RetrogeneDB ID: retro_opri_1103

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_7130:32290..33232(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OGFOD1
• Ensembl ID: ENSOPRG00000006697
• Aliases: None
• Description: 2-oxoglutarate and iron-dependent oxygenase domain containing 1 [Source:HGNC Symbol;Acc:25585]

Sequence

>retro_opri_1103
AAGCTCATGTTTGAAGATTTCCGAGCCTGGCTTTCAGATGTCTCTCAGATTGACCTGGAACCAACCATTGACATGTGCTG
TGCTAAATATGAATTCACCGATGCCCTGCTGTGCCATGATGATGAGCTGGAGGGGTGCTGAATCGCCTTCATTCTGTACC
TCATTCCTTCCTGGGACAGGAGTTTTGGGGGCACCCTGGATCTGTGCCACACTGACGAACACTTTCAGCCGAAACAGATT
GTCATGTCTCTTATCCCTTCATGGAACAAACTGATTTTCTTTGAAGTGTCTCCGTGTCCTTTCATCAGGTGTCTGAAGTC
CTCTCTGAAGAGAAGTCCCGTCTGTCTATAAGCGGCTGGTTTCATGGTGCTTCGCTAACCAGGACCCCCATATACTTTGA
ACCCTTCATTCCTTGGAACCCTCACATCCCAAAAGATCATGAGATTTTGTATGATTGGATCAATCCTCCTTATCTGGACA
TGGAGTACCAAGTTCAAATTCAAGAGGAATTTGAAGAAAGTTCTGAAATTCTCCTGAAAGAATTTCTTAAGCCTGAGAAA
TTTGCAAAGGTCTGTGAGGTCTTGGAGAAAGCAGATGTGGAATGAACACTCTCAGTCCTCCTAACAAAAGGTTTTACTAG
AAGGCTGAGGAAAGCACACTGCCTGACATCCTGAAGGAGTGCATGGAGTTATTTCGCTCTGAGGCAATGTCCTTGCTGCT
GTCCAACTTCACAGGCCTGAAGCTTCACTTCCTGGCCCCCTCAGAGGACAGTGAGACTGAGGACAAAAAGAGGGAGAAGC
AGCCTCAACTGCAGAGAACACAGAAGAGGGGGCCAGCCAGAGCTCCTCTGAGCCTGGGCTTCCTGAGGTGGCCATCAGCA
GCAGCAGCAGCCAGCAGAGTGATGGAGAAGTGGAGTAAGAGTTTGAGGAGAAAGAAGCAAAG

Alignment

ORF - retro_opri_1103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.94 %
• Parental protein coverage: 63.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLMFEDFRAWLSDVSQIDLEPTIDMSCAKYEFTDALLCHDDELEGRRIAFILYLVPSWDRSFGGTLDLYD
          KLMFEDFRAWLSDVSQIDLEPTIDM.CAKYEFTDALLCHDDELEG..IAFILYL.PSWDRSFGGTLDL..
Retrocopy KLMFEDFRAWLSDVSQIDLEPTIDMCCAKYEFTDALLCHDDELEGC*IAFILYLIPSWDRSFGGTLDLCH

Parental  TDEHFQPKQIVKSLIPSWNKLIFFEVSP-VSFHQVSEVLSEEKSRLSISGWFHGASLTRPPIYFEPLIPR
          TDEHFQPKQIV.SLIPSWNKLIFFEVSP.VSFHQVSEVLSEEKSRLSISGWFHGASLTR.PIYFEP.IP.
Retrocopy TDEHFQPKQIVMSLIPSWNKLIFFEVSP<VSFHQVSEVLSEEKSRLSISGWFHGASLTRTPIYFEPFIPW

Parental  NPHIPKDHEILYDWINPTYLDMEYQVQIQEEFEESSEILLKEFLKPEKFAKVCEALEKADVE-WNTRSPP
          NPHIPKDHEILYDWINP.YLDMEYQVQIQEEFEESSEILLKEFLKPEKFAKVCE.LEKADVE..NT.SPP
Retrocopy NPHIPKDHEILYDWINPPYLDMEYQVQIQEEFEESSEILLKEFLKPEKFAKVCEVLEKADVE<MNTLSPP

Parental  NKRFYEKAEESTLPDILKECMELFRSEAMFLLLSNFTGLKLHFLAPSEDSETEDK-KEGEAASTAENTEE
          NKRFY.KAEESTLPDILKECMELFRSEAM.LLLSNFTGLKLHFLAPSEDSETEDK.KEGEAASTAENTEE
Retrocopy NKRFY*KAEESTLPDILKECMELFRSEAMSLLLSNFTGLKLHFLAPSEDSETEDK<KEGEAASTAENTEE

Parental  GAGQSSSEPGLPEAA-ISSSSQQSDGEVESQSEEKEAK
          GA.QSSSEPGLPE.A........SDGEVE...EEKEAK
Retrocopy GASQSSSEPGLPEVAXXXXXXXXSDGEVE*EFEEKEAK

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_1103 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013378	1 retrocopy	retro_mdom_777,
Otolemur garnettii	ENSOGAG00000014894	1 retrocopy	retro_ogar_2808,
Ochotona princeps	ENSOPRG00000006697	1 retrocopy	retro_opri_1103 ,