RetrogeneDB ID: retro_opri_1115

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_7247:41344..42396(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUVBL1
• Ensembl ID: ENSOPRG00000011261
• Aliases: None
• Description: RuvB-like 1 (E. coli) [Source:HGNC Symbol;Acc:10474]

Sequence

>retro_opri_1115
GACGAGAGCTGCTTGGCCAAGCAGGCGGCCTCAGGACTCGTGGGCCAGGAGAACGTGCGGGAGGCACGTGGCGTCATTGA
ATTAATCAAAAGCAAGAAAATGGCTGAAAGAGCTGACTTGTTGGCAGGACCTCCTGGAACTGGCAAGACAGCTCTAGCCC
TGGCTGTTGCTCAGGAGCTGGGTACTAAGGTCCTTGTCTGTCCAATGGTGGGGAGTTGAAGTTTACTCGACGGAGATCAA
GAAGACAGAGGTGCTGATGGAGAATTCCCGCAGGGCCATCGGGCTGTGGATAAAGGAGACCAAGTAAGTTTATGTAGGTG
AAGTCACAGAGCTGACTCCGTGTGAGACAGAGAACCCCATGGGAGGGTATGGCAAAACCATCAGCCACGTGATCATAGGA
CTCAAGCAAGCCAAAGGAATCAAGCAGTTGCAACTGGACCCTGGCATTTTTGAAAGTTTGCAGAAAGAGCGAGTGGAGGC
TGGGTATGTATTTCACATCGAGGCCAACAGCGGAGCTGTGAAGAGGCAAGGCAGGTGTGATACTCATGCCACAGAATTCG
GCCTTGAAGCTGAAGAGTAGGTGCCCTTGCCAAAGGGGGACGTGCACAAGAAGGAGATCATCCAGGACGTGACCTTGCAC
GACTTGGATGTGGCTAATGAGCGACCCCAGGGAGGACAAGACATTCTGTCCATCATGGACCAGGTAATGAAACCAAAGAA
GACAAATTACAAACTTCGAGGGGAAATTAACAAGGTGGTGAACAAGTACATCGAGCAGGGCATTGCCGAGCTGGTTCCAG
GTGTTCTGTTTATTGATGAAGTGCATATTGCTGGACGTTGTGTGCTTCACCTACCTGCACCGGGCCCTAGAATCTTCTAT
CACCCCCATCGTCATCTTCGCATCCAACCAAGGCAACTGTGTCATCAGAGGCACCAAGGATATTACCACTCCTCACAGCA
TTCCGCTCGACCTCCTGGACCGAGTGATGATCATCCGGACCATGCTGTACACTCTGCAGGAAATGAAGCAGATTGTTAAA
ATCCGAGCCCAG

Alignment

ORF - retro_opri_1115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 77.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPM
          DES.LAKQAASGLVGQEN.REA.GVI.ELIKSKKMA.RA.LLAGPPGTGKTALALA.AQELG.KV..CPM
Retrocopy DESCLAKQAASGLVGQENVREARGVI-ELIKSKKMAERADLLAGPPGTGKTALALAVAQELGTKVLVCPM

Parental  VGS-EVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAK
          VGS.EVYSTEIKKTEVLMEN.RRAIGL.IKETK.VY.GEVTELTPCETENPMGGYGKTISHVIIGLK.AK
Retrocopy VGS>EVYSTEIKKTEVLMENSRRAIGLWIKETK*VYVGEVTELTPCETENPMGGYGKTISHVIIGLKQAK

Parental  GTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEII
          G.KQL.LDP.IFESLQKERVEAG.V..IEANSGAVKRQGRCDT.ATEF.LEAEE.VPLPKGDVH.KKEII
Retrocopy GIKQLQLDPGIFESLQKERVEAGYVFHIEANSGAVKRQGRCDTHATEFGLEAEE*VPLPKGDVH-KKEII

Parental  QDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVH
          QDVTLHDLDVAN.RPQGGQDILS.M.Q.MKPKKT....KLRGEINKVVNKYI.QGIAELVPGVLF.DEVH
Retrocopy QDVTLHDLDVANERPQGGQDILSIMDQVMKPKKTNY--KLRGEINKVVNKYIEQGIAELVPGVLFIDEVH

Parental  -MLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQI
          ..LD..CFTYLHRALESSI.PIVIFASN.GNCVIRGT.DIT.PH.IPLDLLDRVMIIRTMLYT.QEMKQI
Retrocopy >LLDVVCFTYLHRALESSITPIVIFASNQGNCVIRGTKDITTPHSIPLDLLDRVMIIRTMLYTLQEMKQI

Parental  IKIRAQ
          .KIRAQ
Retrocopy VKIRAQ

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_1115 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000004254	1 retrocopy	retro_mluc_1421,
Mus musculus	ENSMUSG00000030079	1 retrocopy	retro_mmus_493,
Ochotona princeps	ENSOPRG00000011261	1 retrocopy	retro_opri_1115 ,
Rattus norvegicus	ENSRNOG00000013195	2 retrocopies	retro_rnor_2883, retro_rnor_424,