RetrogeneDB ID: retro_opri_1165

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_83812:274..1170(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000000800
• Aliases: None
• Description: None

Sequence

>retro_opri_1165
CCATTTGATGAGTTCCAGATGATATGATGCTAAAGGAAATTCTGAAGGGTCTGGAATATCTGCACTCAGAAACTCACTGA
GACATCAAAGCTGCCAACATCTTGCTGTTAGAACAAGGAGATGTTAAACTTGCTGACTTTGGAATGGCTGGCCAGCTGAC
AGATACACAAATTAAAATAAATTCTTTTGTGGGAACTCCATTTTGGATGGCTGCTGAAGTTATTCAACAGTCAGTTATGA
CTCAAAAGCTGACATATGGTCTTTGAAGATTACTGCTATTGAACTAGCTAAGGGAGAGCCACCTAACTCTGATATGTATC
CAATCAGAGTTCCGTTTCTTATTCCCAAAACAACCCTCCAATCCTTGTTGGAAATTTTAATAAGTCGTTTAAGGAGTTTA
TTGATGCTTGCTGAACAAAGATACATCATTCCATCCTACAGCTAAATGGCTTCTGAAACACAAATTCATTGTAAAAAATT
CAAAGGAGACTTTTTATCTGACCAAACTGATAGATCGCTTCAAGAGATGGAAGGCAGAAGGGCACAGTGATGAGGAATCT
GATTCCAAGGGCTCTGACTTGAAGTCCACCAGCAGGGAAAATATTCATCATGAATGGAGCACAAGAAGCACTGTGCACAA
GAAGGCTGATCCAAAGAAACTACAGAATGGGGCAGAGCAAGATCTGGTGCAAACCCTGAGCAGTTTGTCTATGATAATCA
CCACTGCGTTTGCTGAACTAAAACAGCAGGGTGAGAATAATGCCGGCCGAAACCAGGCTACTGAAGAACTTGAGAAAAGC
ACTGTGGTGGCTGAAGCCACCTGTCCTGGATTTACAAATAAAATGGTGAAGAAACTAACTGAAAAGTTTCAAAAGCGTTC
AGCAAATGAATCACCC

Alignment

ORF - retro_opri_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.76 %
• Parental protein coverage: 60.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PFDEFQIA-TMLKEILKGLDYLHSEKKIHRDIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTP
          PFDEFQ....MLKEILKGL.YLHSE...H.DIKAAN.LL.EQGDVKLADFG.AGQLTDTQIK.N.FVGTP
Retrocopy PFDEFQMI<MMLKEILKGLEYLHSET--H*DIKAANILLLEQGDVKLADFGMAGQLTDTQIKINSFVGTP

Parental  FWMAPEVIQQS-AYDSKADIWSLGITAIELAKGEPPNSDMHPMRVLFLIPK-NNPPTLVGDFTKSFKEFI
          FWMA.EVIQQS..YDSKADIWSL.ITAIELAKGEPPNSDM.P.RV.FLIPK.NNPP.LVG.F.KSFKEFI
Retrocopy FWMAAEVIQQS<SYDSKADIWSLKITAIELAKGEPPNSDMYPIRVPFLIPK<NNPPILVGNFNKSFKEFI

Parental  DAC-LNKDPSFRPTAKELLKHKFIVKNSKKTSYLTELIDRFKRWKAEGHSDEESDSEGSDSESTSRENNT
          DAC.LNKD.SF.PTAK.LLKHKFIVKNSK.T.YLT.LIDRFKRWKAEGHSDEESDS.GSD..STSRE.N.
Retrocopy DAC<LNKDTSFHPTAKWLLKHKFIVKNSKETFYLTKLIDRFKRWKAEGHSDEESDSKGSDLKSTSRE-NI

Parental  HPEWSF-TTVRKKPDPKKLQNGAEQDLVQTLSCLSMIITPAFAELKQQDENNASRNQAIEELEKSIAVAE
          H.EWS...TV.KK.DPKKLQNGAEQDLVQTLS.LSMIIT.AFAELKQQ.ENNA.RNQA.EELEKS..VAE
Retrocopy HHEWSTRSTVHKKADPKKLQNGAEQDLVQTLSSLSMIITTAFAELKQQGENNAGRNQATEELEKSTVVAE

Parental  AACPGITDKMVKKLIEKFQK-SADESP
          A.CPG.T.KMVKKL.EKFQK.SA.ESP
Retrocopy ATCPGFTNKMVKKLTEKFQKRSANESP

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_1165 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013597	1 retrocopy	retro_meug_307,
Ochotona princeps	ENSOPRG00000000800	1 retrocopy	retro_opri_1165 ,