RetrogeneDB ID: retro_tbel_4454

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_84107:7837..9244(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX21
• Ensembl ID: ENSTBEG00000002310
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 21 [Source:HGNC Symbol;Acc:2744]

Sequence

>retro_tbel_4454
TCGTCCTTAGATAGTTCTCATAAATCAAGTGATAATAAACTAGAGGAGACCCTAACATGTGAACAGAAAGAAGGAGACTT
CTCCAATTTCCCTATTTCTGAAGAGACGATAAAGCTTCTGAAAGGTTGAGGGGTAACATATCTCTTTCCTATTAAAGTTA
AGACCTTTGTTCCTGTATGTGAAGGAAAATATTTAATTGCTCAAGCACGGACAGGAACAGGAAAGACATTCTCTCTTGCT
ATCCCCTTGATTGAAAGGCTCCAAAGAAATCAAGAAATGATTTTTAAAAGCTGCTCTCCAAAGGTACTTGTTTTGGCTCC
AACAGGGGAACTGGCAAATCAGGCAGCCAAAGATTTCAAAGATATAACTAGAAAACTTAGCATGGCATGTTTTTATGGTG
GGACATCATGTCGAAGCCAAATTAATCTTATTTGAAATGGTATTGACATCTTGATTGGGACTGTTGGTCGAATAAAAGAT
TATCTGCAAAGTCGCCCATTGGATCTTTCTAAACTACGCCATGTTGTGCTTGATGAAGTGGATCAAATGTTAGATTTAGT
TTTTTCTGAACAAGTTGAAGATATTATCCACTAATCCTACAAAACTGAGTCTGAAGACAATCCTCACACTTCACTGTTTT
CGGCAGCTGGCCCACAGTGGGTGTATAGAGTCACAAACAAATATTTGAAATCCAGATAAGAACAGGTTGATTTGGTGGGA
AAATGACTCAAAAAGCTGCAACTACTGTGGAATATTTAGCCATCCAATGCCATTGGTCTCAGAGACCAGCAGTTATTGGT
GAAGTCCTTCAAGTCTACAGTGGATCTGAAGGGAGGGCTATTATTTTCTCTGAGACCAAGAAGATTGTAACTGAAATGGC
CATGAATCCTCACATAAAACAGAATGCTCAGTGTTTACATGGGGACATTGCACAGTCACAAAGAGAAATTACACTGACAG
GTTTCAGAGAAGGCAGTTTTAAAGTTTTGGTGGAAACCAATGTGGCTGCCCATGGTTTGGACATTTCTGAGGTTGACCTG
GTGATCCCAAGTTCTTCTCCACAGAATGTGGAGTCCTATATCCATCGCACAGGTAGAGCTGGTCGGACAGGGATTTGCAT
ATGTTTTTAGCAACCAAGAGAAAGAGGTCAACTAAGATATGTGGAACAAAAAGCAGGAATTACTGTTAAACATGTAGGTG
TTCCTGCTGCGATGGATTTAGTTAAATTTAAAAGCATGGATGCCATCAGGTCTCTGGCTTCTGTTTCTTATACTGCTGTT
GATTTTTTTCCAACCACCAGCTCAGAGACTGATAGAAGAGAAAGGGGCAGCGGATGCATTAGCTGCAGCATTTGCACACA
TTTCTGGTGCATCAAGCTTTGAACCACGATCTTTGATCACCTCTGAT

Alignment

ORF - retro_tbel_4454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.47 %
• Parental protein coverage: 60.76 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSNEAASEESNSEAEQEISVEQKEGAFSNFPISEETIKLLKGRGVTFLFPIQAKTFHHVYSGKDLIAQAR
          .S.......S....E.....EQKEG.FSNFPISEETIKLLKG.GVT.LFPI..KTF..V..GK.LIAQAR
Retrocopy SSLDSSHKSSDNKLEETLTCEQKEGDFSNFPISEETIKLLKG*GVTYLFPIKVKTFVPVCEGKYLIAQAR

Parental  TGTGKTFSFAIPLIEKLQGEMQDKKRGRSPQVLVLTPTRELASQVSRDFSDITKKLSVACFYGGTPYGGQ
          TGTGKTFS.AIPLIE.LQ..........SP.VLVL.PT.ELA.Q...DF.DIT.KLS.ACFYGGT....Q
Retrocopy TGTGKTFSLAIPLIERLQRNQEMIFKSCSPKVLVLAPTGELANQAAKDFKDITRKLSMACFYGGTSCRSQ

Parental  IERMRNGIDILVGTPGRIKDHLQNGKLDLTKLKHVVLDEVDQMLDMGFADQVEEILCVAYK--KDENRQT
          I....NGIDIL.GT.GRIKD.LQ...LDL.KL.HVVLDEVDQMLD..F..QVE.I....YK.....N..T
Retrocopy INLI*NGIDILIGTVGRIKDYLQSRPLDLSKLRHVVLDEVDQMLDLVFSEQVEDIIH*SYKTESEDNPHT

Parental  LLFAC---HWVFNVAKKYMKPSYEQVDLI-GKKTQKTAITVEHLAIKCHWTQRAAVIGDVIRVYSGHQGR
          .LF......WV..V..KY.K...EQVDL..GK.TQK.A.TVE.LAI.CHW.QR.AVIG.V..VYSG..GR
Retrocopy SLFSAAGPQWVYRVTNKYLKSR*EQVDLV<GKMTQKAATTVEYLAIQCHWSQRPAVIGEVLQVYSGSEGR

Parental  TIIFCETKKEAQELSQNTSIKQDAQSLHGDIPQKQREITLKGFRNGNFGVLVATNVAARGLDIPEVDLVV
          .IIF.ETKK...E...N..IKQ.AQ.LHGDI.Q.QREITL.GFR.G.F.VLV.TNVAA.GLDI.EVDLV.
Retrocopy AIIFSETKKIVTEMAMNPHIKQNAQCLHGDIAQSQREITLTGFREGSFKVLVETNVAAHGLDISEVDLVI

Parental  QCSPPKXXXXXXXRSGTGRAGRTGVCICFYQHKEEYQLALVEQKAGIKFKRIGVPSATEIIKASSKDAIR
          ..S.P........R..TGRAGRTG.CICF.Q..E..QL..VEQKAGI..K..GVP.A....K..S.DAIR
Retrocopy PSSSPQNVESYIHR--TGRAGRTGICICF*QPRERGQLRYVEQKAGITVKHVGVPAAMDLVKFKSMDAIR

Parental  LLDSVPPTAIS-HFKQSAEKLIEEKGAVEALAAALAHISGATSVDQRSLINSN
          .L.SV..TA....F...A..LIEEKGA..ALAAA.AHISGA.S...RSLI.S.
Retrocopy SLASVSYTAVD>FFQPPAQRLIEEKGAADALAAAFAHISGASSFEPRSLITSD

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_4454 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4454 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013791	2 retrocopies	retro_cfam_1024, retro_cfam_1925,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912,
Macropus eugenii	ENSMEUG00000010586	1 retrocopy	retro_meug_1383,
Microcebus murinus	ENSMICG00000015112	1 retrocopy	retro_mmur_95,
Mus musculus	ENSMUSG00000020075	2 retrocopies	retro_mmus_582, retro_mmus_662,
Procavia capensis	ENSPCAG00000016697	1 retrocopy	retro_pcap_346,
Pongo abelii	ENSPPYG00000002389	1 retrocopy	retro_pabe_3816,
Tupaia belangeri	ENSTBEG00000002310	2 retrocopies	retro_tbel_1590, retro_tbel_4454 ,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,