RetrogeneDB ID: retro_tbel_238

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1532:267264..268392(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSTBEG00000016911
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 [Source:HGNC Symbol;Acc:9561]

Sequence

>retro_tbel_238
ATGGTATTGGAAAGCACTATGGTTTGTGGGGACAATAGTGAGTATATGTGGAATGGGTACGTCTTACCTACCCAGCTGCA
GGATGCTGTCAACATAGTGTGTCACTTGAAATCCCACAACAACCCGGAAAATAATGTGGGCCTTATCACACAGTCAGTGA
CTGTGAAGTGCTGACCATGCTCACCCCCAACACCGGCCACGTCCTCTCCAAGCTCCACATGTCCAGTCCAAGGGCAAGAT
CACTTTTGCACTGGCATCCTTGTGGCCCACTTGGCACTGAAGCACCAGCAGGGCAAGAACCACAAGGTATGCATCATCGC
CTTCGTGGGGAGCCCCATGGAGGACAGCGAAAAGGATCTGGTGAAATTGGCTAAATGCCTCAAAAAGGAGAAAGTAAATG
TTGACATCATCAACTTTGGGGAAGAGGAGGTGAACATGGAAGAGTGAACTGCCTTTGTAAACACTTTGAATGGCAAAGAT
GGAAGCATTTCTCATCTGGTGACAGTTCCTCCTGACCCCAGCTTGGCTGATACTCTCATCAGCTCTCTGATTCTGGCTGG
CGAGGGTGGTGCCATGCTGGGTCTTGGTGCCAGTGACTTTGAATTTGGAGTGGATCCCAGTGCTGGTCCTGAGTTGACTC
TGGCCCTTTGTTTCTCCGTGGAGGAGCAGCAGCAGTGGCAGGGGAGGAGACTCAGCAGGCAGCAGCTGCCTCTGCTGCTG
AAACTGGGATAGCTGCAGCTGGGGCTGAAGGTGAACGAGGCCTAGACAATGCCCTGTTGAAGACGACCATCAGCCAGCAG
GAGTTTAGCTACATGAGGCTCCCTGAACTGAGCAGTATGACTGAGGCAGAGCAGAGTGCCTAGACCATAGGGATGTCCCT
GTAGGGAGCAGGGTCTGGCCAGGCAGAATCAGCAGATCTTGATGCCAGCTCAGCCATGGACACATCTGAGCCAACCAAGG
GGTAGGATGATTATGACATGAGGCAGGACCTGGAGTTCCCTTCAGAGTGTCCTAGAGAAACTTCTGGTTGTGGATCCCAA
CAACAAAGTCATTCAAAATGCCATGGGCTCTCTGGCCTCCCAGATCATGAAGGATGGCAAGAAAGACAAGAAGGAGGAGT
ACAAGAAG

Alignment

ORF - retro_tbel_238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLA-NDCEVLTTLTPDTG
          MVLESTMVC.DNSEYM.NG..LPT.L...QDAVNIVCH.K...NPENNVGLIT....DCEVLT.LTP.TG
Retrocopy MVLESTMVCGDNSEYMWNGYVLPTQL---QDAVNIVCHLKSHNNPENNVGLITQS<SDCEVLTMLTPNTG

Parental  RILSKLHT-VQPKGKITF-CTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVN
          ..LSKLH..VQ.KGKITF.CTGI.VAHLALKH.QGKNHK..IIAFVGSP.ED.EKDLVKLAK.LKKEKVN
Retrocopy HVLSKLHM<VQSKGKITF<CTGILVAHLALKHQQGKNHKVCIIAFVGSPMEDSEKDLVKLAKCLKKEKVN

Parental  VDIIXXXXXEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLADALISSPILAGEGGAMLGLGASDFEFG
          VDII.....EVN.E..TAFVNTLNGKDG..SHLVTVPP.PSLAD.LISS.ILAGEGGAMLGLGASDFEFG
Retrocopy VDIINFGEEEVNMEE*TAFVNTLNGKDGSISHLVTVPPDPSLADTLISSLILAGEGGAMLGLGASDFEFG

Parental  VDPSADPELALALRVSMEEQRQRQ-EEEARRAAAASAAEAGIAPAGAEGERDSDDALLKMTISQQEFSRA
          VDPSA.PEL.LAL..S.EEQ.Q.Q..EE...AAAASAAE.GIA.AGAEGER..D.ALLK.TISQQEFS..
Retrocopy VDPSAGPELTLALCFSVEEQQQWQ<GEETQQAAAASAAETGIAAAGAEGERGLDNALLKTTISQQEFSYM

Parental  GLPDLSSMTEEEQIAYAMQMSLQGAEFGQAESADLDASSAMDTSEPAKEEDDYDVMQDPEF-LQSVLENL
          .LP.LSSMTE.EQ.A....MSL.GA..GQAESADLDASSAMDTSEP.K..DDYD..QD.EF.LQSVLE.L
Retrocopy RLPELSSMTEAEQSA*TIGMSL*GAGSGQAESADLDASSAMDTSEPTKG*DDYDMRQDLEF>LQSVLEKL

Parental  PGVDPNNEAIRNAMGSLASQATKDGKKDKKEEDKK
          ..VDPNN..I.NAMGSLASQ..KDGKKDKKEE.KK
Retrocopy LVVDPNNKVIQNAMGSLASQIMKDGKKDKKEEYKK

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_238 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_238 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012565	1 retrocopy	retro_cfam_591,
Callithrix jacchus	ENSCJAG00000007357	1 retrocopy	retro_cjac_2808,
Dasypus novemcinctus	ENSDNOG00000007446	1 retrocopy	retro_dnov_1556,
Homo sapiens	ENSG00000159352	1 retrocopy	retro_hsap_2531,
Nomascus leucogenys	ENSNLEG00000010139	1 retrocopy	retro_nleu_1450,
Pongo abelii	ENSPPYG00000000871	1 retrocopy	retro_pabe_1862,
Pan troglodytes	ENSPTRG00000013893	1 retrocopy	retro_ptro_1474,
Sus scrofa	ENSSSCG00000006628	1 retrocopy	retro_sscr_981,
Tupaia belangeri	ENSTBEG00000016911	1 retrocopy	retro_tbel_238 ,
Tursiops truncatus	ENSTTRG00000007019	1 retrocopy	retro_ttru_903,