RetrogeneDB ID: retro_tbel_2279

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_10841:81739..82319(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000013600
• Aliases: None
• Description: None

Sequence

>retro_tbel_2279
AGAGTAGTAAGACTCTGTGAACAGCTAGAGAGCTGTTATACCAAACTCACATGTTTGTTACAAAAGAGGACTTGTTCTGA
AAAAAACTGATTCCACAGTGCATCTCAAGAGATTTCATAGATCTGATCATTATTAATGAAGATTGTAAAACACCAAATGG
ACTTATTTTGAGTTGATTGCTAAATAGTCCAACTGCTCATTTTAAAATGAGAATGTTCAACTTTATAAAGAAATTAGATG
TAAGGACCCCACGGAACACATCCTCGAAATAATTATGAATAATTTTACAACACGGCTAGGTCATTCAATTGGAGGAATGT
TTGCATCTCTCTTCCACCATGATCCTCAGTTTATTGGCAGGCAGGTTGCCACATTCCACAATCAGCGGGATTATATTTTC
TTCAGATTTCATAGATACATATTCAAGAGGGAAAAGAAAGTAGGAATTCAGGAACTTGGCCCACGGTTTACCTTAAAATT
AAGATCTCTTCAGAAAGGAACCTTTGATTCTAAATACGGGGAGTATGAATGGGTCCATAAGCCCCAGAAAATGGCCACAA
GTAGAAGAAAATTCCATTTA

Alignment

ORF - retro_tbel_2279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.84 %
• Parental protein coverage: 55.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RTVRLCEQLST-VIPNSHVYYRRGLALKK-IIPQCISRDFTDLIVINEDRKTPNGLILSHLPNGPTAHFK
          R.VRLCEQL...VIPNSHV.Y.RGL.LKK..IPQCISRDF.DLI.INED.KTPNGLILS.L.N.PTAHFK
Retrocopy RVVRLCEQLES>VIPNSHVCYKRGLVLKK>LIPQCISRDFIDLIIINEDCKTPNGLILS*LLNSPTAHFK

Parental  M-SSVRLRKEIKRRGKDPTEHKPEIILNNFTTRLGHSIGRMFASLFPHDPQFIGRQVATFHNQRDYIFFR
          M...V.L.KEI..R.KDPTEH..EII.NNFTTRLGHSIG.MFASLF.HDPQFIGRQVATFHNQRDYIFFR
Retrocopy M<ENVQLYKEI--RCKDPTEHILEIIMNNFTTRLGHSIGGMFASLFHHDPQFIGRQVATFHNQRDYIFFR

Parental  FHRYIFKSEKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPREMDTSRRKFHL
          FHRYIFK.EKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKP..M.TSRRKFHL
Retrocopy FHRYIFKREKKVGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPQKMATSRRKFHL

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_2279 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2279 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001097	1 retrocopy	retro_eeur_17,
Myotis lucifugus	ENSMLUG00000016028	2 retrocopies	retro_mluc_681, retro_mluc_942,
Mus musculus	ENSMUSG00000028187	1 retrocopy	retro_mmus_3026,
Oryctolagus cuniculus	ENSOCUG00000014803	1 retrocopy	retro_ocun_1133,
Pteropus vampyrus	ENSPVAG00000003729	1 retrocopy	retro_pvam_1489,
Rattus norvegicus	ENSRNOG00000015969	1 retrocopy	retro_rnor_1372,
Tupaia belangeri	ENSTBEG00000013600	4 retrocopies	retro_tbel_1027, retro_tbel_2204, retro_tbel_2279 , retro_tbel_63,