RetrogeneDB ID: retro_opri_574

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_178370:381..738(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S6
• Ensembl ID: ENSOPRG00000007310
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 6, pallidin [Source:HGNC Symbol;Acc:8549]

Sequence

>retro_opri_574
GGCCTGACAGGGCCGCCCGGCAGCCTGGAGGCCAGGGAATTGATGCCGGGTTTGAGTGACGCTTCTCCAGATGGAGGGTT
CCTAGAAGGGCTTGAGTGAAGGGAGACAGAGCTGGCCGCAGGATTGCTTTCTCACTACGTGCTAGACCTGCAGAGATCAA
AACAAGCCCTCCAGGAACTCACACAAAACCAAGCTGTCTTATTAGACACCCTGGAACAAGAGATTTCAAAATTTAAAGAA
TGCCATTCTCTGTTGGACATGAATGCTTCGTTCACTGAGGCCACACGTTACCATGCCAAGTTGGTGGACGTAAGGAAAGA
GATGTTGACGCTTCATGAGAAGACGTCGAAGTTAAAG

Alignment

ORF - retro_opri_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.69 %
• Parental protein coverage: 70.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLTGPPGSLEVRELMPGLSDASPDEGLIEDLSVEDRAVEQLAEGLLSHYLPDLQRSKQALQELTQNQVVL
          GLTGPPGSLE.RELMPGLSDASPD.G..E.L.........LA.GLLSHY..DLQRSKQALQELTQNQ.VL
Retrocopy GLTGPPGSLEARELMPGLSDASPDGGFLEGLE*RET---ELAAGLLSHYVLDLQRSKQALQELTQNQAVL

Parental  LDTLEQEISKFKECHSMLDINALFTEAKHYHAKLVNIRKEMLMLHEKTSKLK
          LDTLEQEISKFKECHS.LD.NA.FTEA..YHAKLV..RKEML.LHEKTSKLK
Retrocopy LDTLEQEISKFKECHSLLDMNASFTEATRYHAKLVDVRKEMLTLHEKTSKLK

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_574 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 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012059	7 retrocopies	retro_chof_1342, retro_chof_20, retro_chof_2054, retro_chof_2102, retro_chof_211, retro_chof_248, retro_chof_600,
Dasypus novemcinctus	ENSDNOG00000019785	5 retrocopies	retro_dnov_1687, retro_dnov_1885, retro_dnov_2009, retro_dnov_2411, retro_dnov_275,
Echinops telfairi	ENSETEG00000007378	1 retrocopy	retro_etel_404,
Macropus eugenii	ENSMEUG00000012636	1 retrocopy	retro_meug_778,
Monodelphis domestica	ENSMODG00000017628	2 retrocopies	retro_mdom_1673, retro_mdom_561,
Otolemur garnettii	ENSOGAG00000013706	1 retrocopy	retro_ogar_206,
Ochotona princeps	ENSOPRG00000007310	1 retrocopy	retro_opri_574 ,