RetrogeneDB ID: retro_opri_437

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_11970:49151..49491(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS26
• Ensembl ID: ENSOPRG00000005721
• Aliases: None
• Description: ribosomal protein S26 [Source:HGNC Symbol;Acc:10414]

Sequence

>retro_opri_437
ACAAAGAACAGGAGGAAAAACCACTATGCTAAAAAAGGGTGTAGCCACATGCACCATATACACTGCACCAACTGGGTGTG
GTGCATGCCCAAAGACAAAGCCAGCAAGAAGTTCATCAACCAGAACGTAGTGGAGGCCATGGCTGTGAGGGATGTCTCAG
AAGCAAGCTTGTTCAACATCTACATGCTTCCCAATCTGTACGTGAAGTGTTACTGTGTGAGCTGTACCATTCACAGCCAG
GTGGTTAGAAACTGATCTCATGAAACCTGCTAGGACTGGACCCCACCACCCTGATTTCAGACCTGCTCATGCTGCTCCAC
GTCCTCCACTGAAACCCATG

Alignment

ORF - retro_opri_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDAYVLPKLYVKL
          TK.RR.N..AKKG..H...I.CTN...C.PKDKA.KKF...N.VEA.AVRD.SEAS.F..Y.LP.LYVK.
Retrocopy TKNRRKNHYAKKGCSHMHHIHCTNWVWCMPKDKASKKFINQNVVEAMAVRDVSEASLFNIYMLPNLYVKC

Parental  HYCVSCAIHSKVVRNRSREARKDRTPP-PRFRPAGAAPRPPPKPM
          .YCVSC.IHS.VVRN.S.E...D.TPP.P.FRPA.AAPRPP.KPM
Retrocopy -YCVSCTIHSQVVRN*SHETC*DWTPP>PDFRPAHAAPRPPLKPM

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_437 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 11 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038896	3 retrocopies	retro_btau_191, retro_btau_25, retro_btau_724,
Cavia porcellus	ENSCPOG00000023630	6 retrocopies	retro_cpor_115, retro_cpor_1231, retro_cpor_134, retro_cpor_173, retro_cpor_48, retro_cpor_992,
Echinops telfairi	ENSETEG00000004510	35 retrocopies	retro_etel_1072, retro_etel_1145, retro_etel_1149, retro_etel_1175, retro_etel_1321, retro_etel_1357, retro_etel_1407, retro_etel_1423, retro_etel_1469, retro_etel_1498, retro_etel_155, retro_etel_162, retro_etel_1647, retro_etel_1691, retro_etel_1703, retro_etel_1734, retro_etel_1801, retro_etel_181, retro_etel_1859, retro_etel_1913, retro_etel_1963, retro_etel_2006, retro_etel_2043, retro_etel_2138, retro_etel_2146, retro_etel_2175, retro_etel_269, retro_etel_354, retro_etel_38, retro_etel_424, retro_etel_462, retro_etel_741, retro_etel_77, retro_etel_894, retro_etel_898,
Homo sapiens	ENSG00000197728	13 retrocopies	retro_hsap_1000, retro_hsap_1665, retro_hsap_2289, retro_hsap_2301, retro_hsap_2691, retro_hsap_2977, retro_hsap_3978, retro_hsap_4120, retro_hsap_481, retro_hsap_4853, retro_hsap_498, retro_hsap_605, retro_hsap_946,
Gorilla gorilla	ENSGGOG00000011566	6 retrocopies	retro_ggor_106, retro_ggor_121, retro_ggor_19, retro_ggor_55, retro_ggor_56, retro_ggor_63,
Loxodonta africana	ENSLAFG00000013329	8 retrocopies	retro_lafr_180, retro_lafr_240, retro_lafr_40, retro_lafr_464, retro_lafr_513, retro_lafr_768, retro_lafr_835, retro_lafr_962,
Myotis lucifugus	ENSMLUG00000029968	10 retrocopies	retro_mluc_1153, retro_mluc_149, retro_mluc_1925, retro_mluc_2065, retro_mluc_2163, retro_mluc_2462, retro_mluc_266, retro_mluc_309, retro_mluc_332, retro_mluc_477,
Ochotona princeps	ENSOPRG00000005721	3 retrocopies	retro_opri_437 , retro_opri_497, retro_opri_860,
Pan troglodytes	ENSPTRG00000005075	1 retrocopy	retro_ptro_74,
Pteropus vampyrus	ENSPVAG00000007559	15 retrocopies	retro_pvam_1008, retro_pvam_1033, retro_pvam_1115, retro_pvam_1167, retro_pvam_1184, retro_pvam_1435, retro_pvam_251, retro_pvam_259, retro_pvam_298, retro_pvam_496, retro_pvam_644, retro_pvam_735, retro_pvam_871, retro_pvam_970, retro_pvam_984,
Sus scrofa	ENSSSCG00000000374	2 retrocopies	retro_sscr_406, retro_sscr_650,