RetrogeneDB ID: retro_opri_958

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_50108:415..1026(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFG
• Ensembl ID: ENSOPRG00000000781
• Aliases: None
• Description: TRK-fused gene [Source:HGNC Symbol;Acc:11758]

Sequence

>retro_opri_958
TTCCTTCATAATTCTAGTAGGATACTAAAACTGATATTTTTTAATTGGCAACCCAGACACTTGGAATCAAGTCAGGTAAA
ATACCTTTGTCAAGAACTGATAGAGCTTCAAAATAAAGTGAACTGATTGTTGGATAGCTTGGAGCCACCTGGAGAGTCTG
GACCTTCTACCAGTGTTCCTGAAAATGATGCTGTGAATGGTATAGAAGAAAAGCCTGATGCTTCTGATTTTTCTGGAAAA
CAGTTAACTCAGGTTATGGCAACAAGTATTTCAACTTTTGATCTTTTGAAAAATTAAGATGAAATCAACAAAAATATCAT
GTCAGTTTTTGGCTTAATTGATGATCAGGTTTCAGGGCTGCCCAGTGATGCTGTCCAAAATCATTCAGGCTTTCCTGATA
GCATTGCATCCTCCACTTCGGCAGCTCACCCATCAGGAGTTCAGCCACAGCAGCTACTGCACACAAGAACATAGACACAA
GCAGGTCACACTGAAGGCCAGCCATACCAGCAGTACCAGCAGCAGGCTGGTTGTGGTGCACAGCCACCATAGGCTCCCCC
TCAGCCACCTCACAGCATGATGTTCAGTATTCAGTCAGTTGCAGTGGGCAA

Alignment

ORF - retro_opri_958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.42 %
• Parental protein coverage: 51.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FAIQCSRILKLTLFVNGQPRPLESSQVKYLRRELIELRNKVNRLLNSLGPPGRPGPSTGILEIDAVDGRE
          F....SRILKL..F.N.QPR.LESSQVKYL..ELIEL.NKVN.LL.SL.PPG..GPST...E.DAV.G.E
Retrocopy FLHNSSRILKL-IFFNWQPRHLESSQVKYLCQELIELQNKVN*LLDSLEPPGESGPSTSVPENDAVNGIE

Parental  EKPAASDASGKQSTQVMAASMSAFDPLKNQDEISKNVMSAFGLTDDQVSGPPSAPAEDRSGTPDSIASSS
          EKP.ASD.SGKQ.TQVMA.S.S.FD.LKN.DEI.KN.MS.FGL.DDQVSG.PS......SG.PDSIASS.
Retrocopy EKPDASDFSGKQLTQVMATSISTFDLLKN*DEINKNIMSVFGLIDDQVSGLPSDAVQNHSGFPDSIASST

Parental  SAAHPPGVQPQQPPYTGTQTQAGQSEGQLYQQYQQQAGYGAQQPQAPPQPP-QQYGVQYSASYSQQ
          SAAHP.GVQPQQ...T.T.TQAG..EGQ.YQQYQQQAG.GAQ.P.APPQPP..Q..VQYS.S.S.Q
Retrocopy SAAHPSGVQPQQLLHTRT*TQAGHTEGQPYQQYQQQAGCGAQPP*APPQPP<SQHDVQYSVSCSGQ

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_958 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958 ,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457,