RetrogeneDB ID: retro_opri_1162

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8225:119346..119857(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPRE1
• Ensembl ID: ENSOPRG00000006707
• Aliases: None
• Description: microtubule-associated protein, RP/EB family, member 1 [Source:HGNC Symbol;Acc:6890]

Sequence

>retro_opri_1162
AAAAAGAAATTTCAAGACAATTTTGAATTTGTTCAGTGGTTCAAGAAGTTTTTTTGATACAAACTATGATGGAAAAGGCT
ATGACCCTGTGGCTGCCAGGCAAGGTCAAGAAACTGCTGTGGCTCCCTCTCTTGTCGCTCCAGCTCTGAAAAAACCGAGG
AAACCTCTCTGTTCTAGTGGTGCAGCATCACAGAGGCCCTTTCAACACAGAGAACTACGGTAATTCCTAAGGCTGGCCTA
GGGGTGTTGCGCAAGAATCCCGGGGTGGGCCATGGAGGTGATGAAGCAGCTGAGTTGATGCAGCAGGTCAATGTACTGAA
ACTTACCGTCCAAGACTTGGAGAGAGAGAGATTTGTACTTCGGAAAGCTAAGAAACATTGAATTGATTTGCCAGAAGGAC
GAGGGGGAAAATGACCCTGTTTTGCAGAGGATTGTGGACATTCTATATGCTACAGACGAAGGCTTTGTGATACCTGATGA
AGGCGGCCCGCAGGAAGAACAAGAAGAATAC

Alignment

ORF - retro_opri_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.63 %
• Parental protein coverage: 63.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KGKFQDNFEFVQWFKKFF-DANYDGKDYDPVAARQGQETAVAPSLVAPALNKPKKPLSSGGAASQRP-IS
          K.KFQDNFEFVQWFKKFF.D.NYDGK.YDPVAARQGQETAVAPSLVAPAL.KP.KPL.S.GAASQRP..S
Retrocopy KKKFQDNFEFVQWFKKFF>DTNYDGKGYDPVAARQGQETAVAPSLVAPALKKPRKPLCSSGAASQRP<LS

Parental  TQRTTATPKAGAGVVRKNPGVGNGDDEAAELMQQVNVLKLTVEDLEKERDFYFGK-LRNIELICQENEGE
          TQRTT..PKAG.GV.RKNPGVG.G.DEAAELMQQVNVLKLTV.DLE.ER.F...K.LRNIELICQ..EGE
Retrocopy TQRTTVIPKAGLGVLRKNPGVGHGGDEAAELMQQVNVLKLTVQDLERER-FVLRK>LRNIELICQKDEGE

Parental  NDPVLQRIVDILYATDEGFVIPDEGGPQEEQEEY
          NDPVLQRIVDILYATDEGFVIPDEGGPQEEQEEY
Retrocopy NDPVLQRIVDILYATDEGFVIPDEGGPQEEQEEY

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_1162 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 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013238	3 retrocopies	retro_amel_1187, retro_amel_1436, retro_amel_848,
Canis familiaris	ENSCAFG00000007306	13 retrocopies	retro_cfam_1338, retro_cfam_1554, retro_cfam_1665, retro_cfam_1804, retro_cfam_1808, retro_cfam_2084, retro_cfam_2163, retro_cfam_241, retro_cfam_547, retro_cfam_762, retro_cfam_774, retro_cfam_806, retro_cfam_913,
Choloepus hoffmanni	ENSCHOG00000006737	10 retrocopies	retro_chof_1064, retro_chof_1075, retro_chof_1113, retro_chof_1138, retro_chof_1514, retro_chof_2248, retro_chof_2557, retro_chof_2591, retro_chof_643, retro_chof_704,
Callithrix jacchus	ENSCJAG00000015601	10 retrocopies	retro_cjac_1424, retro_cjac_1647, retro_cjac_1946, retro_cjac_2077, retro_cjac_2084, retro_cjac_2366, retro_cjac_2861, retro_cjac_3259, retro_cjac_3271, retro_cjac_3308,
Cavia porcellus	ENSCPOG00000023542	1 retrocopy	retro_cpor_194,
Dasypus novemcinctus	ENSDNOG00000007431	2 retrocopies	retro_dnov_730, retro_dnov_822,
Felis catus	ENSFCAG00000007783	2 retrocopies	retro_fcat_1335, retro_fcat_970,
Gorilla gorilla	ENSGGOG00000022496	1 retrocopy	retro_ggor_2765,
Loxodonta africana	ENSLAFG00000015453	1 retrocopy	retro_lafr_975,
Microcebus murinus	ENSMICG00000001965	3 retrocopies	retro_mmur_1125, retro_mmur_1179, retro_mmur_129,
Myotis lucifugus	ENSMLUG00000016403	6 retrocopies	retro_mluc_1212, retro_mluc_1811, retro_mluc_1812, retro_mluc_1883, retro_mluc_635, retro_mluc_931,
Macaca mulatta	ENSMMUG00000001816	2 retrocopies	retro_mmul_1938, retro_mmul_2374,
Monodelphis domestica	ENSMODG00000019445	3 retrocopies	retro_mdom_1213, retro_mdom_1946, retro_mdom_431,
Mustela putorius furo	ENSMPUG00000017867	3 retrocopies	retro_mputfur_1240, retro_mputfur_1304, retro_mputfur_341,
Oryctolagus cuniculus	ENSOCUG00000024265	1 retrocopy	retro_ocun_582,
Otolemur garnettii	ENSOGAG00000026557	2 retrocopies	retro_ogar_226, retro_ogar_2290,
Ochotona princeps	ENSOPRG00000006707	4 retrocopies	retro_opri_1161, retro_opri_1162 , retro_opri_1212, retro_opri_807,
Pteropus vampyrus	ENSPVAG00000015887	1 retrocopy	retro_pvam_1035,
Tarsius syrichta	ENSTSYG00000000833	1 retrocopy	retro_tsyr_2018,
Tursiops truncatus	ENSTTRG00000014809	2 retrocopies	retro_ttru_1683, retro_ttru_1917,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,