RetrogeneDB ID: retro_opri_200

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_350:106540..106935(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: N6AMT1
• Ensembl ID: ENSOPRG00000001551
• Aliases: None
• Description: N-6 adenine-specific DNA methyltransferase 1 (putative) [Source:HGNC Symbol;Acc:16021]

Sequence

>retro_opri_200
ATGGCGGCGCCCAGCCTCCCCACGCCTCTGCATGGGCACGTGTGCCACGGGGCCTTTCTCGACGTGCACGAGCCCGCGGA
GGACACATTCCTGCTGCTGGATGCGCTCGAGGCGGCTGCGGCCGAGCTGGCGGGTGTGGAAATATGCCTGGAAGTAGGGT
CCGAGTCTGGAGTGTTGTCTGCGTTCCTCGCTTCTCTTATCGGCCCCCGGGCTCTGTACATGTGCACTGACATCAATCCC
GAGGCCGCAGCCTGTACACTGGAAACAGCACGCTGCAACCAAGTTCATATTCAACCAATCATTACAGATTTGGTCAAAGG
CTTGCTACCGAGACTGAAGGGGAAAGTTGATCTTCTCGTGTTCAATCCCCCCATGTGGTGACTCCCCCTGAAGAG

Alignment

ORF - retro_opri_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.98 %
• Parental protein coverage: 61.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPSLPTPLHGHVGRGVFRDVYEPAEDTFLLLDALEAAAAELAGVEICLEVGSGSGVVSAFLASLLGPR
          MAAPSLPTPLHGHV..G.F.DV.EPAEDTFLLLDALEAAAAELAGVEICLEVGS.SGV.SAFLASL.GPR
Retrocopy MAAPSLPTPLHGHVCHGAFLDVHEPAEDTFLLLDALEAAAAELAGVEICLEVGSESGVLSAFLASLIGPR

Parental  ALYLCTDINPEAAACTLETARCNRVHIQPIITDLVKGLLPRLKGKVDLLVFNP-PYVVTPPEE
          ALY.CTDINPEAAACTLETARCN.VHIQPIITDLVKGLLPRLKGKVDLLVFNP.P.VVTPPEE
Retrocopy ALYMCTDINPEAAACTLETARCNQVHIQPIITDLVKGLLPRLKGKVDLLVFNP<PHVVTPPEE

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_200 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005227	1 retrocopy	retro_chof_1139,
Homo sapiens	ENSG00000156239	1 retrocopy	retro_hsap_916,
Gorilla gorilla	ENSGGOG00000022382	1 retrocopy	retro_ggor_739,
Nomascus leucogenys	ENSNLEG00000002845	1 retrocopy	retro_nleu_282,
Oryctolagus cuniculus	ENSOCUG00000001084	1 retrocopy	retro_ocun_521,
Ochotona princeps	ENSOPRG00000001551	3 retrocopies	retro_opri_200 , retro_opri_867, retro_opri_925,
Pongo abelii	ENSPPYG00000011314	1 retrocopy	retro_pabe_790,
Pan troglodytes	ENSPTRG00000013817	1 retrocopy	retro_ptro_635,
Pteropus vampyrus	ENSPVAG00000012777	2 retrocopies	retro_pvam_1166, retro_pvam_1200,
Sus scrofa	ENSSSCG00000026046	1 retrocopy	retro_sscr_130,
Ictidomys tridecemlineatus	ENSSTOG00000021743	1 retrocopy	retro_itri_497,
Tupaia belangeri	ENSTBEG00000001269	1 retrocopy	retro_tbel_777,