RetrogeneDB ID: retro_opri_1051

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_62478:451..1028(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABHD10
• Ensembl ID: ENSOPRG00000009517
• Aliases: None
• Description: abhydrolase domain containing 10 [Source:HGNC Symbol;Acc:25656]

Sequence

>retro_opri_1051
TTTGATTATTTGGGACTCAGAAGTTCAGATGGCATCTTAGAAGAATACATAGTGGGAAACCAAGAAAAGATGCTCTTTCT
ATAGTTGATGAAGCTGTAGGACCACAGACAGTAACTGGATCGAGCTTTGGTGGATGGCTTCATGCTTCATGCTGCAATAG
CACAGGCAGAAAAAGTCACGGCACTTATTGGTGTAGCTGTAGCTGCAGATGGCCTGGTGAAAAACTTTTACATGTTGAGG
TAAAGAAGAAAGAAGATGAAATGTGAGTGGACCCTGTCATCAAAATATCATGAAGAAGGAATTTACCCTATTCAATACGG
TTTCATTGAGGCAGTGAAGCACCAATGCTTGTTGCAAAGCCCTCTTCCCATGAAATGCCCTATCAGACTGTTCTATGGCA
TGAAGGACAACATCCCATCTTGGCATACATCTATACAGGTTCCTCACAGGAAGTCAGCACAGATGTGGATGTGATCCTCC
AAAAACACAGTGGTCACAGAATAAGGGAAAAAGCCACATTCAACTTCTTCTTTATACTATTGGTGATGTAATGGATAAAC
TTTGAACTGTAGTTAAC

Alignment

ORF - retro_opri_1051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.18 %
• Parental protein coverage: 64.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FDYSGVGSSEGNLEECTVG-KWRKDVLSIIDELAVGPQILVGSSLGGWL-MLHAAIARPEKVMALIGVAT
          FDY.G..SS.G.LEE..VG.K.RKD.LSI.DE.AVGPQ...GSS.GGWL.MLHAAIA..EKV.ALIGVA.
Retrocopy FDYLGLRSSDGILEEYIVG<KPRKDALSIVDE-AVGPQTVTGSSFGGWL>MLHAAIAQAEKVTALIGVAV

Parental  AADGLVTKFNQLPVEVKKEVEMKGVWTMPSKYHEEGVYHIRYSFIKEAEHHCLLHSPIPVTCPVRLLHGM
          AADGLV..F..L....KK...MK..WT..SKYHEEG.Y.I.Y.FI....H.CLL.SP.P..CP.RL..GM
Retrocopy AADGLVKNFYMLR*RRKK---MKCEWTLSSKYHEEGIYPIQYGFIEAVKHQCLLQSPLPMKCPIRLFYGM

Parental  KDDIIPWHTSMQVADR-VVSKDVDVILRKDSDHRMREKA-DIQLLVYTIDDLIDKLSTVVN
          KD.I..WHTS.QV..R..VS.DVDVIL.K.S.HR.REKA..IQLL.YTI.D..DKL.TVVN
Retrocopy KDNIPSWHTSIQVPHR<EVSTDVDVILQKHSGHRIREKA<HIQLLLYTIGDVMDKL*TVVN

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_1051 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020230	1 retrocopy	retro_cjac_2973,
Cavia porcellus	ENSCPOG00000005650	1 retrocopy	retro_cpor_1498,
Dipodomys ordii	ENSDORG00000014818	1 retrocopy	retro_dord_28,
Felis catus	ENSFCAG00000029739	1 retrocopy	retro_fcat_176,
Ochotona princeps	ENSOPRG00000009517	1 retrocopy	retro_opri_1051 ,
Tursiops truncatus	ENSTTRG00000016358	1 retrocopy	retro_ttru_778,