RetrogeneDB ID: retro_tbel_3216

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_134043:139368..140039(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM2
• Ensembl ID: ENSTBEG00000013758
• Aliases: None
• Description: MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973]

Sequence

>retro_tbel_3216
CTTAGTTAAGAAGGACAAGAGCTCTCAGACGGGGATGAAGAAGTGTATTGATTTATTGTATATAGGGCAGGGTAGAGTGA
TACAAATTCATTTGAAGAAGACATTGAAATTTCCTTAGCTGACTACTGGAAGTGTACTACATTCAATGAGATGAATCCTC
CCCTTCCGCCACATTGCGATAGATGTTGGGCCCTTTGTGAGAATTGACTTCCTGAAGATAAGGGAAGAATAAAGGGGAAA
TCCCTGTAAAAGACTAATTAGAAAACTCTACCCAAGCAAGAGAGGTATTTGATGTTTCTGACTGTAAAAAATTGCAGCTA
ATCATTCTGAAGAGTCACACATTGAAGAAAATGATGATAAAATCACACAAGCCTCCCTATCATGAGAAAGTGAGGGCTAT
TCTCAGCCATAAACTTCTAATAGTATTATTTTTAGCAGACAAGATGATGTCAATGAGTTTGGGAGGAAAGAAACACATGA
CAAAGAAGAAAGAATGGAATCTAATTTCTCCTTAATGCCATTGGACCTTGTGTGATTGGTCAGGGTTGATCTAAAAATGG
TGCATTGTCCATGGCAAAACAGGACATCTTATGGCATGCTTTAGCAAAGAAGCTAAAAAAAGGAATAAGCCCTGCTGAGT
GTGTAGATGACCAATTTAATTAATTGTGTTA

Alignment

ORF - retro_tbel_3216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 50.11 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSEEGQELSDEDDEVYRVTVYQAGESDTDSFEDDPEISLADYWKCTSCNEMNPPLPPHCNRCWALRENWL
          LS.EGQELSD.D.EVY...VY.AG.SDT.SFE.D.EISLADYWKCT..NEMNPPLPPHC.RCWAL.EN.L
Retrocopy LS*EGQELSDGDEEVY*FIVYRAG*SDTNSFEEDIEISLADYWKCTTFNEMNPPLPPHCDRCWALCEN*L

Parental  PEDK-GKDKGEIPEKNKLENPTRAEEGFDVPDCKKTPV-NDSKESRGEENDDKITQASLSQGSEDYSQPS
          PEDK.GK.KGEIP.K..LEN.T.A.E.FDV.DCKK....N.S.ES..EENDDKITQASLS..SE.YSQP.
Retrocopy PEDK<GKNKGEIPVKD*LENSTQAREVFDVSDCKKLQL<NHSEESHIEENDDKITQASLS*ESEGYSQP*

Parental  TSNSIICSSQDDVKEFGREETQDKEESMESSFP-LNAIEPCVICQGRPKNG-CIVHGKTGHLMACFTCAK
          TSNSII.S.QDDV.EFGR.ET.DKEE.MES.F..LNAI.PCVI.QG..KNG.CIVHGKTGHLMACF...K
Retrocopy TSNSIIFSRQDDVNEFGRKETHDKEERMESNFS<LNAIGPCVIGQG*SKNG<CIVHGKTGHLMACF--SK

Parental  KLKKRNKPCPVCRQPIQLIVL
          ..KKRNKPC.VCR.PI.LIVL
Retrocopy EAKKRNKPC*VCR*PI*LIVL

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_3216 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3216 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000005885	1 retrocopy	retro_lafr_715,
Otolemur garnettii	ENSOGAG00000034779	2 retrocopies	retro_ogar_1210, retro_ogar_49,
Ochotona princeps	ENSOPRG00000009677	1 retrocopy	retro_opri_891,
Ictidomys tridecemlineatus	ENSSTOG00000014702	1 retrocopy	retro_itri_1731,
Tupaia belangeri	ENSTBEG00000013758	2 retrocopies	retro_tbel_3216 , retro_tbel_915,
Tarsius syrichta	ENSTSYG00000002908	2 retrocopies	retro_tsyr_1343, retro_tsyr_984,