RetrogeneDB ID: retro_opri_120

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2459:84019..84247(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPE
• Ensembl ID: ENSOPRG00000015415
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide E [Source:HGNC Symbol;Acc:11161]

Sequence

>retro_opri_120
GCTGTGGCAAACCAGGGCCAGAAAGCACAGGACGTGATGGTTCAGTCCATCCGATACCTGCAAACTTGATCTTGCATTCA
GGTGTGGCTGTATGAACACGTGAACAGGCAGACAGAGGGCTGCAGCACTGGTTTTGATGAATACATCAAGCAACCTGTAC
TAGATAATGCAGAAGAGATTCATTCTAAAACGAAGTAAAGAAAACAACTGGGTGGGATCATGTTAAAA

Alignment

ORF - retro_opri_120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 85.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNL-VLDDAEEIHSKTKS
          A...QGQK.Q.VMVQ.I....RYLQ..S.IQVWLYE.VN...EGC..GFDEY....VLD.AEEIHSKTK.
Retrocopy AVANQGQKAQDVMVQSI----RYLQT*SCIQVWLYEHVNRQTEGCSTGFDEYIKQPVLDNAEEIHSKTK*

Parental  RKQLGRIMLK
          RKQLG.IMLK
Retrocopy RKQLGGIMLK

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_120 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 9 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006735	1 retrocopy	retro_cjac_3163,
Dasypus novemcinctus	ENSDNOG00000004490	24 retrocopies	retro_dnov_1009, retro_dnov_1141, retro_dnov_122, retro_dnov_1223, retro_dnov_1312, retro_dnov_1314, retro_dnov_1362, retro_dnov_1438, retro_dnov_163, retro_dnov_191, retro_dnov_2398, retro_dnov_2671, retro_dnov_360, retro_dnov_414, retro_dnov_513, retro_dnov_579, retro_dnov_796, retro_dnov_828, retro_dnov_898, retro_dnov_900, retro_dnov_902, retro_dnov_93, retro_dnov_967, retro_dnov_983,
Echinops telfairi	ENSETEG00000014015	24 retrocopies	retro_etel_1136, retro_etel_1244, retro_etel_138, retro_etel_1443, retro_etel_1530, retro_etel_1636, retro_etel_1739, retro_etel_1781, retro_etel_1947, retro_etel_2143, retro_etel_234, retro_etel_258, retro_etel_310, retro_etel_377, retro_etel_466, retro_etel_546, retro_etel_56, retro_etel_579, retro_etel_581, retro_etel_582, retro_etel_76, retro_etel_776, retro_etel_799, retro_etel_80,
Gorilla gorilla	ENSGGOG00000000755	7 retrocopies	retro_ggor_1462, retro_ggor_1626, retro_ggor_1700, retro_ggor_2221, retro_ggor_228, retro_ggor_2892, retro_ggor_91,
Loxodonta africana	ENSLAFG00000009349	3 retrocopies	retro_lafr_796, retro_lafr_814, retro_lafr_873,
Myotis lucifugus	ENSMLUG00000013244	8 retrocopies	retro_mluc_1639, retro_mluc_1650, retro_mluc_1994, retro_mluc_2045, retro_mluc_2088, retro_mluc_2326, retro_mluc_85, retro_mluc_919,
Ochotona princeps	ENSOPRG00000015415	11 retrocopies	retro_opri_120 , retro_opri_1215, retro_opri_314, retro_opri_359, retro_opri_450, retro_opri_453, retro_opri_580, retro_opri_601, retro_opri_613, retro_opri_786, retro_opri_856,
Pongo abelii	ENSPPYG00000000326	8 retrocopies	retro_pabe_1375, retro_pabe_20, retro_pabe_2023, retro_pabe_228, retro_pabe_3015, retro_pabe_3620, retro_pabe_56, retro_pabe_610,
Sorex araneus	ENSSARG00000003311	9 retrocopies	retro_sara_171, retro_sara_173, retro_sara_183, retro_sara_214, retro_sara_219, retro_sara_37, retro_sara_664, retro_sara_697, retro_sara_750,