RetrogeneDB ID: retro_opri_1063

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_64337:1051..1619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C5orf45
• Ensembl ID: ENSOPRG00000015567
• Aliases: None
• Description: chromosome 5 open reading frame 45 [Source:HGNC Symbol;Acc:30817]

Sequence

>retro_opri_1063
CGCGTCCTGAGGTGCCGCTGCTGCGACCTCTTCTAACCGCCCCACCTCAAAAAGAGTTCCAAATGGACATGCAAAGCATG
CGCTAAGAGCAGTCGTTTTTGCAGAGCTACAGTGAGGGCTGCGGTGCTGTGCACAGACGCCATGTCCAAAAGTTACATCG
GCTGCAAAGACAGGTTTCACAGCTGTAGCTCAAGCCTCTGGAAGGTTCTGGAAGTGTCAGTGAAGAACTGGAAGATCACC
AGCAGGCAGAGAATGTGGATCCTCAACCCTCTAGGTGCCGCTGGCTGAAGTTTCTAGACAAGGACTCCCCAGGACTGCAG
CTGGGAGGAGAGTGTTTCCATGAACAGTCCTCATCCGACATGGAGAACCCGGACCCTCCCTTCAGTTGGGAGCTGCCCAG
AAAAAGGAAATGGCGCCTGAGCCCAGCCCAGCTGTCACACAAGCGTGACATCCCAGACTTGGGCACTCCAAGGGACACCT
GGCACCCCAGAAGGACACTCGTGGCCTGACCTTGAAGGTGAAGGAAGGTGGCAGCCACTGCCTCTGGAGCCCTGTGGACC
CACCACCC

Alignment

ORF - retro_opri_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.18 %
• Parental protein coverage: 59.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVLRCCSCGLCQAHQLKKSPKWTCKACGK-KQSFLRSYGEGSGADCRRHVQKLNLLQGQISELPLRSLEG
          RVLRC..C.L.....LKKS.KWTCKAC.K..QSFL.SY.EG.GA..RRHVQKL..LQ.Q.S.L.L..LEG
Retrocopy RVLRCRCCDLF*PPHLKKSSKWTCKACAK<EQSFLQSYSEGCGAVHRRHVQKLHRLQRQVSQL*LKPLEG

Parental  SGSVSEEEIEDHHEAENVHPQQPSESRWLKFLHKDSPELELGGGVCFRGQSSSDMEESDPAFSQELPRKR
          SGSVSEE..EDH..AENV.PQ.PS..RWLKFL.KDSP.L.LGG..CF..QSSSDME..DP.FS.ELPRKR
Retrocopy SGSVSEE-LEDHQQAENVDPQ-PSRCRWLKFLDKDSPGLQLGGE-CFHEQSSSDMENPDPPFSWELPRKR

Parental  KWSPSPAQLSHNCDIPDLATPRGTW-PPQQDSPGLNVKVKAGSSHRLWNHEDPRP
          KW..SPAQLSH..DIPDL.TPR.TW..PQ.D..GL..KVK.G.SH.LW...DP.P
Retrocopy KWRLSPAQLSHKRDIPDLGTPRDTW<APQKDTRGLTLKVKEGGSHCLWSPVDPPP

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_1063 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000015567	1 retrocopy	retro_opri_1063 ,