocun_1880, retro_ocun_356,
Otolemur garnettii	ENSOGAG00000033478	2 retrocopies	retro_ogar_1388, retro_ogar_3454,
Ochotona princeps	ENSOPRG00000004283	5 retrocopies	retro_opri_138, retro_opri_199 , retro_opri_488, retro_opri_567, retro_opri_716,
Pan troglodytes	ENSPTRG00000001078	2 retrocopies	retro_ptro_155, retro_ptro_436,
Sus scrofa	ENSSSCG00000006807	1 retrocopy	retro_sscr_986,
Ictidomys tridecemlineatus	ENSSTOG00000003401	5 retrocopies	retro_itri_1196, retro_itri_154, retro_itri_198, retro_itri_587, retro_itri_86,
Tupaia belangeri	ENSTBEG00000009117	5 retrocopies	retro_tbel_1220, retro_tbel_1427, retro_tbel_1756, retro_tbel_2289, retro_tbel_2329,
Tarsius syrichta	ENSTSYG00000006011	5 retrocopies	retro_tsyr_305, retro_tsyr_306, retro_tsyr_318, retro_tsyr_560, retro_tsyr_870,
Tursiops truncatus	ENSTTRG00000001319	1 retrocopy	retro_ttru_602,