RetrogeneDB ID: retro_opri_911

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_44054:4877..5383(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM76A
• Ensembl ID: ENSOPRG00000017049
• Aliases: None
• Description: family with sequence similarity 76, member A [Source:HGNC Symbol;Acc:28530]

Sequence

>retro_opri_911
ATGGCGACTCTCTAAGCCTGCACCAAGTGTCACCAGCGCTTCCCCTTCGAGACACTGTCTCAGGGGCAGCAGCTGTGCAA
GGAATATCGGATTGCCCACCCCGTGGTGAAGTGTACCTACTGCAGGACTGAGTACCAGCAAGAGAGTAAAACCAATACAA
TACGCAAGAAATGCACTCAGAACGTGCAGTTGTATGGAACGCCAAACCATGCCAGTAATGCTACATAATCGCAGAGTTTA
TTGGCAATAAATGCCCGCTCTGTATGAATTCAGAGAAGTATGCTCACCGTATTCCTGGGAGTAGGGCAAGCAGCAGTGTG
CATTTGACAGGAAAGATGATAGGAAAAAGGTCAATGGCAAGTTGGCTGTGCTGGCTGTGTACGCTGTTGCACAAACGGGT
CCTGCAGAAGGCCAAGGAGCAGAGGAAGCACCTGAACAGCTCTTCCCTGGCCAGCCACCAGCAGAAGGAGCAATACAGTT
GCCTCAGTGGCAGTGGCCATTACAAC

Alignment

ORF - retro_opri_911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.24 %
• Parental protein coverage: 55.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAALYACTKCHQRFPFEALSQGQQLCKECRIAHPVVKCTYCRTEYQQESKTNTICKKCAQNVQLYGTP-K
          MA.L.ACTKCHQRFPFE.LSQGQQLCKE.RIAHPVVKCTYCRTEYQQESKTNTI.KKC.QNVQLYGTP.K
Retrocopy MATL*ACTKCHQRFPFETLSQGQQLCKEYRIAHPVVKCTYCRTEYQQESKTNTIRKKCTQNVQLYGTP<K

Parental  PCQYCNIIAAFIGNKCQRCTNSEKKYG-PPYSCEQCKQQCAFDRKDDRKKVDGKL-LCWLCTLSYKRVLQ
          PCQ.C.IIA.FIGNKC..C.NSE.KY...PYS.E..KQQCAFDRKDDRKKV.GKL.LCWLCTL..KRVLQ
Retrocopy PCQ*CYIIAEFIGNKCPLCMNSE-KYA<SPYSWE*GKQQCAFDRKDDRKKVNGKL>LCWLCTLLHKRVLQ

Parental  KTKEQRKHLSSSSRASHQEKEQYSRLSGSGHYN
          K.KEQRKHL.SSS.ASHQ.KEQYS.LSGSGHYN
Retrocopy KAKEQRKHLNSSSLASHQQKEQYSCLSGSGHYN

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_911 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009327	1 retrocopy	retro_cjac_3197,
Mus musculus	ENSMUSG00000028878	2 retrocopies	retro_mmus_1689, retro_mmus_2783,
Ochotona princeps	ENSOPRG00000017049	1 retrocopy	retro_opri_911 ,