RetrogeneDB ID: retro_tbel_94

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1099:478974..479764(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf29
• Ensembl ID: ENSTBEG00000005256
• Aliases: None
• Description: chromosome 12 open reading frame 29 [Source:HGNC Symbol;Acc:25322]

Sequence

>retro_tbel_94
GGGACATATTGTTACATGACTACCTACAAAGGGCACCCATACCTTTGGGTTCAACTAGATAGAAAACACAACAAACAAGC
TAATAATTTCAAATCTTCTCCATTCGAAAGAAAACCCAAAAGAATCTTTTTTGGAATGTTGAAGAGGACTTCAAACCTGT
TCCAGAGGACTGGGTACCAGTGAAGGAAATAGAACAACTAAATGGGAATCTAGTGCCTGATAAAATGGACACATTCCTGG
CTGTGTACCAGTAAAGAAAAACGACAAACAGTATCGCTGGCACTCTTCTGTAGTTCATTATGCAATTGAAATTGTCTTGG
AACTAAAGCATCATCCTGATGATTCTGGACTTTGGAAATTAGTGCAATGGCACTATCAGATCTCTCAGAACAAACACTGG
GGCTTTTAGGAAAAAGTATCAATGGAAACACGTATGGGTTAGGAAGCAAGAAGCATCCCTTACATCTTCTTATACCACAT
GGGGCATTTCAAATAAATCTACTTGCATTGAAGCACAATGACCTATTGTCCTGGTTTGAAGGTTGCAGAGAGGCTAAAAT
CAAAGGAATAGTATGACATTGAAGTGAAGGCTGTTTAATTAAGGACCATCACGATCGTGTTGGCTTATGCTGGCCAGTTT
CAGATACTTACATGAATTCAAAACCAGTTATTTTCTACATGAACCTGGACAAATATGATTATACTTTTGATACTCGGTGT
ATGTTTTATCATTTTTCAAAAATAGATCATTAGAAATCTGGTAGGGCTCAAAGATATAATACTGAATGTA

Alignment

ORF - retro_tbel_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.38 %
• Parental protein coverage: 82.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GTVCQEGA-SGQPYLWARLDRPNKQADKRFKN-FLHSKENSKEFFWNVEEDFKPVPEYWMPAKEIEQLNG
          GT.C......G.PYLW..LDR........FK..F...K...K..FWNVEEDFKPVPE.W.P.KEIEQLNG
Retrocopy GTYCYMTTYKGHPYLWVQLDRKHNKQANNFKS<FSIRKKTQKNLFWNVEEDFKPVPEDWVPVKEIEQLNG

Parental  NPVPDE-NGHIPGWVPVEKNNKQYCWHSSVVNYEFEIALVLKHHPDDSGL-LEISAVPLSDLLEQTLELV
          N.VPD..NGHIPG.VPV.KN.KQY.WHSSVV.Y..EI.L.LKHHPDDSGL.LEISA..LSDL.EQTL.L.
Retrocopy NLVPDK<NGHIPGCVPVKKNDKQYRWHSSVVHYAIEIVLELKHHPDDSGL<LEISAMALSDLSEQTLGLL

Parental  GTNINGNPYGLGSKKHPLHLLIPHGAFQIRNLPPLKHNDLLSWFEGCREGKIEGIVWHCSDGCLIKVHRH
          G..INGN.YGLGSKKHPLHLLIPHGAFQI.NL..LKHNDLLSWFEGCRE.KI.GIV.H.S.GCLIK.H..
Retrocopy GKSINGNTYGLGSKKHPLHLLIPHGAFQI-NLLALKHNDLLSWFEGCREAKIKGIV*H*SEGCLIKDHHD

Parental  HLGLCWPISDTYMNSKPVIINMNLNKYDYTFDTKCLFYHFSKIDNQKFGR-LKDIMLDV
          ..GLCWP.SDTYMNSKPVI..MNL.KYDYTFDT.C.FYHFSKID..K.GR.LKDI.L.V
Retrocopy RVGLCWPVSDTYMNSKPVIFYMNLDKYDYTFDTRCMFYHFSKIDH*KSGR>LKDIILNV

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_94 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_94 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011011	1 retrocopy	retro_chof_1262,
Homo sapiens	ENSG00000133641	1 retrocopy	retro_hsap_3984,
Gorilla gorilla	ENSGGOG00000005986	1 retrocopy	retro_ggor_2674,
Loxodonta africana	ENSLAFG00000013286	1 retrocopy	retro_lafr_706,
Macaca mulatta	ENSMMUG00000015860	1 retrocopy	retro_mmul_715,
Nomascus leucogenys	ENSNLEG00000005396	1 retrocopy	retro_nleu_1905,
Pan troglodytes	ENSPTRG00000005277	1 retrocopy	retro_ptro_2704,
Rattus norvegicus	ENSRNOG00000006973	1 retrocopy	retro_rnor_1625,
Tupaia belangeri	ENSTBEG00000005256	1 retrocopy	retro_tbel_94 ,
Tarsius syrichta	ENSTSYG00000014665	1 retrocopy	retro_tsyr_1572,