RetrogeneDB ID: retro_opri_386

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1052:229820..230522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB1B
• Ensembl ID: ENSOPRG00000009133
• Aliases: None
• Description: MOB kinase activator 1B [Source:HGNC Symbol;Acc:29801]

Sequence

>retro_opri_386
CCTCCGAGTCCTGAGCAGGGCAGGGGCTGGCGGCCCTCCGTCTCTTCCGCCAAGATGAGCTTCCTCTTCAGCAGCCATTC
TTCTAAAACATTCAAACCAAAGAAGAATATCCCAGAAGGGTCCCATCAGTATGAGCTCCTGAAGCATGTGGAAGCGACTC
TAGAAAGAGGGAATCTGAGACAAGCCGTTATGTTGCCAGAGGGAGAGGACCTCAATGAGTGGATTGCTGTTAACACTGTG
GACTTCTTCAACCAGATCAACATGCTATATGGAACTATTACAGAATTCTGCACTGAAGCAAGCTGTCTAGTCATGTCTGC
TGGGCCAAGATATGAATATCACTGGGCAAATGATACTGATATTAAAAAGCCAATCAAATGTTCTGCACCAAAGTACATTG
ACTATCTGATGACTTGGGTTCAGGATCAGTTTGATGATGAAACTCTTTTTCCTTCTAAGATTGGTGTCCCATTTCCCAAA
AATTTTATGTCTGTGGCAAAGACCATCCTGAAGTGCCTGTTCAGGGTTTATGCCCATATGTATCACCAGCTCTTTGATTC
CATGATGCAGCTCCAAGAGGAGGTCCATCTCAACACCTCCTTTAAGCACTTTATTTTCTTTGTTCAGGAGTTTAACCTGA
TTGATAGGCGTGAGTTGGCACCTCTTCAGGAATTAATTGAGAAGCTTGGATCAAAAGACAGA

Alignment

ORF - retro_opri_386 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 95.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PVLPRPPPGPAPAHAAADMSFLFGSRSSKTFKPKKNIPEGSHQYELLKHAEATLGSGNLRMAVMLPEGED
          P..P....G..P....A.MSFLF.S.SSKTFKPKKNIPEGSHQYELLKH.EATL..GNLR.AVMLPEGED
Retrocopy PPSPEQGRGWRPSVSSAKMSFLFSSHSSKTFKPKKNIPEGSHQYELLKHVEATLERGNLRQAVMLPEGED

Parental  LNEWVAVNTVDFFNQINMLYGTITDFCTEESCPVMSAGPKYEYHWADGTNIKKPIKCSAPKYIDYLMTWV
          LNEW.AVNTVDFFNQINMLYGTIT.FCTE.SC.VMSAGP.YEYHWA..T.IKKPIKCSAPKYIDYLMTWV
Retrocopy LNEWIAVNTVDFFNQINMLYGTITEFCTEASCLVMSAGPRYEYHWANDTDIKKPIKCSAPKYIDYLMTWV

Parental  QDQLDDETLFPSKIGVPFPKNFMSVAKTILKRLFRVYAHIYHQHFDPVIQLQEEAHLNTSFKHFIFFVQE
          QDQ.DDETLFPSKIGVPFPKNFMSVAKTILK.LFRVYAH.YHQ.FD...QLQEE.HLNTSFKHFIFFVQE
Retrocopy QDQFDDETLFPSKIGVPFPKNFMSVAKTILKCLFRVYAHMYHQLFDSMMQLQEEVHLNTSFKHFIFFVQE

Parental  FNLIDRRELAPLQELIEKLTSKDR
          FNLIDRRELAPLQELIEKL.SKDR
Retrocopy FNLIDRRELAPLQELIEKLGSKDR

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_386 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012418	3 retrocopies	retro_chof_1124, retro_chof_1337, retro_chof_660,
Macropus eugenii	ENSMEUG00000014210	1 retrocopy	retro_meug_384,
Microcebus murinus	ENSMICG00000006469	2 retrocopies	retro_mmur_1622, retro_mmur_653,
Myotis lucifugus	ENSMLUG00000005838	1 retrocopy	retro_mluc_1067,
Ochotona princeps	ENSOPRG00000009133	1 retrocopy	retro_opri_386 ,
Sus scrofa	ENSSSCG00000008941	2 retrocopies	retro_sscr_377, retro_sscr_586,
Vicugna pacos	ENSVPAG00000011892	1 retrocopy	retro_vpac_35,