RetrogeneDB ID: retro_opri_946

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4875:158238..159589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIOK3
• Ensembl ID: ENSOPRG00000004803
• Aliases: None
• Description: RIO kinase 3 [Source:HGNC Symbol;Acc:11451]

Sequence

>retro_opri_946
GCTACTGCTGCTGGACCATCTGCCTCTGGAGAAAGCATTGGCACCTCCAGTGACCTAATGCTGGCCCAGATTCTACAGAT
GGAGCTTCACAGAGAATATGACGCACAGCTGAGGCATGAAGAAAATAAATTCAATGGAGAGGCAAAGTTTTTCTACATTG
TTTGAAAACTATCAAAAAATGCATCCTTATGAAGACAGTGACAGCTATGAAGACAAGGTTGGCTGGCAGGATATACATGA
CGATCCCAGCAAAACCAGCTCCCCCCTTCAAAGGGCTTTATTGAAAAAGGGAAAGACATCAATACCAAACATGATGAGGT
CGAGTGTGTGAGAAAGAATACAGTGAAAATGGAAACTTTTGCACTTGGGTTTCCAGTTGGAGATGGATTTGGAATGGATT
TGAAGCTATGTAACCATGTTTTCAATGTTCTGAATCAGCAGACCTACTCAGAGGAGCACCAAAGCACCTGCCTCCATGAG
AAGAAGGAACATTCTATCACACAAAAAAGCAGTCGATTCTACAACATGTTACTGATGTATAAAATGATCAACTCTGGAAT
GGAGGCAATCACTGGCTGTATTTGTACAACAAAGAAGTCTGTTATCTTTCATAAATTTGGGGGGAGCATGGAGGGTAAGA
AGACGGATAGCAAAGCTATAGCTACAGAATGTGCCATCAATGCATTGAAAACAACCCTTAGTGAGTTTCAGAATCATGAC
ACATATATTAAAGATTATTTCAGGTTTAAGGATAGCTTCAGTAAACTAAATCCACATAAGATCATCCATATGTGGGCAGA
AAAAGAAAAGCACAATTTCACAAGAATGCAGAGAGTTGGAATTCCTCTTCCAAAAGTTGTATTGCTCATGAAACACATTT
TAGCTATGTCTTTCATTGGCCATGATGAAGTTTCAGTGCCTAAATTAAAAGAAATATTTCTCAGTAGTGTAAATTGAAAA
ACACTTACTACTAAACTCTTCATTTGATGCAGCAGTTGTATAACGAATGTACCCAACTGCATGCTAACCGAGCGAGTGTA
ACAGGATGTGGCATCCTGGGAAGGCCTGGTTAATTGATATCAGTCAGTTGTTATAGACAACCCAACCCCATGGCTTGGAA
TTCCTATTCCAGAACTGCAGGAATCTCTCGTAGTTTTTCCAGAAAGAAGGAGTGAAGGAAGTTCCAGACAAATGAGAACT
CTTCATTGTGGTTTCATGCTTAAGGTTCTCAGCAGATATCAAGGCAGATTTCTTAGCTGAGATAGAAACTTTAGAGAAAA
TGAATGAGGGTCAAATTCTCAAGAGTGGAAGAAAAGCTTCTTCATTTTTGAAAGACAATGGTGGCCCACCA

Alignment

ORF - retro_opri_946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.23 %
• Parental protein coverage: 87.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AAADGPFVSGENVDTSSDLMLAQMLQMEFDREYDAQLRREEKKFNGDSK-VSISFENYRKVHPYEDSDSS
          A.A.GP..SGE...TSSDLMLAQ.LQME..REYDAQLR.EE.KFNG..K..S..FENY.K.HPYEDSDS.
Retrocopy ATAAGPSASGESIGTSSDLMLAQILQMELHREYDAQLRHEENKFNGEAK>FSTLFENYQKMHPYEDSDSY

Parental  EDEVDWQDTRDDPYRPAKPVPTPKKGFIGKG-KDITTKHDEVVCGRKNTARMENFAPGFQVGDGIGMDLK
          ED.V.WQD..DDP.....P..........KG.KDI.TKHDEV.C.RKNT..ME.FA.GF.VGDG.GMDLK
Retrocopy EDKVGWQDIHDDPSKTSSPL---QRALLKKG<KDINTKHDEVECVRKNTVKMETFALGFPVGDGFGMDLK

Parental  LSNHVFNALKQHAYSEERRSARVHEKKEHSTAEKAVDPKTRLLMYKMINSGMLEAITGCISTGKESVVFH
          L.NHVFN.L.Q..YSEE..S...HEKKEHS...K.......LLMYKMINSGM.EAITGCI.T.K.SV.FH
Retrocopy LCNHVFNVLNQQTYSEEHQSTCLHEKKEHSITQKSSRFYNMLLMYKMINSGM-EAITGCICTTKKSVIFH

Parental  AYGGSMDEEKEDCKAIPTECAIKVFKTTLNEFKNRDKYIKDDFRFKDRFSKLNPRKIIRMWAEKEMHNLT
          ..GGSM...K.D.KAI.TECAI...KTTL.EF.N.D.YIKD.FRFKD.FSKLNP.KII.MWAEKE.HN.T
Retrocopy KFGGSMEGKKTDSKAIATECAINALKTTLSEFQNHDTYIKDYFRFKDSFSKLNPHKIIHMWAEKEKHNFT

Parental  RMQRAGIPCPTVVLLKKHILVMSFIGQDQVPAPKLKEVKLSSE-ELKDAYYQTLHLMQQLYNECTLVHAD
          RMQR.GIP.P.VVLL.KHIL.MSFIG.D.V..PKLKE..LSS...LK..YY.TLHLMQQLYNECT..HA.
Retrocopy RMQRVGIPLPKVVLLMKHILAMSFIGHDEVSVPKLKEIFLSSV<KLKNTYY*TLHLMQQLYNECTQLHAN

Parental  L-SEYNMLWHAGKVWLIDVSQSVEPTHPHGLEFLFRDCRNVSQFFQKGGVKEALGERELFNAVSGLNISA
          ..SE.N..WH.GK.WLID.SQ....T.PHGLEFLF..CRN.S.FFQK.GVKE.....ELF..VS.L..SA
Retrocopy R<SECNRMWHPGKAWLIDISQLL*TTQPHGLEFLFQNCRNLS*FFQKEGVKEVPDK*ELFIVVSCLRFSA

Parental  DNEVDFLAEIEALEKMNEDHVQKNGRKAASFLKDDGGPP
          D...DFLAEIE.LEKMNE....K.GRKA.SFLKD.GGPP
Retrocopy DIKADFLAEIETLEKMNEGQILKSGRKASSFLKDNGGPP

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_946 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008343	1 retrocopy	retro_chof_1788,
Callithrix jacchus	ENSCJAG00000020556	1 retrocopy	retro_cjac_2617,
Echinops telfairi	ENSETEG00000003689	1 retrocopy	retro_etel_2181,
Macropus eugenii	ENSMEUG00000006292	1 retrocopy	retro_meug_1278,
Macaca mulatta	ENSMMUG00000021478	1 retrocopy	retro_mmul_1291,
Ochotona princeps	ENSOPRG00000004803	2 retrocopies	retro_opri_1034, retro_opri_946 ,
Pongo abelii	ENSPPYG00000009062	1 retrocopy	retro_pabe_1011,