RetrogeneDB ID: retro_opri_723

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_26:1029681..1030231(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2A2
• Ensembl ID: ENSOPRG00000011847
• Aliases: None
• Description: casein kinase 2, alpha prime polypeptide [Source:HGNC Symbol;Acc:2459]

Sequence

>retro_opri_723
TTGGTATTTGAATATATCAGCAATACTGATTTTAAGCAATTCTGCCAGATCCTCACAGATTTGATGTCCAGTTTTATGTG
TATGAGCTACTTACAGCTCTGGATTACTTCCACAGCAAGGGAATCACACACAAGGATATGAAACCACGCAATGTCATGAT
AGAGCCCCAATGAAAAAGCCACAGCTGATAGACTGGGGCCTGGCTGAGTTCTGTCAGTCTGCTTAGGAGTATTCTGTCTG
CATAGCTTTGAGGTATTCTCAGGAGCCAGGGTTTCTTGTGGACTATCAGATGTACGATTACAGTTTGGACAACTGGAGTT
TGGACTGAATGATAGCAAGCATGGTCTTCTGAATGGAGCCTTTCTTCCAGGGGCAAGAAAACGCTGAGCAGCTTGCTCAT
ATTGCCAAGGTGCTGGGCATGAATGAACTGTATGGATATCTGAAGTGCCACATAGACCTAGATCCGCACTTCATTGATAT
CCTGGGACAACGTTCATGGAAATGCTGGGACAACTTTATCGATAGTGAAGACAGACACCTTGCCAGCCCA

Alignment

ORF - retro_opri_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 53.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVFEYINNTDFKQLYQILTD-FDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQ-QQKLRLIDWGL
          LVFEYI.NTDFKQ..QILTD.FD..FY.YELL.ALDY.HSKGI.H.D.KP.NVMI..Q...K..LIDWGL
Retrocopy LVFEYISNTDFKQFCQILTD<FDVQFYVYELLTALDYFHSKGITHKDMKPRNVMIEPQ<MKKPQLIDWGL

Parental  AEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGQDNYDQLVRIAKV
          AEF...A.EY.V..A.RY...P..LVDYQMYDYSLD.WSL..M.ASM.F..EPFF.GQ.N..QL..IAKV
Retrocopy AEFCQSA*EYSVCIALRYSQEPGFLVDYQMYDYSLDNWSLD*MIASMVF*MEPFFQGQENAEQLAHIAKV

Parental  LGTDELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSP
          LG..ELYGYL.K.HIDLDPH...............FI.SE.RHL.SP
Retrocopy LGMNELYGYL-KCHIDLDPHXXXXXXXXXXXXXXXFIDSEDRHLASP

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_723 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000000930	1 retrocopy	retro_eeur_442,
Macropus eugenii	ENSMEUG00000013416	1 retrocopy	retro_meug_1470,
Myotis lucifugus	ENSMLUG00000000283	2 retrocopies	retro_mluc_1999, retro_mluc_2562,
Mustela putorius furo	ENSMPUG00000004713	1 retrocopy	retro_mputfur_1121,
Ochotona princeps	ENSOPRG00000011847	2 retrocopies	retro_opri_149, retro_opri_723 ,
Ictidomys tridecemlineatus	ENSSTOG00000003538	1 retrocopy	retro_itri_1769,