RetrogeneDB ID: retro_shar_794

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864864.1:2300899..2301364(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSSHAG00000016996
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_shar_794
CTTCTCTGTGTCAGAGAGGCTGAAGACACCGTTCATTTGCTGAATATATTCAGAAAAGCAGACAGCTCTTCAAGATGTAA
TAAAGGGTATGAACTGTCTCCCACAGCAGCAGGTAACTTCACATGTCACAGTCTGCTGACTGCTTCTGGAGTCAGACCCA
TCCCATATCAACCTCCTGGTACCCACTATGATAAGCATGAAGAAACTTACTGCACTATATGGATTATCTGGTAACCCTGG
CCAAAGTTCCATTTGCTTTCCCCTGTGATAGCTTCTTAACCCTCAGCATCCTAGCTTGCCGTTGCAAACTAAGTATTACT
CAAGAGGAGACAGAACTCCTGAAGAAGTGTCTGAAAGAGTTCCCAACGTGCTTCATCTTGGACCTACCATCCTTAAGTAT
CTAGATCATTGACAAAAAATGGCATTTATGACCTGGATGTCATCCTCCCTTCCAAGAGGAGTACT

Alignment

ORF - retro_shar_794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.61 %
• Parental protein coverage: 94.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LLCVGEAGDTVQ-FAEYIQKNVQLYKM-RNGYELSPTAAANFTRRNL-ADYLRSRT-PYHVNLLL-AGYD
          LLCV.EA.DTV..FAEYIQK..QL.KM...GYELSPTAA.NFT...L.AD...S.T.P.H.NLL....YD
Retrocopy LLCVREAEDTVH<FAEYIQKSRQLFKM>NKGYELSPTAAGNFTCHSL<ADCFWSQT<PSHINLLV<THYD

Parental  EHEGP-ALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYKPSITREEAVELLKKCLEELQKRFILNLPS
          .HE....L.YMDYL..LAK.PF.A.....FLTLSIL....K.SIT.EE..ELLKKCL.E....FIL.LPS
Retrocopy KHEET<LLHYMDYLVTLAKVPF-AFPCDSFLTLSILACRCKLSITQEE-TELLKKCLKEFPTCFILDLPS

Parental  FSVRIID-KDGIHELDTILPSKKSS
          .S..IID.K.GI..LD.ILPSK.S.
Retrocopy LSI*IID>KNGIYDLDVILPSKRST

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_794 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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,