RetrogeneDB ID: retro_opri_1194

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_9249:40075..41394(-)
• 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_1194
GGCCAGGCTGGTGTCCAGATCAGCAATGCCTGCTGGGAGCTCTACTGCCTGGAACATGGGATCCAACCTGATGGCTAGAT
GTCAAGTAACAAGCCAATTGGGGTATTAGACCAGTCCCTCAACACCTTCTTCAGCGAGACAAGCACTGGCAAGCATGTGC
CCAGGGCCGTGTTTGCAGACTTGGAGCCCACAGTCATTGATGAAGTTCGCACTGGCACCTACCACCAGCTGTTCCACCCC
AAGCAACTCATTACTGGCAAGGAAGATGCTGCCAATAACTATGCCCGTGGCTACTACACTGTCGGCAGGGAGATCATCAA
ACCTGTCCAAGAGCACATCCGCAAGCTGGCAGAGCAGTGCTCGGGCCTGCAGGGTTTCCTGGGTTTCCACAGCTTTGGTG
GGGGTACCGGTTCAGGGTTCACCTCGCTTCTGATGGAACGCCTCTCTGTCGATCACGGCAAGAAGTCCAAGCTGGAGTTC
TCTATCTACCCGGCCCCTCAGGTCTCCACAGCTGTGGTGGAGCCATACAAAGCCATCCTCACCATCCACTCCACCCTGGA
GCACTCCGACTGTGCCTTCCTGGTGGACAATGAGGCTATCTATGACATCTGTTGGAGAAAACTCGACATTGGGTGCCCCC
GTTACACTAACCTTAACCACCTTATGAGCCAGGTAAATATCCTCCATCACAGCCTCTCTCCGGGTTGGATGGAAATCTGA
ATGTTGACCTGTAGGAGTTCCAGACCAACCTGGTGCCCTATCCCCACATCCACTTCCCTCTGGCAAGTTATGCCCCAGTT
ATATCTGTTGAGAAAGCCTACCACAAACAGCTTTCTGTAGCAGAGCTCACCAATGCTTGCTTTGAGCCAGCTAACCAGAT
GGTAAAGTGTGACCCTTGCCACAGGAAATATATGGCATGCTGCCTGTTGTACTATGGGGATGTAGTTCCCAAAGACATCA
ACACTGCCATTGCTACCATTAAGACCAAGCTGGAGCATCCAGTTTGTGGACTGGTGCCCCACTGCTTTAAGGTTGGCATT
AATTACCAGCCTCTTACTGTGGTGCCCAGTGGAGACCTGGCCAGGGTCCCGCGAGCTGCATGCATGCTCAGCAACACCAC
CACCATTGCCCAGGCCTGGGCTCGCCTGAACCACAAGTTTGACCTCATGTTCGCGAAGCGGGCATTTGTGTACTGCTATG
TGGGTGAGGGCATGGAGGAGGGAGAGTTTACTGAGGCTCGCGAGGACATGGCTGCTCTGGAAAAGTATCATGAGGAGGTG
GCAGCTGACTACGCAGAGAGGGATGAGGATGAGGAGTAT

Alignment

ORF - retro_opri_1194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.74 %
• Parental protein coverage: 98.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GQAGVQIGNACWELYCLEHGIQPDGQMSSEKPIGVLDQSLDTFFSDTGTGKHVPRAVFADLEPTVIDEVR
          GQAGVQI.NACWELYCLEHGIQPDG.MSS.KPIGVLDQSL.TFFS.T.TGKHVPRAVFADLEPTVIDEVR
Retrocopy GQAGVQISNACWELYCLEHGIQPDG*MSSNKPIGVLDQSLNTFFSETSTGKHVPRAVFADLEPTVIDEVR

Parental  TGTYRQLFHPEQLITGKEDAANNYARGYYTVGREIIEPVQERIRKLAEQCSGLQGFLVFRSFGGGTGSGF
          TGTY.QLFHP.QLITGKEDAANNYARGYYTVGREII.PVQE.IRKLAEQCSGLQGFL.F.SFGGGTGSGF
Retrocopy TGTYHQLFHPKQLITGKEDAANNYARGYYTVGREIIKPVQEHIRKLAEQCSGLQGFLGFHSFGGGTGSGF

Parental  TSLLMERLSVDHGKKSKLEFSIYPAPQVSTAVVEPYNAILTTHTTLEHSDCAFMVDNEAIYDICRRNLDI
          TSLLMERLSVDHGKKSKLEFSIYPAPQVSTAVVEPY.AILT.H.TLEHSDCAF.VDNEAIYDIC.R.LDI
Retrocopy TSLLMERLSVDHGKKSKLEFSIYPAPQVSTAVVEPYKAILTIHSTLEHSDCAFLVDNEAIYDICWRKLDI

Parental  GRPRYTNLNRLMSQV-VSSITASLR-FQGALNVDLKEFQTNLVPYPRIHFPLATYAPVISVEKAYHEQLS
          G.PRYTNLN.LMSQV..SSITASLR...G.LNVDL.EFQTNLVPYP.IHFPLA.YAPVISVEKAYH.QLS
Retrocopy GCPRYTNLNHLMSQV>ISSITASLR>LDGNLNVDL*EFQTNLVPYPHIHFPLASYAPVISVEKAYHKQLS

Parental  VAELTNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKR-SIQFVDWCPTG-FKVGI
          VAELTNACFEPANQMVKCDP.H.KYMACCLLY.GDVVPKD.N.AIATIKTK..SIQFVDWCPT..FKVGI
Retrocopy VAELTNACFEPANQMVKCDPCHRKYMACCLLYYGDVVPKDINTAIATIKTKL>SIQFVDWCPTA<FKVGI

Parental  NYQPPTVVPGGDLARVPRAACMLSNTTAIAQAWARLNHKFDLMYAKRAFVHWYVGEGMEEGEFTEAREDM
          NYQP.TVVP.GDLARVPRAACMLSNTT.IAQAWARLNHKFDLM.AKRAFV..YVGEGMEEGEFTEAREDM
Retrocopy NYQPLTVVPSGDLARVPRAACMLSNTTTIAQAWARLNHKFDLMFAKRAFVYCYVGEGMEEGEFTEAREDM

Parental  AALEKDYEEVAADYGEGEDEDEEY
          AALEK..EEVAADY.E..DEDEEY
Retrocopy AALEKYHEEVAADYAE-RDEDEEY

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_1194 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 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,