RetrogeneDB ID: retro_opri_1011

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5717:79389..80588(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOR3A
• Ensembl ID: ENSOPRG00000012889
• Aliases: None
• Description: torsin family 3, member A [Source:HGNC Symbol;Acc:11997]

Sequence

>retro_opri_1011
ATGCCTCGCGGCCCCCGGCGCCCCTTTTGCCTTTGCTTTCTCCTCTTGCTGCTGCTGCACCCGGGCGCTCTGGACGGCCC
CGGTGCCGCGAGGCCGGGTGAGGGCGCCGAGGAGCCGGGCTGGGCATCGCCGTGGCCAGGCTTGCATCACCTGCAACAGC
AGCAGTTCAGGACGGCCGGGGCCCTCTCCAGGCGGTACTGAGCGCTTTTCAGCTGCCGGGTGTGGCCCGGAGAGTGCGAG
GAAGATGAGGTTGCCGCGACAACCCTAGCCTGGAGCCTGCCCGTGTTGGGCCAGCGGTATGTGGATATGCTAGCTGCGTG
GTACTGCCGCTTCTGGGACTGCTGCGACTCTGACGACTGCAGGATCTCCAACAACTTCACAGGCTTAGACTCAGACCTGA
GTGTGCGACTGCATGGCCAGCATCTGGCCCGGGAACTGGTCCTGCAAACGGTGAGGGGCTACTTGGAAATTCCACTGCCA
GACAAGGCCCTGGCTCTGTCATTCCACGGCTGGTCGGGGACCGGCAAGAACTTTGTGGCCCGGATATTGGCAGAGAACCT
ATATCGGGATGGACAGAAGAGCCCCTGTGTCAGGGTGTTCATTGCCACAATCCACTTCCCGCACTCCAAGTACGTGGATC
TGTACCAGGACTGGCTGCTGGGCCAGATGCAGGAGGCACAGCAGCGCTGCCGCCAGACCCTGTCATCTTTGATGAAGTCA
AGAAGCTGCACCCCGAGCTGCTGGAGCTCCTGGGGCTGCAGCTGGAGCACCGAGCCCCTGAGAAGCCGGGCGCCAGGCCT
CAGAGAAGCATCTTTGTTTTTCTCAGTAACCTCGGGGGCAATGCCATCAACCAGGCGGTCCTGGATCTGCTGAAGGCTGG
AAGGTCCCGGGAAGAAATCACCATGGATCACCTGGGACCCATGCTTCAGGCTGAGATGGCGGCATCCCCAGGCAGCAGCT
TTGGCCACAGCCATCTTGTGAAGGAAAACCTGATCGACACCTTCGTTCCCTTCCTGCCTCTGGAGTTCCACCATGTGAGG
CTGTGTGTACGCGATGCCTTCCTGAGCCAGGACCTGGCATACACAGAAGAGACCTTGGACAGAGTTGCCAGGACAATGAC
CTACATTCCCAAGGAGGAGCAGCGCTTCTCGTCCCAGGGATGCAAGTCCATCTCCCAGAGAATCCACTACTTTCAGCCC

Alignment

ORF - retro_opri_1011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPRGPRRPLCLCFLLLLLLHPGAPDGPGAARPGEGAEEPGWASPWPGLQHLQQQ-LRTAGALSRRYWALF
          MPRGPRRP.CLCFLLLLLLHPGA.DGPGAARPGEGAEEPGWASPWPGL.HLQQQ..RTAGALSRRY.ALF
Retrocopy MPRGPRRPFCLCFLLLLLLHPGALDGPGAARPGEGAEEPGWASPWPGLHHLQQQQFRTAGALSRRY*ALF

Parental  SCRVWPGECEEDEVAATPLGWSLPVLGQRYVDMLAAWYCRFRDCCDSDDCRISNNITGLDSDLSVRLHGQ
          SCRVWPGECEEDEVAAT.L.WSLPVLGQRYVDMLAAWYCRF.DCCDSDDCRISNN.TGLDSDLSVRLHGQ
Retrocopy SCRVWPGECEEDEVAATTLAWSLPVLGQRYVDMLAAWYCRFWDCCDSDDCRISNNFTGLDSDLSVRLHGQ

Parental  HLARELVLQTVRGYLETPLPDKALALSFHGWSGTGKNFVARILAENLYRDGQKSPCVRVFIATIHFPHSK
          HLARELVLQTVRGYLE.PLPDKALALSFHGWSGTGKNFVARILAENLYRDGQKSPCVRVFIATIHFPHSK
Retrocopy HLARELVLQTVRGYLEIPLPDKALALSFHGWSGTGKNFVARILAENLYRDGQKSPCVRVFIATIHFPHSK

Parental  YVDLYQDWLLGQMQEAQQRCRQTL-FIFDEAEKLHPELLELLGLQLEHRAPEKPGARPQRSIFVFLSNLG
          YVDLYQDWLLGQMQEAQQRCRQTL..IFDE..KLHPELLELLGLQLEHRAPEKPGARPQRSIFVFLSNLG
Retrocopy YVDLYQDWLLGQMQEAQQRCRQTL<VIFDEVKKLHPELLELLGLQLEHRAPEKPGARPQRSIFVFLSNLG

Parental  GSAINQAVLDLLKAGRSREEITMDHLGPKLQAEMAASPGSSFGHSHLVKENLIDTFVPFLPLEFRHVRLC
          G.AINQAVLDLLKAGRSREEITMDHLGP.LQAEMAASPGSSFGHSHLVKENLIDTFVPFLPLEF.HVRLC
Retrocopy GNAINQAVLDLLKAGRSREEITMDHLGPMLQAEMAASPGSSFGHSHLVKENLIDTFVPFLPLEFHHVRLC

Parental  ARDAFLSQDLAYTEETLDRVARTMTYIPKEEQRFSSQGCKSISQRIHYFQP
          .RDAFLSQDLAYTEETLDRVARTMTYIPKEEQRFSSQGCKSISQRIHYFQP
Retrocopy VRDAFLSQDLAYTEETLDRVARTMTYIPKEEQRFSSQGCKSISQRIHYFQP

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_1011 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000012889	1 retrocopy	retro_opri_1011 ,