RetrogeneDB ID: retro_tbel_2388

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109838:258..1017(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSPC1
• Ensembl ID: ENSTBEG00000002361
• Aliases: None
• Description: paraspeckle component 1 [Source:HGNC Symbol;Acc:20320]

Sequence

>retro_tbel_2388
CCACTGTGTGTGCACTTTGTCTGCCATGGTGCATCCCTTATCATCTGAAAACTTTCTCAGCACGTGTCCAACAAATTGTT
GGAAGAAGCATTTTCTGTGTTTGTCCAGGTGGAAAGGGCTGTCATCATTGTGGATGATCAAAAAAGGCCCTCAGTAAAAG
GCATTGTTGAGCTCTCAGGAAAGCCGGCTGCTTGAAAAGCTCTGGACAGATGTGGTAAAGGCTCCTTTCTGCCAACCACA
TATCCTCGACCTGTGACTGTGGAAACCATGGACCAGTTATATGATCTAGAAGGACTTCTAGAGAAGGTGGTTAAAAAGAA
TCAGCAATTTCAAAGGAGTGAGAGCAGCCACCCAGATCTGCACAGTCCAGGTGCTTTGAGTATGAGTATGCCATGCCGAA
AGGCAAACACTGAGATGGAGAAGCAGCAGCAAGACCAAGTAGACCGCAATATCCAGGAGGCTCATGAGAAGCTGGAGATG
GAGATGGAGGCTGCCCAACATGAGCACCAGGTCATGCTAATGAGGCAGGATTAGATGAAGTGCCACGGAGAACTTCAGAG
GACAAAAGAGCTGCATAGCCAAGAGGTACCAAAAAGAAAGCAACTGGAGCTCAGGCAGGAGAAGTGCCGGCATCATGAGG
AAGAGATGCGATGACAGCAGGAAGAAGGCAACAGCAGGAAGGATTCAAGGGAACCTTCTCTGATGCAAGAGCAGGAGATA
CAGATGGGTCAGATGGCTATGGGTGGCGCCATGGGCATA

Alignment

ORF - retro_tbel_2388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.02 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER
          PL...F..HGA.L....LS..VSN.LLE.AFS.F..VE.AV..VDD..R...KG.VE...KP.A.KAL.R
Retrocopy PLCVHFVCHGASLII*KLSQHVSNKLLEEAFSVFVQVERAVIIVDDQKRPSVKGIVELSGKPAA*KALDR

Parental  CGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYH-KEREQPPRFAQ-PGTFEFEYASRWKALD
          CG.G.FL.TT.PRPV.VE.M.Q..D..GL.EK...K.QQ...KE.EQPPR.AQ.PG........R.KA..
Retrocopy CGKGSFLPTTYPRPVTVETMDQLYDLEGLLEKVVKKNQQFQ<KE*EQPPRSAQ>PGALSMSMPCR-KANT

Parental  EMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLMLMRQDLMRRQEELRRLEELRNQELQKRKQIQLRHE
          EMEKQQ..QVDRNI.EA.EKLE.EMEAA.HEHQ.MLMRQD.M....EL.R..EL..QE..KRKQ..LR..
Retrocopy EMEKQQQDQVDRNIQEAHEKLEMEMEAAQHEHQVMLMRQD*MKCHGELQRTKELHSQEVPKRKQLELR-Q

Parental  EEHRRREEEMMRHREQEELRRQQEGFKPNYMENREQEMRMGDMGPRGAINM
          E..R..EEEM.....QEE.........P..M...EQE..MG.M...GA...
Retrocopy EKCRHHEEEM--R*QQEEGNSRKDSREPSLMQ--EQEIQMGQMAMGGAMGI

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_2388 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2388 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011078	2 retrocopies	retro_dnov_1278, retro_dnov_488,
Tupaia belangeri	ENSTBEG00000002361	2 retrocopies	retro_tbel_2388 , retro_tbel_3616,
Xiphophorus maculatus	ENSXMAG00000007929	1 retrocopy	retro_xmac_3,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,