RetrogeneDB ID: retro_opri_573

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1780:2238..3359(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000009578
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTA1
• Ensembl ID: ENSOPRG00000002854
• Aliases: None
• Description: actin, alpha 1, skeletal muscle [Source:HGNC Symbol;Acc:129]

Sequence

>retro_opri_573
GATGATGAGCTGTCTGCCTTAGTAGTAGATAATGGGTCAGGGATGTGTAAGGCAGGCTTTGGTGGAGATGATGCCCACGG
GCTGTGTTCCCCTCCATGGTGGGGCGTCCACGACACCAGGGGGTCATGGTAGGCATGGGCCAGAAGGACTGCTACGTCGG
GGATGAGGCGCAGAGCAAGAGAGGCATCCTGACCCTGAAGTATCCCATTGAACACGGAGTAGTCACCAACTGGGACGACA
TGGAGAAAATCTGGTACCACACTTTCTACAACGAGCTTCGGGTGGCACCTGACGAGCATCCCATCCTCCTCACCGAGGCC
CCCCTCAACCCTAAGATCAACCGCGAAAAGATGACTCAGATTATGTTCGAGGCCTTCAATACACCAGCCATGTATGTGGC
TATCCAAGCTGTGCTGTCCCTCTATGCCTCCGGACGGACCACAGGCATAGTCATGGATTCTGGGGACGGGGTCACTCATA
CCGTGCCCATCTATGAAGGCTACGCCTTGTCCCATGCCATCCTGCGTCTGGATCTGGCAGGCAGAGATCTGACGGATTAC
CTCATGAAGATCCTGACAGAGAGAGGCTATAGTTTCACCACCACGGCTGAGCGGGAGATTGTGCGGGATGTCAAAGAGAA
GCTGTGCTACGTGGCCCTGGACTTTGAACAGGAGATGGTCAGCGCAGCTGCATCCTCCTCGCTGGAAAGAAGCTATGAGC
TTCCGGATGGGCAGGTGATCACCATCGGGAATGAACGCTTCCGCTGTCCTGAGGCCATTTTCCAGCCTTCCTTCCTGGGC
TTCGAGTCCAGCGGCATCCACGAGGCGACCTTTAACTCAATCATGAAGTGTGATGTGGATATTCGCAAGGATTTGTATGC
CAACACTGTGCTGTCTGGGGGCAGCACTATGTACCCAGGCATTGCTGACCGGATGCAGAAGGAAATCTTAACCCTGACAC
CAAGCACCATGAAAGTGAAGATCATCGCTCCCCCAGAACGGAAGTATTCCGTCTGGATCGGGGGCTCCATCCTGGCCAGC
CTGTCTACGTTCCAGCAGATGTGGATCAGTAAGCAAGAATATGATGAAGCTGGTCCTCCTATTGTTCATAGGAAATGCTT
C

Alignment

ORF - retro_opri_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.73 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDETTALVCDNGSGLVKAGFAGDDA-PRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          .DE..ALV.DNGSG..KAGF.GDDA.PRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLKYP
Retrocopy DDELSALVVDNGSGMCKAGFGGDDA<PRAVFPSMVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLKYP

Parental  IEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVL
          IEHG..TNWDDMEKIW.HTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FN.PAMYVAIQAVL
Retrocopy IEHGVVTNWDDMEKIWYHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVL

Parental  SLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVR
          SLYASGRTTGIV.DSGDGVTH.VPIYEGYAL.HAI.RLDLAGRDLTDYLMKILTERGYSF.TTAEREIVR
Retrocopy SLYASGRTTGIVMDSGDGVTHTVPIYEGYALSHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR

Parental  DIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYN
          D.KEKLCYVALDFE.EM..AA.SSSLE.SYELPDGQVITIGNERFRCPE..FQPSF.G.ES.GIHE.T.N
Retrocopy DVKEKLCYVALDFEQEMVSAAASSSLERSYELPDGQVITIGNERFRCPEAIFQPSFLGFESSGIHEATFN

Parental  SIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
          SIMKCD.DIRKDLYAN.V.SGG.TMYPGIADRMQKEI..L.PSTMK.KIIAPPERKYSVWIGGSILASLS
Retrocopy SIMKCDVDIRKDLYANTVLSGGSTMYPGIADRMQKEILTLTPSTMKVKIIAPPERKYSVWIGGSILASLS

Parental  TFQQMWITKQEYDEAGPSIVHRKCF
          TFQQMWI.KQEYDEAGP.IVHRKCF
Retrocopy TFQQMWISKQEYDEAGPPIVHRKCF

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_573 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
Nomascus leucogenys	ENSNLEG00000014347	1 retrocopy	retro_nleu_1585,
Ochotona princeps	ENSOPRG00000002854	1 retrocopy	retro_opri_573 ,
Xenopus tropicalis	ENSXETG00000021417	1 retrocopy	retro_xtro_24,