RetrogeneDB ID: retro_opri_691

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_24286:41782..42415(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIGMAR1
• Ensembl ID: ENSOPRG00000009222
• Aliases: None
• Description: sigma non-opioid intracellular receptor 1 [Source:HGNC Symbol;Acc:8157]

Sequence

>retro_opri_691
TGGGCCCCGCTGCTTCTGACCACCGCGGCTGTGCTGACCCAGGTGCTCTGGCTGGGGATGCAGAACTTCGTCTTCCAGCG
CGAAGAGATGGCGCTGCTGGCGAGGAAGTACGCAGGGCTGGACCATGAGCTGGCTTTCTCTCGGCTGATTGTGGAGCTGT
GGCGGCTGCGCCCAGGCCACATGCTGCCTGACGAGGAGCTGCAGTGGGTGTTTGTGAACGCGGGAAGCTGGATGGGTGCC
ATGTGCCTTCTGCACGCCTTGCTGTCCGAGTACGTGCTGTTGTTTGGCACCGCCCTGGGCTCCCGCGGCCATTAGAGCCG
CTGTTGGGCTGAGATCTCTGATACCATCATCTCTGGCACCTACCACTAGTCGAGAGAGGGCACTACCAAAAGTGAGAGCT
TCTACCCAGGAGAGATGGTGGTCCATAGGCCTGGAGTAGCGACAGCTGTGGAGTGGGGACCCAACACGTGGATGGTGGAG
TACGGCGGGGGTGTCATCCCATGTTCCCTGGCATTCATGCTGGCCGACACAGTCTTCAGCACCCAAGACTTGCTCACTCT
CTTCTACACCCTTCGTGCATATGCCCGGGGCTTCCGACTTGAACTTGCCACCTACCTCTTTGGCCAGGACCCT

Alignment

ORF - retro_opri_691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.15 %
• Parental protein coverage: 95.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WAALLLAAAAVLTQVLWLGTQNFVFEREEIALLARKYAGLDHELAFSRLIVELRRLHPGHVLPDEELQWV
          WA.LLL..AAVLTQVLWLG.QNFVF.REE.ALLARKYAGLDHELAFSRLIVEL.RL.PGH.LPDEELQWV
Retrocopy WAPLLLTTAAVLTQVLWLGMQNFVFQREEMALLARKYAGLDHELAFSRLIVELWRLRPGHMLPDEELQWV

Parental  FVNAGGWMGAMCLLHASLSEYVLLFGTALGSRGHSGRYWAEISDII--STFHQWXXXXXXXXXXXXXETV
          FVNAG.WMGAMCLLHA.LSEYVLLFGTALGSRGH..R.WAEISD.I...T.H...............E.V
Retrocopy FVNAGSWMGAMCLLHALLSEYVLLFGTALGSRGH*SRCWAEISDTIISGTYH*SREGTTKSESFYPGEMV

Parental  VHGPGEATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRAYARGLRLELTTYLFGQD
          VH.PG.ATAVEWGPNTWMVEYG.GVIP..LAF.LADTVFSTQD.LTLFYTLRAYARG.RLEL.TYLFGQD
Retrocopy VHRPGVATAVEWGPNTWMVEYGGGVIPCSLAFMLADTVFSTQDLLTLFYTLRAYARGFRLELATYLFGQD

Parental  P
          P
Retrocopy P

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_691 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008767	1 retrocopy	retro_cjac_155,
Microcebus murinus	ENSMICG00000002386	1 retrocopy	retro_mmur_119,
Ochotona princeps	ENSOPRG00000009222	1 retrocopy	retro_opri_691 ,