RetrogeneDB ID: retro_opri_360

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_916:390236..390805(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM18
• Ensembl ID: ENSOPRG00000010381
• Aliases: None
• Description: RNA binding motif protein 18 [Source:HGNC Symbol;Acc:28413]

Sequence

>retro_opri_360
ATGGAAGCGGAAACGAAATCTTTTTCCCTGGAGAATGCATCTATCCTCTCAGAGGGCTCATAGCACGAAGGCCGGCGGTT
ATGGATTGGCAGCCTGGACCCCAAGATCACAGAATACCGTCTACTCAAGCTCCTCCAGAAGTTTGGCAAAGTGAAGCAGT
TTGACTTCCTCTTCCACAAATCAAGTGCCCTGGAGTGATAGCCACGAGGATACTGTTTTGTTAACTTTGAAACTAAACAG
AAGGCAGAAGAAGCCATCCAATGTCTCAATGGCAAGCTGGCTCTGTCGAAGAAGCTGGTAGTGCGATGGGCATATGCACA
GGTAAAGAGATATGATCATAACGAGAATGATAAGATCCTTCCAATTAGTCTAGAGCCGCCCACTAGCACAGAGCCCGCTC
AGTCTAACCTAAGTGTCACTGTGAGGATCAAAGCCATTGAAGCAAAGCTGAAAATGATGGCAGAAAATCGTGATGCAGAG
TACCCAGCAGCACCTCTTTATTCCTACTTAAAACCACCAGATAAAAAAGGACTACTCCTTATTCCAGAACAGCTTGGAAA
TCCTGAAGA

Alignment

ORF - retro_opri_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEAETKSLPLENASILSEGSLQEGHRLWIGNLDPKITEYHLLKLLQKFGKVKQFDFLFHKSGALEGQPRG
          MEAETKS..LENASILSEGS..EG.RLWIG.LDPKITEY.LLKLLQKFGKVKQFDFLFHKS.ALE..PRG
Retrocopy MEAETKSFSLENASILSEGS*HEGRRLWIGSLDPKITEYRLLKLLQKFGKVKQFDFLFHKSSALE**PRG

Parental  YCFVNFETKQEAEQAIQCLNGKLALSKKLVVRWAHAQVKRYDHNKNDKILPISLEPSSSTEPAQSNLSVT
          YCFVNFETKQ.AE.AIQCLNGKLALSKKLVVRWA.AQVKRYDHN.NDKILPISLEP..STEPAQSNLSVT
Retrocopy YCFVNFETKQKAEEAIQCLNGKLALSKKLVVRWAYAQVKRYDHNENDKILPISLEPPTSTEPAQSNLSVT

Parental  AKIKAIEAKLKMMAENPDAEYPAAPVYSYFKPPDK-KRTTPYSRTAWKSRR
          ..IKAIEAKLKMMAEN.DAEYPAAP.YSY.KPPDK.KRTTPYSRTAWKS.R
Retrocopy VRIKAIEAKLKMMAENRDAEYPAAPLYSYLKPPDK<KRTTPYSRTAWKS*R

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_360 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013811	1 retrocopy	retro_cpor_237,
Myotis lucifugus	ENSMLUG00000004794	1 retrocopy	retro_mluc_298,
Monodelphis domestica	ENSMODG00000019688	1 retrocopy	retro_mdom_1462,
Oryctolagus cuniculus	ENSOCUG00000008527	1 retrocopy	retro_ocun_290,
Otolemur garnettii	ENSOGAG00000015104	1 retrocopy	retro_ogar_846,
Ochotona princeps	ENSOPRG00000010381	2 retrocopies	retro_opri_1123, retro_opri_360 ,
Ictidomys tridecemlineatus	ENSSTOG00000022388	1 retrocopy	retro_itri_1882,
Tupaia belangeri	ENSTBEG00000016520	1 retrocopy	retro_tbel_2898,