RetrogeneDB ID: retro_opri_1034

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_60598:0..1224(-)
• 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_1034
ATGGATCCTGTTGGAGTGGCATCGCCTGAGCCAGGGCCAGCAGCAGCCTGGGGCCCCAGCAAGTGTCCGTGGGCCACACC
TCAAAATACAGCATCCTGTTCTTTGGCTGACGTCATGAGCAAACAGCTGGCTAAAGAACTGCAGTTAGAAGAAGAAGCTG
CTGCTTTTCCTGAAGTTGCTGCTGCTGATGGACCGTTTGTCTCTGGAGAAAATGTTGACACCTCCAGTGATCTAATGCTA
CAGATGCTACAGATAGAATTTGACAGAGAATATGACGCACAGCTGAGGCATGAAGAAAAGAAGTTCAATGGAGATAGCAA
AGTTTCTGTCTCTTTTGAAAATTATCGAAAAGTGCATCCTTATGAAGACAGTGATAGCTCTGAAGACGAGGTTGAATGGC
AGGACATGCGTGATGATCCCTACAGACCAGCAAAACCAGTTCCCACTCCCAAAAAGGGCTTTATTGGAAAAGGAAAAGAC
ATCACTACTAAACACGATGAGGTTGTGTGTGGGAGAAAGAACACAGCAAGATGGAAAATTTTGCGCCTGGCTTTCAGGTT
GGAGATGGAATTGGAATGGATTTGAAACTATCCAACCACGTTTTCAATGCCCTGAAACAGCATGCCTACTCTGAGGAGCG
CTGGAGCGCCCACGTGCATGAAAAGAAGGAGCATTCTACTGCGGAAAAAGCAGTTGATCCTAAGACATGTCTACTTATAT
ATAAAATGATCAACTCTGGAATGTTGGAGGCAATCACTGGCTGTATTAGTACAGGAAAGGAATCTGTTGTCTTCCATGCC
GATGGCGGGAGCATGGAGGAAGAGAAGGAAGATTGTAAAGCTATACCCACAGAATGTGCCATCAAGGTATTTAAAACAAC
CCCTTAATGAATTTAATAATCATGACAAATATATTAAAGATGATTTCAGGTTTAAAGATAGCTTCAGTAAACTAAATCCA
CGTAAGATAATCCGCATGTGGGCAGAAAAAGAAATGCACAATCTCACCAGAATGCAGAGAGCTGGAATTCCTTGTCCAAC
AGTTGTACTGCTCAAGAAGCACATTTTAGTTATGTCTTTTATTGGCCAAGATCAAGTTCCAGCCCCTAAATTAAAAGAAG
TAAAGCTCAGTAGTGAAGAACTGAAAGACGCTTATTACCAAACTCTTCATTTGATGCAGCAGCGGTATAATGAGTGCACT
CTTGTCCATGCTGACTTCAGCGAG

Alignment

ORF - retro_opri_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.19 %
• Parental protein coverage: 78.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDPVGVASPEPGTAAAWGPSKCPWATPQNTMSCSLADVMSEQLAKELQLEEEAAAFPEVAAADGPFVSGE
          MDPVGVASPEPG.AAAWGPSKCPWATPQNT.SCSLADVMS.QLAKELQLEEEAAAFPEVAAADGPFVSGE
Retrocopy MDPVGVASPEPGPAAAWGPSKCPWATPQNTASCSLADVMSKQLAKELQLEEEAAAFPEVAAADGPFVSGE

Parental  NVDTSSDLMLAQMLQMEFDREYDAQLRREEKKFNGDSKVSISFENYRKVHPYEDSDSSEDEVDWQDTRDD
          NVDTSSDL........EFDREYDAQLR.EEKKFNGDSKVS.SFENYRKVHPYEDSDSSEDEV.WQD.RDD
Retrocopy NVDTSSDLXXXXXXX-EFDREYDAQLRHEEKKFNGDSKVSVSFENYRKVHPYEDSDSSEDEVEWQDMRDD

Parental  PYRPAKPVPTPKKGFIGKGKDITTKHDEVVCGRKNTAR-MENFAPGFQVGDGIGMDLKLSNHVFNALKQH
          PYRPAKPVPTPKKGFIGKGKDITTKHDEVVCGRKNTAR.MENFAPGFQVGDGIGMDLKLSNHVFNALKQH
Retrocopy PYRPAKPVPTPKKGFIGKGKDITTKHDEVVCGRKNTAR<MENFAPGFQVGDGIGMDLKLSNHVFNALKQH

Parental  AYSEERRSARVHEKKEHSTAEKAVDPKTRLLMYKMINSGMLEAITGCISTGKESVVFHAYGGSMDEEKED
          AYSEER.SA.VHEKKEHSTAEKAVDPKT.LL.YKMINSGMLEAITGCISTGKESVVFHA.GGSM.EEKED
Retrocopy AYSEERWSAHVHEKKEHSTAEKAVDPKTCLLIYKMINSGMLEAITGCISTGKESVVFHADGGSMEEEKED

Parental  CKAIPTECAIKVFKTT-LNEFKNRDKYIKDDFRFKDRFSKLNPRKIIRMWAEKEMHNLTRMQRAGIPCPT
          CKAIPTECAIKVFKTT.LNEF.N.DKYIKDDFRFKD.FSKLNPRKIIRMWAEKEMHNLTRMQRAGIPCPT
Retrocopy CKAIPTECAIKVFKTT>LNEFNNHDKYIKDDFRFKDSFSKLNPRKIIRMWAEKEMHNLTRMQRAGIPCPT

Parental  VVLLKKHILVMSFIGQDQVPAPKLKEVKLSSEELKDAYYQTLHLMQQLYNECTLVHADLSE
          VVLLKKHILVMSFIGQDQVPAPKLKEVKLSSEELKDAYYQTLHLMQQ.YNECTLVHAD.SE
Retrocopy VVLLKKHILVMSFIGQDQVPAPKLKEVKLSSEELKDAYYQTLHLMQQRYNECTLVHADFSE

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_1034 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,