RetrogeneDB ID: retro_opri_1175

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8764:41766..43109(-)
• 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_1175
CGTGAGTGCGTCTCCATCCACATTGGTCAGGCTGGTGTCCAGATTGGCAATGCCTGCTGGGAGCTCTGCTGCCTGGAACA
CGGGATCCAACCTGATGGCCAGATGTCAAGTGAAGAGCCAATTGGGGTATTAGACCAGTCCCTTGTCATCTTCTTTAGCG
ACACAGGCACTGGCAAGCATGTGCCCAGGGCTGTGTTTGCAGACCTGGAGCCCACGGTCATTGATGAAGTTCGCACTGGC
ACCTACCGCCAGCTGTTCCACCCCGAGCAGTTCATTAGTGGCAAGGAAGATGCAGCCAATAACTATGCCCATGACTACTA
CACTGTTGGCAGGGAGATCATTGAACCTGTCCAAGAGCACATCCGCAAGCTGGCTGAGCAGTGCTCGGGCCTGCAGGGTT
TCCTGGTGTTCCGCAGCTTTGGTGGGGGTACCGGTTCTGGGTTCACCTTGCTTCTGATGGAACGCCTCTCTGTCGATCAC
GGCAAGAAGTCCAAGCTGGAGTTCTCCATCTACCCGGCCCCTCAGGTCTCCACAGCTGTAGTGGAGCCCTACAACTCCAT
CCTCACCACGCACACCACCCTGGAGCACTCAGACTGTGTCTTCATGGTGGACAATGAGGTTATCTATGACATCTGTCGGA
GAAACCTCGACATTGGGCGCCCCCGTTACACTTACCTGAACCGCCTTATGAGCCAGGTTGTGTCCTCCATCACAGCCTCG
CTGCGGTTTCAAGGAGCCCTGAATGTTGACCTGCAGGAGTTCTAGACCAATTTGGTCCCCTATCCTCGCATCCACTTCCC
TCTGGCCACTTATGCCCCAGTTATCTCCGTTGAGAAAGCCTACCACGAACAGTTTTCTGTAGCAGAGCTCACCAATGCTT
GCTTTGAGCCAGCTAACCAAATGGTAAAATGTGACCCTCACCACGGGAAATACATGGCTTGCTGCCTGTTGTACTGTGGG
GATGTGGTTCCCAAAGATGTCAACGCGGCCATTGCTACCATCAAGACCAAGCGGAGCATCCAGTTTGTGGACTGGTGCCC
CACTGGCTTTAAGGTAGGCATTAACTACCAGCCTCCCACTGTGGTGCCTGGTGGAGACCTGGCCAGTGTCCCGCGAGCTG
CATGTATGCTCAGCAACACCACAGCCATTGCCCAGGCCTGGGCTCGTCTGAACCACAAGTTTGACCTCATGTATGCCAAA
CGTGCATTTGTTCACTGGTACATGGGTAAGGGCATGGAGGAAGGAGAGTTTACTGAGGCTCGTGAGGACATGGCTGCCCT
GGAGAAGGATTATGAAGAGGTGGCAGCAGACTATGGTAGGGAGAGGATGAGGAAGAGGAGTAT

Alignment

ORF - retro_opri_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RECISIHIGQAGVQIGNACWELYCLEHGIQPDGQMSSEKPIGVLDQSLDTFFSDTGTGKHVPRAVFADLE
          REC.SIHIGQAGVQIGNACWEL.CLEHGIQPDGQMSSE.PIGVLDQSL..FFSDTGTGKHVPRAVFADLE
Retrocopy RECVSIHIGQAGVQIGNACWELCCLEHGIQPDGQMSSEEPIGVLDQSLVIFFSDTGTGKHVPRAVFADLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGYYTVGREIIEPVQERIRKLAEQCSGLQGFLVFRSF
          PTVIDEVRTGTYRQLFHPEQ.I.GKEDAANNYA..YYTVGREIIEPVQE.IRKLAEQCSGLQGFLVFRSF
Retrocopy PTVIDEVRTGTYRQLFHPEQFISGKEDAANNYAHDYYTVGREIIEPVQEHIRKLAEQCSGLQGFLVFRSF

Parental  GGGTGSGFTSLLMERLSVDHGKKSKLEFSIYPAPQVSTAVVEPYNAILTTHTTLEHSDCAFMVDNEAIYD
          GGGTGSGFT.LLMERLSVDHGKKSKLEFSIYPAPQVSTAVVEPYN.ILTTHTTLEHSDC.FMVDNE.IYD
Retrocopy GGGTGSGFTLLLMERLSVDHGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCVFMVDNEVIYD

Parental  ICRRNLDIGRPRYTNLNRLMSQVVSSITASLRFQGALNVDLKEFQTNLVPYPRIHFPLATYAPVISVEKA
          ICRRNLDIGRPRYT.LNRLMSQVVSSITASLRFQGALNVDL.EF.TNLVPYPRIHFPLATYAPVISVEKA
Retrocopy ICRRNLDIGRPRYTYLNRLMSQVVSSITASLRFQGALNVDLQEF*TNLVPYPRIHFPLATYAPVISVEKA

Parental  YHEQLSVAELTNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF
          YHEQ.SVAELTNACFEPANQMVKCDP.HGKYMACCLLY.GDVVPKDVNAAIATIKTKRSIQFVDWCPTGF
Retrocopy YHEQFSVAELTNACFEPANQMVKCDPHHGKYMACCLLYCGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF

Parental  KVGINYQPPTVVPGGDLARVPRAACMLSNTTAIAQAWARLNHKFDLMYAKRAFVHWYVGEGMEEGEFTEA
          KVGINYQPPTVVPGGDLA.VPRAACMLSNTTAIAQAWARLNHKFDLMYAKRAFVHWY.G.GMEEGEFTEA
Retrocopy KVGINYQPPTVVPGGDLASVPRAACMLSNTTAIAQAWARLNHKFDLMYAKRAFVHWYMGKGMEEGEFTEA

Parental  REDMAALEKDYEEVAADYGE-GEDEDEEY
          REDMAALEKDYEEVAADYG..GEDE.EEY
Retrocopy REDMAALEKDYEEVAADYGR<GEDEEEEY

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_1175 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,