RetrogeneDB ID: retro_meug_1235

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold336437:66..575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSMEUG00000000421
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_meug_1235
TGCCCCACATCACTTGCTACAGAGTACCTTATTGGTATCCAGGGTCCTGGCTACATCTTAGTGACCTTGAACTGTGTGGC
CACCAGCAATTTCATCCAGAAGGGCAATTATGATTATGCTTAAAATGAGGGAGAAGATCTTACTTCTCTATGTTGGAGAG
TCTTAGAGACACTGTACAGTTTGCTGAATACATTCAGAAAAATGTAGAGCTCTACAAGATGTGCAGTGACTATGAACTGT
CTCCCACAGCAACAGCTAACTTCACACATCAAAATCTGGATGACTACTTCCAGAGTCAGACCCCAAACCATGTCAGCCTC
CTGTTGGCTGGCTATGATGAGCATGAAGGACCTTGACTGTAGTAGATGGGTTAGCTGGAAGTTCAGGCCAAAGTTTCATT
TGCAGCCCATAATTATTGTGTCTTCTTGACCCTCAGCATTCTAGATCACTACTGCAAACCAAGTATCACACATGAATATG
CAGTAGAGCTCCTGAAGAATTGTCTAGAA

Alignment

ORF - retro_meug_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.95 %
• Parental protein coverage: 85.86 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CP-SAAMEYLIGIQGPDYILVASDRVAASNIVQMKDXHDKMFKMSEKILLLC-VGEAGDTVQFAEYIQKN
          CP.S.A.EYLIGIQGP.YILV....VA.SN..Q.K...D......E....LC......DTVQFAEYIQKN
Retrocopy CPTSLATEYLIGIQGPGYILVTLNCVATSNFIQ-KGNYDYA*NEGEDLTSLC<LESLRDTVQFAEYIQKN

Parental  VQLYKMRNGYELSPTAAANFTRRNLADYLRSRTPYHVNLLLSGYDEHEGPALYYMSYLAALAKAPFAAHG
          V.LYKM...YELSPTA.ANFT..NL.DY..S.TP.HV.LLL.GYDEHEGP.L..M..L...AK..FAAH.
Retrocopy VELYKMCSDYELSPTATANFTHQNLDDYFQSQTPNHVSLLLAGYDEHEGP*L**MG*LEVQAKVSFAAHN

Parental  YGAFLTLSILDHYYKPSITREEAVELLKKCLE
          Y..FLTLSILDHY.KPSIT.E.AVELLK.CLE
Retrocopy YCVFLTLSILDHYCKPSITHEYAVELLKNCLE

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1235 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1235 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,