RetrogeneDB ID: retro_opri_1180

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8945:27779..28112(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSOPRG00000015952
• Aliases: None
• Description: H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]

Sequence

>retro_opri_1180
ACCAGTGATAAAGCACTTACAGGGCAGCTGGCTACAAAAGCTGCTCTCCAGAGAGCGCCCTCTACTGGAGGCGTGAAGAA
ACCTCATTGTTACAGACCTGGTACTGCGGCACTTGGTGAAATTAGATATTATCAGAAGTCCTCCAATTTTGTGACTCACA
AACCTCCCCCCAATCTCTAGTGCAAAAAGCTACTCCACAGTTTAGAATGGAACTGAACATTCTACCTTTTGGTGCTTTGC
AGCAGACAAGTGAAGCCTATCTGAGAGGCATTTTTTAAGACATTATCCTGCTGTATCCATGCAAAATGCAAAACGAAAGA
CATCCAACTAGCA

Alignment

ORF - retro_opri_1180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.46 %
• Parental protein coverage: 86.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGGKAPRKQLATKAARKSAPSTGGVKKPHRYRLGTVALREIRRYQKSTELLIRKLP-FQRLVREIAQDFK
          T..KA...QLATKAA...APSTGGVKKPH.YR.GT.AL.EIR.YQKS......K.P..Q.LV......F.
Retrocopy TSDKALTGQLATKAALQRAPSTGGVKKPHCYRPGTAALGEIRYYQKSSNFVTHKPP<PQSLVQKATPQFR

Parental  TDLRFQSAAIGALQEASEAYLVGLFEDTNL-CAIHAKRVTIMPKDIQLA
          ..L.......GALQ..SEAYL.G.F.D..L.C.IHAK..T...KDIQLA
Retrocopy MELNI--LPFGALQQTSEAYLRGIF*DIIL>C-IHAKCKT---KDIQLA

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_1180 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 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
Ochotona princeps	ENSOPRG00000015952	2 retrocopies	retro_opri_1180 , retro_opri_937,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,