RetrogeneDB ID: retro_opri_502

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_14152:23346..23673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSOPRG00000008611
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_opri_502
CCACGGCAGAGTGTGATGATGCCATTTCGCACTAACCTGGCTACTGGAATCCCCAGCAGTAAGGTGAAGTACTCGCGACT
CTCCAGCACAGACGATGGCTACATCGACCTCCAGTTTAAGAAAAGCCCTCCGAAGATCCCGTACAAGGCCATCGCGCTCA
CCACCGTGCTGTTCCTGATCGGTGCCTTTCTCATCATCATCGGCTCTCTCCTGCTGGCGGGCTACATCATCAAGGCGGGG
GCAGACCCAGCCGTTCCCGTGCTGATCACCAGCATCCTGGTGTGCCTGCCAGGATTTTACCACCTGCACATTGCCTACTG
TGCATCC

Alignment

ORF - retro_opri_502 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.82 %
• Parental protein coverage: 95.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRPRVMMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSL
          PR..VMMP.RTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIAL.TVLFLIGAFLIIIGSL
Retrocopy PRQSVMMPFRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKSPPKIPYKAIALTTVLFLIGAFLIIIGSL

Parental  LLAGYISKGGTDWAI-VPILGILLHLPGFHQLQVAFFVS
          LLAGYI.K.G.D.A..V.I..IL..LPGF..L..A...S
Retrocopy LLAGYIIKAGADPAVPVLITSILVCLPGFYHLHIAYCAS

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_502 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009083	1 retrocopy	retro_amel_1818,
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Canis familiaris	ENSCAFG00000006039	1 retrocopy	retro_cfam_981,
Dasypus novemcinctus	ENSDNOG00000005724	5 retrocopies	retro_dnov_1004, retro_dnov_2377, retro_dnov_2534, retro_dnov_373, retro_dnov_803,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Ochotona princeps	ENSOPRG00000008611	1 retrocopy	retro_opri_502 ,
Pteropus vampyrus	ENSPVAG00000002863	1 retrocopy	retro_pvam_44,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,