RetrogeneDB ID: retro_tbel_3266

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_135281:321..879(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSTBEG00000003352
• Aliases: None
• Description: thioesterase superfamily member 4 [Source:HGNC Symbol;Acc:17947]

Sequence

>retro_tbel_3266
GACATTCTTGTAGACTTTGCTCTCCCTAACCCCAGCTGGAGTAAGGACATAAGATTCCTCTTTGACCAGTTTATGAAGAA
ATGTGAAGACAGCTCGTGGAAACAGCTACCTTCATATAAATGTGGATCTACTCAAAGAACTTAAGAGTTCAAAACCTGTT
TTCTTGACCCGAAACTGATGAAGGATGAACTGCCACAGGCCCAGCTCTTCAACAGAAGCATTGAGGATGGCCTAGGTTTT
GAATATGCGATGTTCTATAATAATGCTGAGGAAAGAGTAGTTTGTTTGTTTCAAGGAGGTCCTTACCTACAAGGAGCACC
TGGATTCATTCGTGGAAGTGCAATTGCAACCATGATTGATGCTACCGTTGGTATGACTGCACTTATCGCTGGCGGAATTG
TCATGACTGCCAATCTCAACATCAATTATAAAAGACCCATTCCCCTTTGTTCTGTTGTTGTGATAAATAGCCAACTTGAT
AAAGTTGAAGGAAGGAAATATTTTGTTTCCTGTAAGGTTCAAAGTGTTGATGAGAAGACTCTGCACTCAGAAGCAACA

Alignment

ORF - retro_tbel_3266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 96.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DILVDFALPNPSWSQDIRLLFDQFMKKCEDGSWKRLPSYKRGSTQRTQEFKTRFLDPKLMKDELPQAQLF
          DILVDFALPNPSWS.DIR.LFDQFMKKCED.SWK.LPSYK.GSTQRT.EFKT.FLDPKLMKDELPQAQLF
Retrocopy DILVDFALPNPSWSKDIRFLFDQFMKKCEDSSWKQLPSYKCGSTQRT*EFKTCFLDPKLMKDELPQAQLF

Parental  TRSIEDGLGFEYVMFYNNAEERVVCLFQGGPYLQGAPGFIHGGAIATMIDATVGMTALFAGGIVWTAHLN
          .RSIEDGLGFEY.MFYNNAEERVVCLFQGGPYLQGAPGFI.G.AIATMIDATVGMTAL.AGGIV.TA.LN
Retrocopy NRSIEDGLGFEYAMFYNNAEERVVCLFQGGPYLQGAPGFIRGSAIATMIDATVGMTALIAGGIVMTANLN

Parental  IHYKRPIPLVPVVVINSQLDKVEGRKYFVPCKVQSVDEKTLHSEAT
          I.YKRPIPL..VVVINSQLDKVEGRKYFV.CKVQSVDEKTLHSEAT
Retrocopy INYKRPIPLCSVVVINSQLDKVEGRKYFVSCKVQSVDEKTLHSEAT

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_3266 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3266 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266 ,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,