RetrogeneDB ID: retro_opri_584

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_18223:5216..5801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000014425
• Aliases: None
• Description: None

Sequence

>retro_opri_584
ATGAGGCTTCTGCTGCTCTTCATGGTGGTGGCATTGACAGTGTCCTGGAGCAAGGCTTCTTCCAACCTGGGCAGTGTGCC
CATGAAGATGTTAAAGATGCAGAACGTTACGGGGCCTTTGCCCATGTTCCAGACCTGTGTTTCCTAAGGGTATTGACAGG
TGTCTGAGGGGTCCATGCAGGTTATTAGCCAATGGTACCCAGACATCTGAATTGACGGAGAGAATTACCTCTCTCAACCA
ATATATAGACACATAGCATCTTTCCTGTCAGTCTTCAAACTAGTCTTAATAGGCCTGATCATTGTTGGCAAGGATCCTTT
TGCTGTCTTTGGCGTGCAAGCTCCTAGCATCTGGCAGTGGGGCCAGGGAAAGAAGGTCTATGCTTGTATGATGGTTTTCT
TCTTGAGCAACATGATTGAGTAGCAGTATATGTCAGTAGGTGCATTTGAAATAACTTTAAATGGTGTGCCTGTATGGTCT
CAACTGGAATCTGGTCACCTTCCTTCCATGCAATAACTTGTTTAAATGCTCAACAATGAAATGAAGCTCAACATGAACAT
GGATTCAATACTGCACCGTCGATCA

Alignment

ORF - retro_opri_584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLVLLFLVAASAVARSEASANLGGVPSKRLKMQYATGPLLKFQIC---WYRRVFEEYMRVISQRYPDIR
          MRL.LLF.V.A..V..S.AS.NLG.VP.K.LKMQ..TGPL..FQ.C....Y..V.E..M.VISQ.YPDI.
Retrocopy MRLLLLFMVVALTVSWSKASSNLGSVPMKMLKMQNVTGPLPMFQTCVS*GY*QVSEGSMQVISQWYPDI*

Parental  IEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFLGMQAPSIWQWGQENKVYACMMVFFLSNMIE
          I.GENYL.QPIYRHIASFLSVFKLVLIGLIIVGKDPFA..G.QAPSIWQWGQ..KVYACMMVFFLSNMIE
Retrocopy IDGENYLSQPIYRHIASFLSVFKLVLIGLIIVGKDPFAVFGVQAPSIWQWGQGKKVYACMMVFFLSNMIE

Parental  NQCMSTGAFEITLNGVPVWSKLESGHLPSMQQLDQILDNEMKLNVHMDSIPHHRS
          .Q.MS.GAFEITLNGVPVWS.LESGHLPSMQ.L...L.NEMKLN..MDSI.H.RS
Retrocopy *QYMSVGAFEITLNGVPVWSQLESGHLPSMQ*LV*MLNNEMKLNMNMDSILHRRS

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_584 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384, retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584 ,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,