RetrogeneDB ID: retro_opri_126

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2608:395835..396707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM23
• Ensembl ID: ENSOPRG00000001092
• Aliases: None
• Description: RNA binding motif protein 23 [Source:HGNC Symbol;Acc:20155]

Sequence

>retro_opri_126
CGTAGCAAAAAGAGGGAAAAAAGCAAGAGCAGGAGTCGTAGTCATGAACGGAAGAGAAGCAAATGTAAGGAACGGAAGAA
AAGCAGAGATAGAGAAAGGAAAAAGAGCAGGAGCCGGGAAAGGAAGCGAAGTAGAAGCAAAGGAAGGAGACAGAGCCAAT
CAAGAAGTCGGGACCGCAGATTCCGAGGCCCTTACAGAAACCCCTACAGATGACGTTCCCGAAGCAAAAGTCCCTTCAGA
AAAGACAAGAGCCCTGTGAGAGAACCTGTAGATAATCTAACTCCTGAGGAAAGAGATGCTCGGACAGTGTTCTGTAGGCA
GTTGGCAGCAAGAATTCGACCACAGGATTTGGAAGAATTCTTTTCTACAGTAGAAAAGGTTCGAGAAGTGCGGATGATTT
CTGATAGAAATTCAAGACGTTCCAAGGGAATCGCTTATGTGGAGTTTGTCGATGTGAGCTCAGTGCCTCTAGCAACAGGA
GTAATGGGCCAGCGACTTTCAGGTGTGCCAAACAGTACAAGCTTCACAGGAAGAGAAAAACAGAGCTGCAGCAATGGCGA
ACAATTGACAAAAGGGGAGTGCTGGACCTGTGAGACTTTATGTGGGCTCATCACACTTTAACATAACAGAGGACATGCTT
AGAGGAGTCTCTGAGCCCTTTGGAAAGATTGAAAGTATACAGTTCATGACGGATAGTGAAACGGGTCATTCGAAAGGATA
TGGATTTGTTACATTTTCTGATTCAGAATGTGCCAAAAAAGGCATTAGAACAACTGAACGGATTTGAACTAGCAGGAAGG
CCGATGAAGGTTGGTCATGTTACTGAGCGGACTGATGCTTCCAGTGCTAGTTCATTTTTGGATAGTGATGAA

Alignment

ORF - retro_opri_126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.84 %
• Parental protein coverage: 65.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSRDRKRSRSRDRDRHRRRNS---RSRSRDRQHRHRSRSRDRRHSSESRSRDRRREDRVRYRSSPLAAGP
          RS..R..S.SR.R...R.R.....R..SRDR..R..SRSR.R..S.....R......R.R....P.....
Retrocopy RSKKREKSKSRSRSHERKRSKCKERKKSRDRE-RKKSRSRERKRSRSKGRRQSQSRSRDRRFRGPYRNPY

Parental  R-YGQNKSPHIREKSPVRQPVDNLSPEERDARTVLCMQLAARIRPRDLEEFFSAVGKVRDVRIISDRNSR
          R.....KSP....KSPVR.PVDNL.PEERDARTV.C.QLAARIRP.DLEEFFS.V.KVR.VR.ISDRNSR
Retrocopy R*RSRSKSPFRKDKSPVREPVDNLTPEERDARTVFCRQLAARIRPQDLEEFFSTVEKVREVRMISDRNSR

Parental  RSKGIAYVEFCDIQAVPLAIGLTGQRLLGVPIVVQASQAEKNRLAAAANSLQKG-GGGPIRLYVGSLHCN
          RSKGIAYVEF.D...VPLA.G..GQRL.GVP........EK.........L.KG...GP.RLYVGS.H.N
Retrocopy RSKGIAYVEFVDVSSVPLATGVMGQRLSGVPNSTSFTGREK-QSCSNGEQLTKG>SAGPVRLYVGSSHFN

Parental  ITEDMLRGIFEPFGKIDNIVLMKESDTGRSKGYGFITFSDSECG-RRALEQLNGFELAGRPMRVGHVTER
          ITEDMLRG..EPFGKI..I..M..S.TG.SKGYGF.TFSDSEC....ALEQLNGFELAGRPM.VGHVTER
Retrocopy ITEDMLRGVSEPFGKIESIQFMTDSETGHSKGYGFVTFSDSECA>KKALEQLNGFELAGRPMKVGHVTER

Parental  PDGTTDITFPDGDQ
          .D......F.D.D.
Retrocopy TDASSASSFLDSDE

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_126 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008482	1 retrocopy	retro_cjac_1069,
Myotis lucifugus	ENSMLUG00000012923	1 retrocopy	retro_mluc_2430,
Ochotona princeps	ENSOPRG00000001092	2 retrocopies	retro_opri_126 , retro_opri_412,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55, retro_opri_913,
Pan troglodytes	ENSPTRG00000006151	1 retrocopy	retro_ptro_3108,
Ictidomys tridecemlineatus	ENSSTOG00000010354	1 retrocopy	retro_itri_1902,