RetrogeneDB ID: retro_opri_559

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_17186:14189..14697(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf106
• Ensembl ID: ENSOPRG00000009350
• Aliases: None
• Description: chromosome 6 open reading frame 106 [Source:HGNC Symbol;Acc:21215]

Sequence

>retro_opri_559
CAGTTTGGACATGAGAACATGGTGATGCTGAGATCGCTAGAGCCGCAAGAGATTGCAGATGTTAGGGTCCCGATGTGCAG
CCCCAGCGGAGCAGGAATGTATCAGGGACAGTGGCGGATGTGCACTGCTACAGGACTCTACTATGGAGATGTCATCTGGG
TGATTCTCAGTGTGGAGGTGGGTGTACTTTTAGGAGTAGCACAGCAGCTGTCATTTTGAAATGGAGTTCAACACACAGCC
GCATCACAAGGGTAGAAGGAAACTTCTACCTATTTCCCCTCCCCAAAAGAGCCGAGGAGCAGATGAAAACAACTTATAAG
ACCCTGGGGGTTCCAAGTTCCACTTAATTAGCAAAAACACATGGGCTCCTGCTCCCAACCAAACCAAGCAAGATCAGAAT
AGACTCTCACAGAGCTCTGTAAATTTCTCTCCCAGCAGTCACGCAAACAACTTAGCAGTAGTGACTTACAGTAAGGGGCT
CCACGGGCCTTACCCTTTTGGCCAGTCT

Alignment

ORF - retro_opri_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.92 %
• Parental protein coverage: 58.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QFGHVNMVMVRSLEPQEIADVSVQMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGVTQQL
          QFGH.NMVM.RSLEPQEIADV.V.MCSPS.AGMYQGQWRMCTATGLYYGDVIWVILSVEV.G.L....Q.
Retrocopy QFGHENMVMLRSLEPQEIADVRVPMCSPSGAGMYQGQWRMCTATGLYYGDVIWVILSVEV-GVLLGVAQQ

Parental  SSF-ETEFNTQPHRK-VEGNFN-PFASPQKSRQSDENNLKDPGGSEFDSISKNTWAPAPDQTEQDQNRLS
          .SF.E.EFNTQPH.K.VEGNF..P...PQKSR..DENNL.DPGGS.F..ISKNTWAPAP.QT.QDQNRLS
Retrocopy LSF>EMEFNTQPHHK>VEGNFY<PISPPQKSRGADENNL*DPGGSKFHLISKNTWAPAPNQTKQDQNRLS

Parental  QNSVNLSPSSHANNLSVVTYSKGLHGPYPFGQS
          Q.SVN.SPSSHANNL.VVTYSKGLHGPYPFGQS
Retrocopy QSSVNFSPSSHANNLAVVTYSKGLHGPYPFGQS

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_559 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034493	1 retrocopy	retro_btau_1343,
Callithrix jacchus	ENSCJAG00000015304	1 retrocopy	retro_cjac_2788,
Homo sapiens	ENSG00000196821	1 retrocopy	retro_hsap_2137,
Gorilla gorilla	ENSGGOG00000000388	1 retrocopy	retro_ggor_1653,
Microcebus murinus	ENSMICG00000013442	1 retrocopy	retro_mmur_1615,
Macaca mulatta	ENSMMUG00000022824	1 retrocopy	retro_mmul_2155,
Nomascus leucogenys	ENSNLEG00000008387	2 retrocopies	retro_nleu_1933, retro_nleu_2739,
Otolemur garnettii	ENSOGAG00000011264	1 retrocopy	retro_ogar_3245,
Ochotona princeps	ENSOPRG00000009350	1 retrocopy	retro_opri_559 ,
Pongo abelii	ENSPPYG00000016519	2 retrocopies	retro_pabe_1265, retro_pabe_1928,
Pan troglodytes	ENSPTRG00000018068	1 retrocopy	retro_ptro_1564,