RetrogeneDB ID: retro_opri_76

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1893:53793..54301(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSOPRG00000012259
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_opri_76
TGTTCTGTGGAACCTGCAACCCCCAGCCTCATTGGCACTCAGGGCCCAGGCTATGACCTTGTCACCTTTGGCCAGGTGGA
TGTCAGCAGCATTGTCCAGATGAAAGGTTCATCATGACAAGATGTTTAAGATGAGTGAAAAACTATTTACTCCTGTGTTG
GAGAAGTTGGAGACACTGTACAATTTGCAGAATATATTCATGAAAATGTGCAACTTTATAAGATGCAAAATGTCTGTGAA
CTGTCTCGCACAGCAGCGGCAAATTTCACATGCAGAAACCTGGCTGACTGTCTTCGGAGTCAGACCCTGTATCTCATGAA
CCTCCTCCTGGCTGGCTATGGTGACATGAGGGGCCAGTGCTCTATTATGTGGACCACTGACAGCTTTGGCCGAGGTCCCT
TTTACAGCCCATGGCTGTGGTGCCTTCCTGACTCTCAGTATCCTGGACTGACACTATGCACCCACCATCTCACACGACAA
GGAACTCCCGAGGAAGTGTCTGGAGGAG

Alignment

ORF - retro_opri_76 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.42 %
• Parental protein coverage: 90.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CSPQPTATMEYLIGIQGPDYVLVASDRVAASNIVQMKDD-HDKMFKMSEKI-LLLCVGEAGDTVQFAEYI
          CS..P......LIG.QGP.Y.LV....V..S.IVQMK...HDKMFKMSEK.....CVGE.GDTVQFAEYI
Retrocopy CSVEPATPS--LIGTQGPGYDLVTFGQVDVSSIVQMKGS>HDKMFKMSEKL<IYSCVGEVGDTVQFAEYI

Parental  QKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDE-HEGPALYYMDY-LAALAKAP
          ..NVQLYKM.N..ELS.TAAANFT.RNLADCLRS.T.Y..NLLLAGY...HEGP.LYY.D..L.ALA..P
Retrocopy HENVQLYKMQNVCELSRTAAANFTCRNLADCLRSQTLYLMNLLLAGYGD<HEGPVLYYVDH<LTALAEVP

Parental  FAAHGYGAFLTLSILDRYYTPTISRDKAVELLKKCLEE
          F.AHG.GAFLTLSILD..Y.PTIS.DK..EL..KCLEE
Retrocopy FTAHGCGAFLTLSILD*HYAPTISHDK--ELPRKCLEE

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_76 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76 , retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403, retro_tsyr_912,