RetrogeneDB ID: retro_opri_61

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_159:50950..51854(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXR1
• Ensembl ID: ENSOPRG00000009223
• Aliases: None
• Description: fragile X mental retardation, autosomal homolog 1 [Source:HGNC Symbol;Acc:4023]

Sequence

>retro_opri_61
GGTGTTACTGCCATTGAGCTAGATGAAGATACTGGAACATTTAGAGTCTATGGAGAGAGTGCTGATGCTGTGAAAAAAGT
TAGAGGTTTCTTGGAATTTGTGGAGGACTTTATTCAGGTTCCTAGAAATCTTGTTGGAAAAGTAATTGGGAAAAATGGCA
GTTATTCAAGAAATTATGGACAAATCTGGTGTGGTTCGGGTGAGAATTGAAGGCGACAATGAAAACAAACTACCTGGAGA
AGATGGAATGGTTCCATTTGTGTTTGTTGGCACTAAAGAGAGCATCGGAAATGTGCAGGTTCTTTTAGAGTATCATGTTG
CATGTCTAAAGGAAGTAGAGCAGTTAAGAATGGAACGCCTACAGATTGACGAACAGCTGCGTCAGATTGGTTCTAGGTCT
TACGGTGGAAGAGGCAGAGGTTGTTGGGGCCCTAATTACACCTCCTGTTATGGTACAAATTCTGAGCTGTCTAACCCCTC
TGAAACAGAATCTGAACGTAAAGACGAGCTGAGTGATTGGTCATTGGCAGGAGAATAAGATGGAAAGAACCGACATCAGC
GTGACAGCAGAAGACGCCCAGGAAGAAGAGGCAGAAATGTTTCAGGGGGTCGAGGTCGTGGTGGACCACATGGTGACAAA
TCCTCCATCAGTTATGTGCGCAAAGATGCAGACAGCAATCCATACAGCTTAGTTGATAATACGGAATCAGATCCGACTGC
AGACACTGATGCCAGCGAATCTCCTCACAGTACTGACCGTCGTAGGGGGTCTCGTAGACGAAGGCCTGATGAAGATGCTG
TTCTGATGGATGGAATGAAATCTGAGACAGCTTCAGGTACGGAAAATGGGCTAGTCTCAGAGCAGACAAAGAAATCTCCC
AAGGAAACTTTGGCTAAAAATAAG

Alignment

ORF - retro_opri_61 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVTAIELDEDTGTFRIYGESADAVK-ARGFLDFVEDFIQVPRNLVGKVI-GKNGKVIQEIVDKSGVVRVR
          GVTAIELDEDTGTFR.YGESADAVK..RGFL.FVEDFIQVPRNLVGKVI.GK...VIQEI.DKSGVVRVR
Retrocopy GVTAIELDEDTGTFRVYGESADAVKKVRGFLEFVEDFIQVPRNLVGKVI>GKMA-VIQEIMDKSGVVRVR

Parental  IEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRG
          IEGDNENKLP.EDGMVPFVFVGTKESIGNVQVLLEYH.A.LKEVEQLRMERLQIDEQLRQIGSRSY.GRG
Retrocopy IEGDNENKLPGEDGMVPFVFVGTKESIGNVQVLLEYHVACLKEVEQLRMERLQIDEQLRQIGSRSYGGRG

Parental  RGRRGPNYTSGYGTNSELSNPSETESERKDELSDWSLAGEDDRENRHQRDSRRRPGGRGRSVSGGRGRGG
          RG..GPNYTS.YGTNSELSNPSETESERKDELSDWSLAGE.D..NRHQRDSRRRPG.RGR.VSGGRGRGG
Retrocopy RGCWGPNYTSCYGTNSELSNPSETESERKDELSDWSLAGE*DGKNRHQRDSRRRPGRRGRNVSGGRGRGG

Parental  PRGGKSSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGVTESDTA
          P.G.KSSIS.V.KD.DSNPYSL.DNTESD.TADTDASES.HST.RRR.SRRRR.DEDAVLMDG...S.TA
Retrocopy PHGDKSSISYVRKDADSNPYSLVDNTESDPTADTDASESPHSTDRRRGSRRRRPDEDAVLMDGM-KSETA

Parental  SVNENGLVTVADYISRAESQSRQR
          S..ENGLV......S..E......
Retrocopy SGTENGLVSEQTKKSPKETLAKNK

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_61 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000012105	1 retrocopy	retro_mmul_859,
Nomascus leucogenys	ENSNLEG00000005928	1 retrocopy	retro_nleu_197,
Ochotona princeps	ENSOPRG00000009223	2 retrocopies	retro_opri_61 , retro_opri_779,
Pan troglodytes	ENSPTRG00000015656	1 retrocopy	retro_ptro_691,