RetrogeneDB ID: retro_opri_1121

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_74524:417..875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MND1
• Ensembl ID: ENSOPRG00000015738
• Aliases: None
• Description: meiotic nuclear divisions 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24839]

Sequence

>retro_opri_1121
ATATTTTTGGAGACAAAAGATGTGTTTCAACTAAAAGACATGGAGAAGATTGCTCCTAAAGAAAAAGGCACTAATGCAAT
GTCAGTGACAGAAGTCCTCCAAAGTTTAGTTGATGATGGTATGGTTGATTGTGAGAGGACTGGAATGTCTAATTATTATT
GGGCTTTTCCCAGTAAAGCGCTTCATGCAAGGAAACAGAAGTTGGAGGTTCTCAGTTGTCTGAGGGAAACCAGAAGCATG
CGATCCTGCAGGAAAACAAAAACATTGAGAAATCTAAAATTGGCCGACATGAGACGGAAGAATGAACCATGATAGCAAAA
GAGCTTGCCTCACTGCGGGAACAAAGTGATTTGCTAAGAGCAGAAGTGGACAAATATAAGGAATGTGACCCACAAGTCAT
AGAAGAAATATGTCAAGTAAATAAAGTAGCCAAAGAAGCAGCTAACAGATGGAACGAA

Alignment

ORF - retro_opri_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFFETKDVFQLKDIEKIAPKEKGITAMSVKEVLQSLVDDGMVDCERIGTSNYYWAFPSKALHARKRKLEV
          IF.ETKDVFQLKD.EKIAPKEKG..AMSV.EVLQSLVDDGMVDCER.G.SNYYWAFPSKALHARK.KLEV
Retrocopy IFLETKDVFQLKDMEKIAPKEKGTNAMSVTEVLQSLVDDGMVDCERTGMSNYYWAFPSKALHARKQKLEV

Parental  LESQLSEGNQKHAILQKNI-EKAKIGRHETEERTTLAKELVSLREQREQLRAEVDKYKECDPQVVEEIRQ
          L...............K...EK.KIGRHETEE.T..AKEL.SLREQ...LRAEVDKYKECDPQV.EEI.Q
Retrocopy LSCLRETRSMRSCRKTKTL<EKSKIGRHETEE*TMIAKELASLREQSDLLRAEVDKYKECDPQVIEEICQ

Parental  ANKVAKEAANRWTD
          .NKVAKEAANRW..
Retrocopy VNKVAKEAANRWNE

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_1121 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121 ,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,