RetrogeneDB ID: retro_opri_646

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2162:82816..83530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC109B
• Ensembl ID: ENSOPRG00000017044
• Aliases: None
• Description: coiled-coil domain containing 109B [Source:HGNC Symbol;Acc:26076]

Sequence

>retro_opri_646
TCTCTGCCATCCCGGAAAGAGCGCTGTCAGTTTGTGGTCCAGCCGGTGCTGTCACAGTGGGCTCATTCCCTCCAGGACCT
GCAGAGCGAAGACAAGGGTGTCACGGCTGCAGCCGTGATTGCTGCAGATGGCAGTGAGATACCAGCTTCCACCTTGATGG
GAACTTTGCTCATGAAAGATTTTAAGCTTGTCATCAATGAAGTGGCTTATGATGTGCAGTGCCCTAACAAAGGAAATCTA
ACTAATGAGCACATCCCCGAGATGGAAAGCGTGAAAGCCTTGGTTCACAGGCTCTTCACAGTCTTGCACTTAGAAGAGTT
TCAGAAGAGGAGAGAGCACCTGCTACTGGAGAAAATCGACCACCTGAAGAGACAGCTGCAGCCCCTTGAGCAGGTGAAAG
CTAGACTTGAAGCTCGTTCAGAAGCCAACACCAGCAGGCTCCTCTGGGCTGGCTTAGCACTGCTGTCCACTCAGGGCGGG
GCCCTGGCCTGGCTCACTTGGTGGGTGTACTCCTGGGACATCATGGAGCCAGTCACATACTTCATCACGTTCGCAAATTC
CATGGTCTTTTTTGCATACTTCATAGTCACTCGACAGAGTTACACTTACTCTGCTGTGAGGAGCAGGCAGTTTCTTCAGT
TCTTCCACAAGAAATCAAAGCAACAGCATTTTGATGTGGAGCAGTACAACAGGTTAAAGGAGGACCTTGCCAAG

Alignment

ORF - retro_opri_646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.33 %
• Parental protein coverage: 85.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TLPSRKERCQFVVQPVLS-TVGSF-LQDLQSEDKGVTAAAVIAADGSEIPASTLMGTLLMKDFKLVINEV
          .LPSRKERCQFVVQPVLS.TVGSF.LQDLQSEDKGVTAAAVIAADGSEIPASTLMGTLLMKDFKLVINEV
Retrocopy SLPSRKERCQFVVQPVLS<TVGSF>LQDLQSEDKGVTAAAVIAADGSEIPASTLMGTLLMKDFKLVINEV

Parental  AYDVQCPNKGNLTNEHIPEMESVKALVHRLFTVLHLEEFQKRREHLLLEKIDHLKRQLQPLEQVKARLEA
          AYDVQCPNKGNLTNEHIPEMESVKALVHRLFTVLHLEEFQKRREHLLLEKIDHLKRQLQPLEQVKARLEA
Retrocopy AYDVQCPNKGNLTNEHIPEMESVKALVHRLFTVLHLEEFQKRREHLLLEKIDHLKRQLQPLEQVKARLEA

Parental  RSEANTSRLLWAGLALLSTQGGALAWLTWWVYSWDIMEPVTYFITFANSMVFFAYFIVTR-SYTYSAVRS
          RSEANTSRLLWAGLALLSTQGGALAWLTWWVYSWDIMEPVTYFITFANSMVFFAYFIVTR.SYTYSAVRS
Retrocopy RSEANTSRLLWAGLALLSTQGGALAWLTWWVYSWDIMEPVTYFITFANSMVFFAYFIVTRQSYTYSAVRS

Parental  RQFLQFFHKKSKQQHFDVEQYNRLKEDLAK
          RQFLQFFHKKSKQQHFDVEQYNRLKEDLAK
Retrocopy RQFLQFFHKKSKQQHFDVEQYNRLKEDLAK

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_646 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013586	1 retrocopy	retro_etel_443,
Loxodonta africana	ENSLAFG00000002726	1 retrocopy	retro_lafr_1127,
Ochotona princeps	ENSOPRG00000017044	1 retrocopy	retro_opri_646 ,
Vicugna pacos	ENSVPAG00000009837	1 retrocopy	retro_vpac_642,