RetrogeneDB ID: retro_opri_523

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_150714:2..1070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNGTT
• Ensembl ID: ENSOPRG00000000916
• Aliases: None
• Description: RNA guanylyltransferase and 5'-phosphatase [Source:HGNC Symbol;Acc:10073]

Sequence

>retro_opri_523
ACTCAAGTAACAACTCAACCAAAGCTAGGAGAGGTACAACAGAAGTGTCATCAATTCTGTGGCTGGGAAGGGTCTGGATT
CCCTGGAGCACAGCCCGTTTCCATGGACAAGCAAAATATTACACTTTTAGAGCAGAAGCCATATAAAGTAAGCTGGAAAG
CAGATGGCACTCGTTACATGATGTTGGTTGATGGCACAAATGAAGTCTTTATGATTGATCGAGATAATTCAGTGTTTCAT
GTTTCTAATCTGGAATTTCCATGTCGGAAAGACCTTCAAATCCATTTATCGAATACTCTTTTGGATGGTGAGATGATTAT
TGACAGAGTAAACGGACAGGCTCTTCCTAGATATTTGATATATGACATCATTAAGTTCAATGCACAGCCAGTTGGAGATT
GCGACTTGAATGTCCGCTTGCAGTGTATAGAACGAGAAATTATAAATCCTCGGCACGAAAAAATGAAGACCGGACTCATT
GACAAGACACGGGAACCATTTAGTGTCAGAAAGAAGCCGTTTTTTGACATTCATACTTCAAGAAAGCTGCTTGAAGGAAA
TTTTGCCAAACAAGTCAGTCATGCAGTGGACGGACTTATATTTCAGCCCATCGGGAAGTATAAACCTGGTCGGTGTGATG
ATATTTTGAAGTGGAAACCTCCCAGTTTGAATTCTGTGGATTTCCGCCTGAAGATAACAAGACTGGGAGGAGAAGGGCTA
CTTCCTCAGAATGCCGGTCTTCTCTATGTTGGAGGCTACAAAAGACCCTTTGCCCAAATCAAGGTGACAAAAGAGCTCAA
TCAGTATGACAACAAAATCATAGAATGCAGATTTGAGAAGAACAGCTGGGTCTTCATGAGACAGAGAACAGACAAAAGTT
TTCCGAATGCCTATAACACTGCCATGGCTGTGTGCAATAGCATCTCAAACCCTGTCACCAAGGAGATGCTGTTTGAGTTC
ATCGACGGATGTGCTGCAGCTTTTCAAGGACAGAAGCAAAAGCATCATCTGAACCCCGACACAGAGCTCATGCCCCCGCC
GCCTCCCAAAAGACCGCGCCCTGCCACC

Alignment

ORF - retro_opri_523 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.54 %
• Parental protein coverage: 61.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNIKLLEQKPYKVSWKADGTRYMMLIDGTNEVF
          TQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNI.LLEQKPYKVSWKADGTRYMML.DGTNEVF
Retrocopy TQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNITLLEQKPYKVSWKADGTRYMMLVDGTNEVF

Parental  MIDRDNSVFHVSNLEFPFRKDLRIHLSNTLLDGEMIIDRVNGQAVPRYLIYDIIKFNAQPVGDCDFNIRL
          MIDRDNSVFHVSNLEFP.RKDL.IHLSNTLLDGEMIIDRVNGQA.PRYLIYDIIKFNAQPVGDCD.N.RL
Retrocopy MIDRDNSVFHVSNLEFPCRKDLQIHLSNTLLDGEMIIDRVNGQALPRYLIYDIIKFNAQPVGDCDLNVRL

Parental  QCIEREIINPRHEKMKTGLIDKTQEPFGVRNKPFFDIHTSRKLLEGNFAKAVSHEMDGLIFQPIGKYKPG
          QCIEREIINPRHEKMKTGLIDKT.EPF.VR.KPFFDIHTSRKLLEGNFAK.VSH..DGLIFQPIGKYKPG
Retrocopy QCIEREIINPRHEKMKTGLIDKTREPFSVRKKPFFDIHTSRKLLEGNFAKQVSHAVDGLIFQPIGKYKPG

Parental  RCDDILKWKPPSLNSVDFRLKITRMGGEGLLPQNVGLLYVGGYERPFAQIKVTKELKQYDNKIIECKFEN
          RCDDILKWKPPSLNSVDFRLKITR.GGEGLLPQN.GLLYVGGY.RPFAQIKVTKEL.QYDNKIIEC.FE.
Retrocopy RCDDILKWKPPSLNSVDFRLKITRLGGEGLLPQNAGLLYVGGYKRPFAQIKVTKELNQYDNKIIECRFEK

Parental  NSWVFMRQRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDRCAAAFQGQKRKHHLDPDAELMPPPPPK
          NSWVFMRQRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFID.CAAAFQGQK.KHHL.PD.ELMPPPPPK
Retrocopy NSWVFMRQRTDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDGCAAAFQGQKQKHHLNPDTELMPPPPPK

Parental  RPRPAT
          RPRPAT
Retrocopy RPRPAT

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_523 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000003302	1 retrocopy	retro_mluc_2437,
Ochotona princeps	ENSOPRG00000000916	3 retrocopies	retro_opri_523 , retro_opri_978, retro_opri_979,