RetrogeneDB ID: retro_tbel_4260

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_73511:5503..6407(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX5
• Ensembl ID: ENSTBEG00000009490
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]

Sequence

>retro_tbel_4260
GAGCTGCCCAAATTTGAGAAGAATTTTAACAAGAACACCTGATTTGGCCAGACCCATAGCTCAAGAGGCTGAAACATACA
GAAGAAGCAAGGAAGTATAGTTAGAGGTCACAACTGCCCTAAACCAGTTTTGAAATTTTATAAAGCAAACTTCCCTGCAA
ATGTCATGGATATGATTGCAAGACAGAACTTTACTGAACCCACTGCTGTTCAAGCTCAGGGATGGCCAGTTGCCCCAAGT
GGATTGGATATGGTTGGAGTAGCACAGACTAGATCTGGGAGAACATTGTCTTATTTACTGCCTGCGATTGTCCACATCAA
TCATCAGTCATTCCTAGAGAGAGGTGATGGGCCTATTTGCTTAGTGCTGGCACCAGCCTGGAAACTAGCCCAGTAGGTGC
AGCAAGTAGCTGCTGAATACTGTAGAGCATGCTGCTTGAAGTCTCCCTGCATCTATGGTGGTGCTCTGAAAAGATCACAG
TTAAGTGGTTTGGAGAGAGTTATGGAAATCTGTATTCCAGCACCTGGAAGACTGATTGACTTTTTAGAATGTGGGAAAAC
CAATCTGAAGAACTACTTATCTTGTACTCAGTGAAGCAGACAGAATGCTCGATATGAGCTTTGAACCACAATTAAGGAAG
ATTGTGAATCAGAAAAGACCTGATAGGCAAACCCTAATGTGGAGTGCAACTTGGCCGAAAGAAATAAGATAGCTTGCTGA
AGATTTCTTGAAACACTATATTCATATAAATATTGGTGGACTAGCACTGAGTGCAAACCACAACATTCTTCAGATTGTAG
ATGTGTGTTATGACGTAGAGAGGGATGAAAAACTTACTAGTCTAATGGAAGAGATCATGAATGAGAAGGAGAATAAAACA
ATTGTTTTTTGAAACCAAAAGAAG

Alignment

ORF - retro_tbel_4260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.76 %
• Parental protein coverage: 63.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ELPKFEKNFY-QEH-PDLARRTAQEVETYRRSKEV-TVRGHNCPKPVLNFYEANFPANVMDVIARQNFTE
          ELPKFEKNF..QEH.PDLAR..AQE.ETYRRSKEV..VRGHNCPKPVL.FY.ANFPANVMD.IARQNFTE
Retrocopy ELPKFEKNFN<QEH<PDLARPIAQEAETYRRSKEV<IVRGHNCPKPVLKFYKANFPANVMDMIARQNFTE

Parental  PTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQV
          PTA.QAQGWPVA.SGLDMVGVAQT.SG.TLSYLLPAIVHINHQ.FLERGDGPICLVLAP...LAQ.VQQV
Retrocopy PTAVQAQGWPVAPSGLDMVGVAQTRSGRTLSYLLPAIVHINHQSFLERGDGPICLVLAPAWKLAQ*VQQV

Parental  AAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLEC-GKTNLRRTTYLVLDEADRMLD
          AAEYCRAC.LKS.CIYGGA.K..Q...LER..EICI..PGRLIDFLEC.GK....RTTYLVL.EADRMLD
Retrocopy AAEYCRACCLKSPCIYGGALKRSQLSGLERVMEICIPAPGRLIDFLEC>GKP-I*RTTYLVLSEADRMLD

Parental  MGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEK
          M.FEPQ.RKIV.Q.RPDRQTLMWSATWPKE.R.LAEDFLK.YIHINIG.L.LSANHNILQIVDVC.DVE.
Retrocopy MSFEPQLRKIVNQKRPDRQTLMWSATWPKEIR*LAEDFLKHYIHINIGGLALSANHNILQIVDVCYDVER

Parental  DEKLIRLMEEIMSEKENKTIVFVETKR
          DEKL..LMEEIM.EKENKTIVF...K.
Retrocopy DEKLTSLMEEIMNEKENKTIVF*NQKK

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_4260 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4260 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000002310	2 retrocopies	retro_tbel_1590, retro_tbel_4454,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260 ,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,