RetrogeneDB ID: retro_opri_462

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_126972:678..1316(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX3
• Ensembl ID: ENSOPRG00000017309
• Aliases: None
• Description: glutaredoxin 3 [Source:HGNC Symbol;Acc:15987]

Sequence

>retro_opri_462
ATGGCGGCCAGGCTGGCTAAGGCTGCGGCGACCTTGGTGGTGGGCTCTGCCTAGCAGTTTGAGGAGCTGTGGCGCCTCCG
ATCCGAGTCCCCTCTCGTGGTCCACTTCTGGTCGCAATGGGCTCCTCAGTGTTTGCAAATGAACGAGGTCATGGAGGAGT
TGGCCAAGGAGCACCTGCAAGTTTCATTTGTGAAGTTGGAAGCTGAAGCTGTGGCTGAAGTAGCTGAGAAATACCAGATC
AGTTCTGTCCCCACCTTCCTGTTCTTCAAGAATTCTCAGAAAATCGACCAATTAGATGGTGACCATGCCCCCGAATTGAC
CGAGAAAGTCCAGGGACATGCGGCGAGCGGCTCCTTGCCTCCCACCACCAGTGAGCACCCCAAAGAAGACCTCAGTGTTT
GCTTCAAAAAGCTAACTCACGCCGCCCCCTGTTTATGAAGGGGACCCCTGAAGAGCCCCGCTGTGGGTTCAGCAAGCAGA
TGGTGGAGATCCTGCAGCGGCACAGCATTCAGCTCAGCAGCTTCGATATCTTTTCAGACGAAGAAGTGTGGCAGGGCCTC
AAGGCCTACTCCAACTGGCCCCCATATGCCCAGCTCTGCGTGTCCAGAGAACTCATAGGAGGACTTGACATAGTTAAG

Alignment

ORF - retro_opri_462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 64.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IAAGAAEAAAVVEVGSAQQLEELLRLRAKSLLVVHFWAPWAPQCAQMNEVMAELAKEHRHVSFVKLEAEA
          .AA..A.AAA...VGSA.Q.EEL.RLR..S.LVVHFW..WAPQC.QMNEVM.ELAKEH..VSFVKLEAEA
Retrocopy MAARLAKAAATLVVGSA*QFEELWRLRSESPLVVHFWSQWAPQCLQMNEVMEELAKEHLQVSFVKLEAEA

Parental  VPEVSEKYEITSVPTFLFFKNSQKIDRLDGAHAPELTKKVQRHAASGSFPPTASEHPK-DLSVRLKKLTH
          V.EV.EKY.I.SVPTFLFFKNSQKID.LDG.HAPELT.KVQ.HAASGS.PPT.SEHPK.DLSV..KKLTH
Retrocopy VAEVAEKYQISSVPTFLFFKNSQKIDQLDGDHAPELTEKVQGHAASGSLPPTTSEHPKEDLSVCFKKLTH

Parental  AAPCMLFMKGTPQEPRCG-FSKQMVEILQRHNIQFSSFDILSDEEVRQGLKTFSNWPTYPQLYVSGELIG
          AAPC.....G....P..G.FSKQMVEILQRH.IQ.SSFDI.SDEEV.QGLK..SNWP.Y.QL.VS.ELIG
Retrocopy AAPCL--*RGPLKSPAVG<FSKQMVEILQRHSIQLSSFDIFSDEEVWQGLKAYSNWPPYAQLCVSRELIG

Parental  GLDIVK
          GLDIVK
Retrocopy GLDIVK

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_462 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 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462 ,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,