RetrogeneDB ID: retro_opri_403

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_108574:41..745(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H1FOO
• Ensembl ID: ENSOPRG00000010371
• Aliases: None
• Description: H1 histone family, member O, oocyte-specific [Source:HGNC Symbol;Acc:18463]

Sequence

>retro_opri_403
TCCTCCAGACAGGAGGTTCCCAGCGCCCCCGTTCGCAGGCCAAGGGGCAGCCTCACACAGAGCCGCAAACCCACGATGCT
GCGCATGGTGCTAGAGGCGCTGCAAGCGAGCGAACGGCGCCGAGGCACGTCAGTGATGGCCATCAAGCTCTATATCCTGC
GCAAGTATCCGACTGTGCACAGCCTGCGCTTCAAGTACCTGCTCAAGCAGGCCCTGGCCACCGGCATGAGTCGAGGCCTT
CTCACCAGGCCCCTCCACTCCAAGGCCAAGGGTGCCACTGGCAGCTTCAAATTGGTGTCCGAGCGCAAGAGAACACAACT
CAGCAAGGCCAGGATGCCCAGGAAGGGGAAGGCCGGAAAAGCGGGGAAGGGCCAAGGAGCCAGTCTCCAAGAAACCTAGA
GAGGCCAGACCATTCCAGGTGGGACAGGCACACAAGAAGCCGGGTGCTGTGGGGAAGGTGCCTCCTAAGCCTGGTGCAAC
CAAGAAGGTCCGCAAGAAAGGCAAAGAGGCCAAAGACAGGGAGGTCAAACGGGGCCAGGCCAGGAAGGCTCCCAGGAAGT
CAAACAAGGCCACACAGGCCTCTGCTGGTCCTAAGAACAATGGGAAACCAAAGGTCAAAGGCCACAGGAAAAGCCAAGGA
ATCCAGCCTGCCCCTCCGGGAGAGGCCAAAGCTCCCAGGAAAACCAGTGCCGCCGACAGCAAGA

Alignment

ORF - retro_opri_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.77 %
• Parental protein coverage: 72.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSAPLAPAAKLPDPTEPGSLTQSRKPTMLRMVLEALQASERRQGTSVMAIKLYILRKYPTVHSLRFKYLL
          SS....P.A....P...GSLTQSRKPTMLRMVLEALQASERR.GTSVMAIKLYILRKYPTVHSLRFKYLL
Retrocopy SSRQEVPSAPVRRPR--GSLTQSRKPTMLRMVLEALQASERRRGTSVMAIKLYILRKYPTVHSLRFKYLL

Parental  KQALATGMSRGLLTRPLHSKAKGATGSFKLVSERKNT--TQPRKARKGKAGKAGK-AKEPVSKKPREA-D
          KQALATGMSRGLLTRPLHSKAKGATGSFKLVSERK.T.....R..RKGKAGKAGK.AKEPVSKKPREA..
Retrocopy KQALATGMSRGLLTRPLHSKAKGATGSFKLVSERKRTQLSKARMPRKGKAGKAGK>AKEPVSKKPREARP

Parental  GQVGQAHKKPGAVGKVPPKPGAAKKVSKKGKEAKDTEVKRGQARKAPRKSNKATQASAGPKNNGKPKVKG
          .QVGQAHKKPGAVGKVPPKPGA.KKV.KKGKEAKD.EVKRGQARKAPRKSNKATQASAGPKNNGKPKVKG
Retrocopy FQVGQAHKKPGAVGKVPPKPGATKKVRKKGKEAKDREVKRGQARKAPRKSNKATQASAGPKNNGKPKVKG

Parental  HRKSQGEAKAPRKTSAADSKSS-KPTAR
          HRKSQG...AP.....A..K.S..PTAR
Retrocopy HRKSQGIQPAPPGEAKAPRKTS>PPTAR

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_403 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017209	2 retrocopies	retro_cjac_3976, retro_cjac_981,
Felis catus	ENSFCAG00000000094	2 retrocopies	retro_fcat_1139, retro_fcat_416,
Homo sapiens	ENSG00000178804	1 retrocopy	retro_hsap_2799,
Gorilla gorilla	ENSGGOG00000000735	1 retrocopy	retro_ggor_1946,
Myotis lucifugus	ENSMLUG00000025226	2 retrocopies	retro_mluc_1278, retro_mluc_1318,
Oryctolagus cuniculus	ENSOCUG00000029379	1 retrocopy	retro_ocun_1483,
Ochotona princeps	ENSOPRG00000010371	2 retrocopies	retro_opri_403 , retro_opri_624,
Pongo abelii	ENSPPYG00000013414	1 retrocopy	retro_pabe_2225,
Pan troglodytes	ENSPTRG00000015380	1 retrocopy	retro_ptro_1896,
Pteropus vampyrus	ENSPVAG00000007110	1 retrocopy	retro_pvam_808,
Tursiops truncatus	ENSTTRG00000011276	1 retrocopy	retro_ttru_1111,