RetrogeneDB ID: retro_opri_204

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_358:179790..180141(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP3
• Ensembl ID: ENSOPRG00000011126
• Aliases: None
• Description: FK506 binding protein 3, 25kDa [Source:HGNC Symbol;Acc:3719]

Sequence

>retro_opri_204
GGTCCACCAAAATATACAAAATCTGTTCTCAGAAAAGGAGATAAAACCAACTTTCCCAAAAGAGGAGATGTTGTTCACTG
CTGGTATACAGGAACACTACAGGATGGTACTGTTTTTGATACTAATGTTCAAACAAGTTCAAAGAAGAAGAAAAACACCA
GTCCTTTGAGTTTTAAGATTGGAGTGGGCGAAGTTATCAGAGGATGGGACGAGGCACTCTTTACTATGAGTAAAGGAGAA
AAGGCTTGACTCGAGATTAAACCCGAATGGGCTTATGGAAAGAAAGGACAGCCTGGTGCCAAAATTCCACCAAATGCAAA
ACTCATTTTTGAAGTAGAATTACTGGATATT

Alignment

ORF - retro_opri_204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 52.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPPKYTKSVLKKGDKTNFPKKGDVVHCWYTGTLQDGTVFDTNVQTSSKKKKNAKPLSFKVGVGKVIRGWD
          GPPKYTKSVL.KGDKTNFPK.GDVVHCWYTGTLQDGTVFDTNVQTSSKKKKN..PLSFK.GVG.VIRGWD
Retrocopy GPPKYTKSVLRKGDKTNFPKRGDVVHCWYTGTLQDGTVFDTNVQTSSKKKKNTSPLSFKIGVGEVIRGWD

Parental  EALLTMSKGEKARLEIEPEWAYGKKGQPDAKIPPNAKLIFEVELVDI
          EAL.TMSKGEKA.LEI.PEWAYGKKGQP.AKIPPNAKLIFEVEL.DI
Retrocopy EALFTMSKGEKA*LEIKPEWAYGKKGQPGAKIPPNAKLIFEVELLDI

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_204 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Felis catus	ENSFCAG00000027304	1 retrocopy	retro_fcat_1894,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Microcebus murinus	ENSMICG00000005808	2 retrocopies	retro_mmur_1582, retro_mmur_351,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Ochotona princeps	ENSOPRG00000011126	2 retrocopies	retro_opri_204 , retro_opri_600,
Ictidomys tridecemlineatus	ENSSTOG00000002249	1 retrocopy	retro_itri_650,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tursiops truncatus	ENSTTRG00000006664	1 retrocopy	retro_ttru_1041,