RetrogeneDB ID: retro_opri_348

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5537:2881..3471(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAA2
• Ensembl ID: ENSOPRG00000007567
• Aliases: None
• Description: acetyl-CoA acyltransferase 2 [Source:HGNC Symbol;Acc:83]

Sequence

>retro_opri_348
CACTTTAATGCGCAGATGACACCAGTCGAGGTGAAGACAAGGAAGGGAAAACAGAACATACAAGAAGATGAGCATGCTCG
ACCTGAGACAACCATCGAACAATTATAGAAACTTCCTTCGGTGTTCTAGAAAGATGGCACTATCGCTGCGGGAAGGGCTT
CAGGGGTGTGTGATGGTGCTGCAGCTGTCATCCTGGCTAGTGAAGATGCTGTCCAAAAACACAACTTCACACCGCTGGCC
AGAGTGGTAGGTACTTTGTGTCTGGATGTGTTGCTTCTATCACGGGTATTGGTCCTGTCCTTGCTACCCATGGAGTCCTG
AGGAATGCAGGACTGGGTCTTAAGGACACATGCTTGCTAGAAGTGAATGAAGCCTTTGACCCCCATGTACCTGGCTGTTC
AGAACAATTCAGACCTGGTTCCAAGCAAAACCAATGGAGAAGACATTAGTTTGGGTCACACATGGAGAGGATCTGGTGCA
AGAATTCCTGCATATGTGGTTCATGAATTAAGGCATAGAGGTGGAAAATACACTCTGGGCTCGACCTACACTGGAGGCAG
CCAAGGTGTGCAGTCATCATTCAGAACACA

Alignment

ORF - retro_opri_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.83 %
• Parental protein coverage: 50.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YFNEEMVPIEVKTRKGKQTMQVDEHPRPDTTMEQLQKLPPVFKKDGVVTAGNASGVCDGAGAVILASEDA
          .FN..M.P.EVKTRKGKQ..Q.DEH.RP.TT.EQL.KLP.VF.KDG...AG.ASGVCDGA.AVILASEDA
Retrocopy HFNAQMTPVEVKTRKGKQNIQEDEHARPETTIEQL*KLPSVF*KDGTIAAGRASGVCDGAAAVILASEDA

Parental  VKKHNLTPLARVVS-YFTSGCDPAIMGIGPVPAISGALKKAGLSLKDMDLVEVNEAF-APQYLAVQKSLD
          V.KHN.TPLARVV..YF.SGC...I.GIGPV.A..G.L..AGL.LKD..L.EVNEAF..P.YLAVQ...D
Retrocopy VQKHNFTPLARVVG<YFVSGCVASITGIGPVLATHGVLRNAGLGLKDTCLLEVNEAF>TPMYLAVQNNSD

Parental  LDPSKTNVNGGAIALGHPLASSGSRITAHLVHELRRRGGKYAVGSACIGGGQGI-AVIIQNT
          L.PSKT..NG..I.LGH....SG.RI.A..VHELR.RGGKY..GS...GG.QG..AVIIQNT
Retrocopy LVPSKT--NGEDISLGHTWRGSGARIPAYVVHELRHRGGKYTLGSTYTGGSQGV<AVIIQNT

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_348 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009411	1 retrocopy	retro_amel_602,
Equus caballus	ENSECAG00000019394	1 retrocopy	retro_ecab_454,
Homo sapiens	ENSG00000167315	1 retrocopy	retro_hsap_4829,
Gorilla gorilla	ENSGGOG00000012552	1 retrocopy	retro_ggor_3011,
Myotis lucifugus	ENSMLUG00000022960	1 retrocopy	retro_mluc_654,
Nomascus leucogenys	ENSNLEG00000011576	1 retrocopy	retro_nleu_2706,
Ochotona princeps	ENSOPRG00000007567	2 retrocopies	retro_opri_1224, retro_opri_348 ,
Pan troglodytes	ENSPTRG00000010016	1 retrocopy	retro_ptro_3214,
Vicugna pacos	ENSVPAG00000012121	1 retrocopy	retro_vpac_625,