RetrogeneDB ID: retro_tbel_915

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3306:101903..102634(-)
• 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_915
GAATCTCTTGATTCAGAAGATTATAGCCTTAATGAAGAAGGACAAGAACTCTCAGATGAAGATGATGAGGCATATCGAGT
TACTGTGTATCAGGCAGGGGAGAGTGATACTGATTCATTTGAAGATGATCCTGAAATTTCTTTAGCTGGCTATTGGAAAT
GTACTTCATGCAATGAGATGAACCCTCCCCTTCCACCACACTGCAACAGATGTTGGGCTCTTCGTGAGAATTGGCTTCCT
GAACGTAAAGGGAAGGATAAAGGGGAAATCCTTGAAAAAGTCAAGCTAGAAAACCCAACATAAGCAGAAGAGGGATTTGA
TGTTCCTGACTGTAAAAAAAAAACTCCAGTGAGTGATTTCAAAGAGTCACGTGTTAAAGAAAATGATGATAAAATCACGC
AAGCCTCCCTGTCACAAGGAAGTGAGGACTATTCTCAGCCATAAACTTCTAATAGCATTATTTGTAGCAGCCAAAATGAT
GCCAAAGAGTTTGGGAGGGAAGAAACACAAGACAAAGAAGAAAGTATGGAATCTAGTTTCTCCTTAATGCCATTGAACCT
GTGTGACCTTGTGTGATTTGCCAGGGTGGACCTAAAAATGGTTGCGTTGTCCATGGCAAAACAGGACATCTTATGGCATG
CTTTACATGTGCGGAGAAATTAAAGAAAAGGAATAAGCCCTGCCCAGTGTGTAGACAACCAATTCAATTAATCATGCTAA
CTTACTTCCCC

Alignment

ORF - retro_tbel_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.12 %
• Parental protein coverage: 52.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESTGTPSEPLSEEGQELSDEDDEVYRVTVYQAGESDTDSFEDDPEISLADYWKCTSCNEMNPPLPPHCNR
          ES.......L.EEGQELSDEDDE.YRVTVYQAGESDTDSFEDDPEISLA.YWKCTSCNEMNPPLPPHCNR
Retrocopy ESLDSEDYSLNEEGQELSDEDDEAYRVTVYQAGESDTDSFEDDPEISLAGYWKCTSCNEMNPPLPPHCNR

Parental  CWALRENWLPEDKGKDKGEIPEKNKLENPTRAEEGFDVPDC-KKTPVNDSKESRGEENDDKITQASLSQG
          CWALRENWLPE.KGKDKGEI.EK.KLENPT.AEEGFDVPDC....PV.D.KESR..ENDDKITQASLSQG
Retrocopy CWALRENWLPERKGKDKGEILEKVKLENPT*AEEGFDVPDCXXXXPVSDFKESRVKENDDKITQASLSQG

Parental  SEDYSQPSTSNSIICSSQDDVKEFGREETQDKEESMESSFP-LNAIEP---CVICQGRPKNGCIVHGKTG
          SEDYSQP.TSNSIICSSQ.D.KEFGREETQDKEESMESSF..LNAIEP...CVICQG.PKNGC.VHGKTG
Retrocopy SEDYSQP*TSNSIICSSQNDAKEFGREETQDKEESMESSFS<LNAIEPV*PCVICQGGPKNGCVVHGKTG

Parental  HLMACFTCAKKLKKRNKPCPVCRQPIQLIVLTYFP
          HLMACFTCA.KLKKRNKPCPVCRQPIQLI.LTYFP
Retrocopy HLMACFTCAEKLKKRNKPCPVCRQPIQLIMLTYFP

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_915 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_915 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,