RetrogeneDB ID: retro_tbel_3616

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_146470:44351..45134(+)
• 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_3616
GAAACGCAAACCCTAGTGGAGATTGCCAAAGTAGAACTGGACAATATGCCACTCTGTGGAAAGCAGCCACGTGTATGCTT
TGCCTGCCATAGCGCATCCCTACAGTCTGAAACCTTTAGTATGTGTCCACCGAACTGTTGGAAGAAGCCTTTTCTGTGTT
CATCCAGGTGGAAAGGGCTGTAGTTATTGTGATGATTGAAGAAGACCCTCAGGAAAAGGCATTGATGAGTTCTCAGGGAA
GCCAGCTGCTTAAAAAGCTCTGGACAGATGTAGTGAAGGCTCATTTCTGCTAACTGCATTTCCTCGTCCTATGACTATGG
AGCCCATGGACCAGTTAGATGATGAAGAGGGACTTCCAGAGAAAGTGATTATAAAGAACCAGTGATTTCACAAGGAGCGC
GAGTGGCCCCTCAGCTTTGCACAGCCCAGGTCCTTTGTGAGTGTGCCATGTGCTAGAAGGCCCTCATTGAGATGGAGAAG
CAGCAGCAGAACCAGGTGGGCCACAACATCAAGGAGGCTTGTGAGAAGCTGGTGATGGAGATGGAGGCAGCTTGCCATGA
ACACCAGGTCATGCTAATGAGGCGGGATTTGATGAGGCACCGAGAAGAACTTCGGAGGATGGGAGAGTTGTACAACCAAG
AGGTGCAAAAATGAAAGAAAGCAACTGGAGCTCAGACAGGAGAGGAGCAAAGGTGCAGTGAGGAAGAGATGAGTGGCAGC
AGGAAGAAATGATGCAACAACTGCAGGAAGGATTCAAGGAAACCTGCCTTGATGCGAGTGAGG

Alignment

ORF - retro_tbel_3616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.81 %
• Parental protein coverage: 51.47 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ESRTLAEIAKAELDGTILKSRPLRIRFATHGAAL-TVKNLSPVVSNELLEQAFSQFGPVEKAVVVV-DDR
          E..TL.EIAK.ELD...L.....R..FA.H.A.L.TV.NL...VS.ELLE.AFS.F..VE.AVV.V.DD.
Retrocopy ETQTLVEIAKVELDNMPLCGKQPRVCFACHSASL<TV*NL*-YVSTELLEEAFSVFIQVERAVVIV<DD*

Parental  GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQP
          .R..GKG..EF..KP.A.KAL.RC..G.FLLT..PRP...EPM.Q.DDE.GLPEK...K.Q..HKERE.P
Retrocopy RRPSGKGIDEFSGKPAA*KALDRCSEGSFLLTAFPRPMTMEPMDQLDDEEGLPEKVIIKNQ*FHKEREWP

Parental  PRFAQPGTFEFEYASRWKAL-DEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLMLMRQDLMRRQEEL
          ..FAQP..F......R...L......QQ..QV..NI.EA.EKL..EMEAA.HEHQ.MLMR.DLMR..EEL
Retrocopy LSFAQPRSFVSVPCARRPSL<EMEKQQQ-NQVGHNIKEACEKLVMEMEAACHEHQVMLMRRDLMRHREEL

Parental  RRLEELRNQELQK-RKQIQLRHEEEHRRREEEMMRHREQEELRRQQEGFKPNYMENR
          RR..EL.NQE.QK..K.......EE.R..EEEM...R............KP..M..R
Retrocopy RRMGELYNQEVQK*KKATGAQTGEEQRCSEEEMSGSRKK*CNNCRKDSRKPALMRVR

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_3616 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3616 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.

---

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,