RetrogeneDB ID: retro_opri_1071

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_65850:1374..1850(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000007960
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VPS25
• Ensembl ID: ENSOPRG00000012574
• Aliases: None
• Description: vacuolar protein sorting 25 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28122]

Sequence

>retro_opri_1071
ATGGCGATGAGTTTCAAATGGCCCTGGCAATATCGCTTCCCGCCCTTCTTTACGTTGCAGCCGAACATGGTCACGCGGCA
GAAACAGCTGGCCGCGTGGTGCTCTCTGGTGCTGTCCTTCTGCCGCCTGCACAAGCAGGCCAGCATGACGGTGATGGAGG
CGCAGGAGAGCCCGCTCTTCAACAACGTCAAACTGCAGCGGAAGCTTCCTGTGGAATCCATCCAGATTGTGTTAGAAGAA
CTGAGGAAAAAAGGGAACCTCGAGTGGCTGGATAAGAACAAGTCTAGCTTCCTGCTCATGTGGCGGAGGCCGGAAGAATG
GGGAAACTCATCTACCAGTGGGTTTCCAAGAGTGGCCAGAAGAACTCCGTGTTCACCCTGTATGAACTGACCAATGGGGA
AGACACAGAGGATGAGGAATTCCATGGGCTGGATGAGGCGACCCTCCTGCGGGCTCTGCAGGCCCTCCAGCAGGAA

Alignment

ORF - retro_opri_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMSFEWPWQYRFPPFFTLQPNMDTRQKQLAAWCSLVLSFCRLHKQASMTVMEAQESPLFNNVKLQRKLP
          MAMSF.WPWQYRFPPFFTLQPNM.TRQKQLAAWCSLVLSFCRLHKQASMTVMEAQESPLFNNVKLQRKLP
Retrocopy MAMSFKWPWQYRFPPFFTLQPNMVTRQKQLAAWCSLVLSFCRLHKQASMTVMEAQESPLFNNVKLQRKLP

Parental  VESIQIVLEELRKKGNLEWLDKNKSSFLIMWRRPEEW-GKLIYQWVSKSGQNNSVFTLYELTNGEDTEDE
          VESIQIVLEELRKKGNLEWLDKNKSSFL.MWRRPEEW.GKLIYQWVSKSGQ.NSVFTLYELTNGEDTEDE
Retrocopy VESIQIVLEELRKKGNLEWLDKNKSSFLLMWRRPEEW<GKLIYQWVSKSGQKNSVFTLYELTNGEDTEDE

Parental  EFHGLDEATLL-TLQALQQE
          EFHGLDEATLL..LQALQQE
Retrocopy EFHGLDEATLLRALQALQQE

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_1071 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013276	1 retrocopy	retro_cjac_2959,
Homo sapiens	ENSG00000131475	1 retrocopy	retro_hsap_213,
Gorilla gorilla	ENSGGOG00000016041	1 retrocopy	retro_ggor_284,
Macropus eugenii	ENSMEUG00000011611	2 retrocopies	retro_meug_1247, retro_meug_1681,
Macaca mulatta	ENSMMUG00000002149	1 retrocopy	retro_mmul_406,
Nomascus leucogenys	ENSNLEG00000011797	1 retrocopy	retro_nleu_1862,
Ochotona princeps	ENSOPRG00000012574	1 retrocopy	retro_opri_1071 ,
Pongo abelii	ENSPPYG00000008377	1 retrocopy	retro_pabe_427,
Pan troglodytes	ENSPTRG00000009220	2 retrocopies	retro_ptro_1624, retro_ptro_334,