RetrogeneDB ID: retro_opri_436

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_11944:34845..35477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000002191
• Aliases: None
• Description: None

Sequence

>retro_opri_436
CCCAAAGAGCTGGTCAATGAATGGTCATTGAAGATAAGAAAAGAAATGAGAGTTGTTGACAGGCAAATAAGAGACATACA
AAGAGAAGAGGAAAAAGTGAAGCGGTCTGTGAAAGATGCTGCCAAGAAGGCCAGAAGGACATCTGTGTGGTTCTGGCCAA
GGAGATGATCTGGTCCAGGAAGGCTGTGAGCAAGCTGCACACCTCCAGAGCCCATACGAACTCGATGCTCATGGGGATGA
AGAACCAGCTCGTGGTCCTGCCCGTGGCTGGCTCCCTGCAGAAGAGCACAGAAGTGATGAGGGCCATGCAGAGCCTCGTC
GAGATCCAGGAAATCCTGGCCACCATGAGGGAGCTGTCCAAAGAGATGATGAAGGCTGGGATCGTAAAGGAAATGTTGGA
GGACACCTTTGAGAGCATGGACGACCAGGAAGAAATGGAGGAGGCAGCAGAAATGGAAATCCACACAATTCTGTTTGAAA
TCACAGCAGGGGCCTTGGGCAAAGCACCCAGTAAGGTGACCAACGCCCTTCTGGAGCCAGAACCGCCAGGAGCGATGGCT
GCGTCCAAAGACGAGGAGGAAGAGGAGGAGGCCCTGGAGGCCATGCAGTCGCGCCTGGCCACACTCCAAAGC

Alignment

ORF - retro_opri_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 95.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKK-GQKDVCVVLAKEMIRSRKAVSKLHAS
          PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKK.GQKD.CVVLAKEMI.SRKAVSKLH.S
Retrocopy PKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKK<GQKDICVVLAKEMIWSRKAVSKLHTS

Parental  RAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMRAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFES
          RAH.NS.LMGMKNQL.VL.VAGSLQKSTEVMRAMQSLV.I.EI.ATMRELSKEMMKAGI..EMLEDTFES
Retrocopy RAHTNSMLMGMKNQLVVLPVAGSLQKSTEVMRAMQSLVEIQEILATMRELSKEMMKAGIVKEMLEDTFES

Parental  MDDQEEMEEAAEMEIDRILFEITAGALGKAPNKVTDALPEPELLGAMAASEDEEEEEEALEAMQSRLATL
          MDDQEEMEEAAEMEI..ILFEITAGALGKAP.KVT.AL.EPE..GAMAAS.DEEEEEEALEAMQSRLATL
Retrocopy MDDQEEMEEAAEMEIHTILFEITAGALGKAPSKVTNALLEPEPPGAMAASKDEEEEEEALEAMQSRLATL

Parental  RS
          .S
Retrocopy QS

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_436 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007479	1 retrocopy	retro_cfam_1869,
Callithrix jacchus	ENSCJAG00000019406	2 retrocopies	retro_cjac_2032, retro_cjac_2784,
Cavia porcellus	ENSCPOG00000001723	1 retrocopy	retro_cpor_920,
Dipodomys ordii	ENSDORG00000002851	1 retrocopy	retro_dord_382,
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Macaca mulatta	ENSMMUG00000013134	1 retrocopy	retro_mmul_1797,
Mustela putorius furo	ENSMPUG00000009273	1 retrocopy	retro_mputfur_1508,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683,
Oryctolagus cuniculus	ENSOCUG00000029277	1 retrocopy	retro_ocun_1044,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436 ,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,
Tarsius syrichta	ENSTSYG00000014743	1 retrocopy	retro_tsyr_561,
Tursiops truncatus	ENSTTRG00000010400	1 retrocopy	retro_ttru_638,