RetrogeneDB ID: retro_opri_583

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_18180:3329..4664(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000000398
• Aliases: None
• Description: None

Sequence

>retro_opri_583
CGTGAGTGCATCTCCATCCACGTGGGCCAGGCTGGTGTCCAGATCGGCAATGCCTGCTGGGAGCTCTACTGCCTGGAACA
CGGGATCCAGCCTGATGGCCAGATGTCAAGTGAAAAGCCCATTGGAGTACTAGACCAGTCCCTCGACACCTTCTTCAGTG
ACACAGGCACTGGCAAGCATGTGCCGAGGGCCGTGTTTGCGGACCTGGAGCCCACGGTCATTGATGAAGTTCGCATTGGC
AACTACCGCCAGCTGTTCCACCCCGAGCAGCTCATCACTGGCAAGGAAGATGCCGCCAATAACTATGCCCGTGGCTACTA
CACTGTCGGCAGGGAGATCATTGAACCTGTCCAAGAGCGCATCCGCAAGCTGGCTGAGCAGTGCTCGGGCCTGCAGGGTT
TCCTGGTTTTCCGCAGCTTTGGTGGGGGCACTGGTTCTGGATTCACCTCGCTCCTGATGGAATGCCTCTCTGTTGATCAC
GGCAAGAAGTCCAAGCTGGAGTTCTCCATCTACCCGGCCCCTCAGGTCTCCACAGCTGTGGTGGAGCCCTACAACGCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGACTGTGTCTTCATGGTGGACAACGAGGCCATCTATGACATCTGTCGGA
GAAACCTCGACATTGGGCGCCCCCGTTACACTAACCTGAACCGCCTCATGAGCCAGGTGGTATCCTCCGTCACAGCCTCT
CTCCGGTTTGATGGAGCCCTCAATGTTGACCTGACAGAATTCCAGACCAACCTGGTCCCCTATCCCCGCATCCACTTCCC
TCTGGCCACTTAAGCCCCAGTTATCTCTGTTGAGAAAGCCTACCACGAACAGCTTTCTGTAGCAGAGCTCACCAATGCTT
GCTTTGAGCCAGCCAACCAGATGGTAAAATGTGACCCTCGCCATGGGAAATATATGGCTTGCTGCCTGTTGTACCGTGGG
GATGTAGTTCCCAAAGACGTCAACGCTGCCATTGCAACCATCAAGACCAAGCGGAGCATCCAGTTTGTGGACTGGTGCCC
CACTGGCTTTAAGGTTGGCATTAATTACCAGCCTCCCACTGTGGTGCCCGGTGGAGACCTGGCCAGGGTACCACGAGCTG
CATGCATGCTCAGCAACACCACAGCCATTGCCCAGGCCTGGGCTCGTCTGAACCACAAGTTTGACCTCATGTACGCCAAG
CGTGCATTTGTTCACTGGTACGTGGGTGAGGGCATGGAGGAGGGAGAGTTTACTGAGGCTCGTGAGGACATGGCTGCCCT
GGAGAAGGATTATGAGGAGGTGGCAGCCGACTATGGTGAGGGAGAGGATGAGGAG

Alignment

ORF - retro_opri_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.75 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RECISIHIGQAGVQIGNACWELYCLEHGIQPDGQMSSEKPIGVLDQSLDTFFSDTGTGKHVPRAVFADLE
          RECISIH.GQAGVQIGNACWELYCLEHGIQPDGQMSSEKPIGVLDQSLDTFFSDTGTGKHVPRAVFADLE
Retrocopy RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMSSEKPIGVLDQSLDTFFSDTGTGKHVPRAVFADLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGYYTVGREIIEPVQERIRKLAEQCSGLQGFLVFRSF
          PTVIDEVR.G.YRQLFHPEQLITGKEDAANNYARGYYTVGREIIEPVQERIRKLAEQCSGLQGFLVFRSF
Retrocopy PTVIDEVRIGNYRQLFHPEQLITGKEDAANNYARGYYTVGREIIEPVQERIRKLAEQCSGLQGFLVFRSF

Parental  GGGTGSGFTSLLMERLSVDHGKKSKLEFSIYPAPQVSTAVVEPYNAILTTHTTLEHSDCAFMVDNEAIYD
          GGGTGSGFTSLLME.LSVDHGKKSKLEFSIYPAPQVSTAVVEPYNAILTTHTTLEHSDC.FMVDNEAIYD
Retrocopy GGGTGSGFTSLLMECLSVDHGKKSKLEFSIYPAPQVSTAVVEPYNAILTTHTTLEHSDCVFMVDNEAIYD

Parental  ICRRNLDIGRPRYTNLNRLMSQVVSSITASLRFQGALNVDLKEFQTNLVPYPRIHFPLATYAPVISVEKA
          ICRRNLDIGRPRYTNLNRLMSQVVSS.TASLRF.GALNVDL.EFQTNLVPYPRIHFPLAT.APVISVEKA
Retrocopy ICRRNLDIGRPRYTNLNRLMSQVVSSVTASLRFDGALNVDLTEFQTNLVPYPRIHFPLAT*APVISVEKA

Parental  YHEQLSVAELTNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF
          YHEQLSVAELTNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF
Retrocopy YHEQLSVAELTNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF

Parental  KVGINYQPPTVVPGGDLARVPRAACMLSNTTAIAQAWARLNHKFDLMYAKRAFVHWYVGEGMEEGEFTEA
          KVGINYQPPTVVPGGDLARVPRAACMLSNTTAIAQAWARLNHKFDLMYAKRAFVHWYVGEGMEEGEFTEA
Retrocopy KVGINYQPPTVVPGGDLARVPRAACMLSNTTAIAQAWARLNHKFDLMYAKRAFVHWYVGEGMEEGEFTEA

Parental  REDMAALEKDYEEVAADYGEGEDED
          REDMAALEKDYEEVAADYGEGEDE.
Retrocopy REDMAALEKDYEEVAADYGEGEDEE

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_583 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000000398	4 retrocopies	retro_opri_1175, retro_opri_1194, retro_opri_379, retro_opri_583 ,