RetrogeneDB ID: retro_opri_963

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5076:109142..109682(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI2
• Ensembl ID: ENSOPRG00000015368
• Aliases: None
• Description: desumoylating isopeptidase 2 [Source:HGNC Symbol;Acc:24264]

Sequence

>retro_opri_963
TACTGGATGAACGAATACACCTCATCTATCGGAATTGGAGTTTTTCATTCACGAATTGAAGTTTATGGTAGAGAATTTGC
TTATGGTGGTCATCCTTACCCTTTTTCTGGAATATTTGAGATTTCCCCAGGAAATGCTTCTGAACTAGGAGAAACATTTA
AATTTAAAGAAGCCGTTGTTTTAGGAAGCACTGACTTCCTAGAAGATGATATAGAAAAAATTGTAGAAGAACTGGGAAAA
GAATACAAAGGCAACGCTTATCATTTGATGCATAAAAATTGCAATCACTTCTCTTCAGCTTTATCAGAGATTCTTTGTGG
GAAAGAGATTCCTCGCTGGATCAATCGGCTTGCCTACTTCAGCTCCTGCATACCCTTTCTACAGAGTTGCCTCCCGAAGG
AGTGGCTCACGCCAGCAGCCCTGCAGTCCAGTGTCAGCCAGGAGCTGCAGGATGAACTGGAGGAGGCAGAGGATGCTGCG
GCAGCCGCTTCTATGGCAAGCAGTGCAGCAGGCTCCAGGCCTGGGCGCCACACTAAACTA

Alignment

ORF - retro_opri_963 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YWMNEYTSSIGIGVFHSGIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEAVVLGSTDFLEDD
          YWMNEYTSSIGIGVFHS.IEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEAVVLGSTDFLEDD
Retrocopy YWMNEYTSSIGIGVFHSRIEVYGREFAYGGHPYPFSGIFEISPGNASELGETFKFKEAVVLGSTDFLEDD

Parental  IEKIVEELGKEYKGNAYHLMHKNCNHFSSALSEILCGKEIPRWINRLAYFSSCIPFLQSCLPKEWLTPAA
          IEKIVEELGKEYKGNAYHLMHKNCNHFSSALSEILCGKEIPRWINRLAYFSSCIPFLQSCLPKEWLTPAA
Retrocopy IEKIVEELGKEYKGNAYHLMHKNCNHFSSALSEILCGKEIPRWINRLAYFSSCIPFLQSCLPKEWLTPAA

Parental  LQSSVSQELQDELEEAEDAAAAASMASSAAGSRPGRHTKL
          LQSSVSQELQDELEEAEDAAAAASMASSAAGSRPGRHTKL
Retrocopy LQSSVSQELQDELEEAEDAAAAASMASSAAGSRPGRHTKL

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_963 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000016	1 retrocopy	retro_chof_2439,
Dasypus novemcinctus	ENSDNOG00000003484	3 retrocopies	retro_dnov_1042, retro_dnov_2533, retro_dnov_539,
Erinaceus europaeus	ENSEEUG00000009507	2 retrocopies	retro_eeur_394, retro_eeur_470,
Homo sapiens	ENSG00000121644	1 retrocopy	retro_hsap_2071,
Gorilla gorilla	ENSGGOG00000009797	1 retrocopy	retro_ggor_1493,
Nomascus leucogenys	ENSNLEG00000004019	1 retrocopy	retro_nleu_2734,
Ochotona princeps	ENSOPRG00000015368	2 retrocopies	retro_opri_1007, retro_opri_963 ,
Pongo abelii	ENSPPYG00000000055	1 retrocopy	retro_pabe_1685,
Pan troglodytes	ENSPTRG00000002180	1 retrocopy	retro_ptro_1384,
Sus scrofa	ENSSSCG00000010876	1 retrocopy	retro_sscr_388,
Drosophila melanogaster	FBgn0033551	1 retrocopy	retro_dmel_30,