RetrogeneDB ID: retro_opri_385

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_10518:11144..12220(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFFL
• Ensembl ID: ENSOPRG00000011769
• Aliases: None
• Description: ring finger and FYVE-like domain containing E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:24821]

Sequence

>retro_opri_385
ATGTGGGCAACCTGCTGCAACTGGTTCTGCCTGGGTGGAAGCCTGAGGAGGTGCCAGCATCCCAGGGGACCAGGACGCAA
GCCTATTCCAACCCTGGGTACAGCTCCTTCCCTTTATCGACGGTCTCAGAACCAAGCTGCAAGTCCTGTGGGGCCCACTT
CACCAGCATGGCCAGGAAGCAGACCTGCTTGGACTGTAAGAAGAATTTCTTCCTGACCTGTTGGAACCAAGTGGGGAATG
GGCCCCGCCTCTGTCTGCTCTGCCAACGGTTCCGAGCCACAGCCTTTCAGCGTGAGGAGCTCATGAAGATGAAGGTGAAG
GACCTGAGGGACTATCTCAGCCTCCATGACATTTCCACGGAGATGTGCCAGGAGAAGGAAGAGCTGGCGTTCTTGAGTTT
GGCCAGCAGCCTGCAGTCCCACAGGAGGGCAGGACTCATGCCTTATCCCTGGACTTGCCCGAGCAGCCTTCCTGAGTCAG
TCGCATGCCAGCACAATACCTTCTACCTCGGCCAGCCTCCCACCCTCCCCTGCACAGGCCACCTCTGTTCCCCCAGCCCA
GGCACAGGAACGCCAGCAGGCCAATGGCCATGTGTCTCACGACCAAGAGGAGCCCGTCTGCCTGCAGAGCACAGCCACAG
CAGCTGATGAGAGTGAGACCCAGTCTCTTGACTCGGAGCACAGCTTTGTCCCAGGCCGGAGGGCCTCTCTGTCTGACTTG
ACCCACCTAGAGGACATTGAAGGCCTGACCGTGCGGCAGCTGAGAGAGATCCCGGCTCGCAACTTTGTCAACTACAAAGG
CTGTTGTGAGAAGTGGGAGCTGATGGAGAGAGTGCCGCGGCTGTACAAAGACCAGAAAGGACTGCAGCACCTGGTGTGTG
ATACTGAAATCCAAAATGGGGGAGCAGTACCATCGGCTCTGAGGAGAACCTGTGTAAGATCTGCATGGACTCACCCACTG
ACTGTGTTTTGCTGGAGTGTGGCCACATGGTAACCTGTACCAAGTGTGGCAAGCGCATGAATGAATGCCCCATCTGCCGG
CAGTATGTTATCTGAGCTGTGCACGTCTTCCGGTCT

Alignment

ORF - retro_opri_385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MWATCCNWFCLDG-QPEEVPASQGARTQAYSNPGYSSFPSPTGSEPSCKSCGTHFTNMARKQTCLDCKKN
          MWATCCNWFCL.G..PEEVPASQG.RTQAYSNPGYSSFP..T.SEPSCKSCG.HFT.MARKQTCLDCKKN
Retrocopy MWATCCNWFCLGG<KPEEVPASQGTRTQAYSNPGYSSFPLSTVSEPSCKSCGAHFTSMARKQTCLDCKKN

Parental  FCLTCSNQVGNGPRLCLLCQRFRATAFQREELMKMKVKDLRDYLSLHDISTEMCREKEELVFLVL-GQQP
          F.LTC.NQVGNGPRLCLLCQRFRATAFQREELMKMKVKDLRDYLSLHDISTEMC.EKEEL.FL.L.GQQP
Retrocopy FFLTCWNQVGNGPRLCLLCQRFRATAFQREELMKMKVKDLRDYLSLHDISTEMCQEKEELAFLSL<GQQP

Parental  AVPQE-GRTRALSPDSPEQQAFLSQPHASTIPPTSASLPPSPAQATSVPPAQAQERQQANGHVSQDQEEP
          AVPQE.G....L.P......AFLSQ.HASTIP.TSASLPPSPAQATSVPPAQAQERQQANGHVS.DQEEP
Retrocopy AVPQE<GQDSCLIPGLA-RAAFLSQSHASTIPSTSASLPPSPAQATSVPPAQAQERQQANGHVSHDQEEP

Parental  VCLEGTATASVEDETQSLDSEDSFVPGRRASLSDLTHLEDIEGLTVRQLKEILARNFVNYKGCCEKWELM
          VCL..TATA..E.ETQSLDSE.SFVPGRRASLSDLTHLEDIEGLTVRQL.EI.ARNFVNYKGCCEKWELM
Retrocopy VCLQSTATAADESETQSLDSEHSFVPGRRASLSDLTHLEDIEGLTVRQLREIPARNFVNYKGCCEKWELM

Parental  ERVTRLYKDQKGLQHLVCGAEDQNGGAVPSAL-EENLCKICMDSPIDCVLLECGHMVTCTKCGKRMNECP
          ERV.RLYKDQKGLQHLVC..E.QNGGAVPSAL.EENLCKICMDSP.DCVLLECGHMVTCTKCGKRMNECP
Retrocopy ERVPRLYKDQKGLQHLVCDTEIQNGGAVPSAL<EENLCKICMDSPTDCVLLECGHMVTCTKCGKRMNECP

Parental  ICRQYVIRAVHVFRS
          ICRQYVI.AVHVFRS
Retrocopy ICRQYVI*AVHVFRS

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_385 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001950	2 retrocopies	retro_chof_1069, retro_chof_285,
Macropus eugenii	ENSMEUG00000012628	1 retrocopy	retro_meug_1745,
Otolemur garnettii	ENSOGAG00000024777	1 retrocopy	retro_ogar_621,
Ochotona princeps	ENSOPRG00000011769	1 retrocopy	retro_opri_385 ,
Tarsius syrichta	ENSTSYG00000008923	2 retrocopies	retro_tsyr_1749, retro_tsyr_2060,