RetrogeneDB ID: retro_tsyr_1343

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_40584:13427..13990(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM2
• Ensembl ID: ENSTSYG00000002908
• Aliases: None
• Description: MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973]

Sequence

>retro_tsyr_1343
CCGTCCAGCCCTGATCTTGATGCCAGTGTAAGTGAACATTCAGGTGATTGGTTGGACCAGGATTCAGTTTCAGATCCATT
TAGAGTAGAATCTGAAGTTGAGTCTCTTGATTCAGAAGATTACAGCCTCAGTGAAGAAGGACAGGAACTCTCCACTGAAG
ATGATGAGATGTATCGGGTTACTGTGTCCCAGGCAGGGGAGGACAAAATGGACTCATTTGAAGAAGATCTGAAAATTTCC
TTAGCTGACTACTGGAAGTGCCTCGCGTGCAGGGAAGTGAACCCTCCCGCGCCACCGCATTGCAACAGATACTGGGCCCT
GCATGATATAGCTGGCTTCCCAAGGACAAAGGGAAGGACAGAGGGGACTCCCCTGAGAAGGCCACCCTGGAGCACCCTGC
ACAGACTGAGAAGGGCTTCGACGATCCGGACTGTAAAATGACTGCAGTGAGCAATTTCAAGGAGTCAAGTCCCGAGGAAA
ACTACAAGAAAGCCACACCAGCCTCCCAGTCACAGGAGAGTGAGAACTACTCCCAGCCATCCACTTAATCTAGTAACATC
GTT

Alignment

ORF - retro_tsyr_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.73 %
• Parental protein coverage: 50.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSKLALDAGISEHSGDWLDQDSVSVYFSVELEVESLSSEGYSLSEE-QQLSDEDDEVY-ATVFE-GESDT
          PS...LDA..SEHSGDWLDQDSVS..F.VE.EVESL.SE.YSLSEE.Q.LS.EDDE.Y..TV...GE...
Retrocopy PSSPDLDASVSEHSGDWLDQDSVSDPFRVESEVESLDSEDYSLSEEGQELSTEDDEMYRVTVSQAGEDKM

Parental  DS-EEDPEISLADCWKRTSCNETNRPLPPHCNR-WALPE-NWLPEDKAK-DTGEIPKKVKLE---TAEEG
          DS.EED..ISLAD.WK...C.E.N.P.PPHCNR.WAL......P..K...D.G..P.K..LE.....E.G
Retrocopy DSFEEDLKISLADYWKCLACREVNPPAPPHCNRYWALHDIAGFPRTKGR<DRGDSPEKATLEHPAQTEKG

Parental  FDVPDCKKTTVNDSRESCVEENDDKFT-HSQSQESEDSSQSSAPSSIIV
          FD.PDCK.T.V....ES..EEN..K.T..SQSQESE..SQ.S..SS.IV
Retrocopy FDDPDCKMTAVSNFKESSPEENYKKATPASQSQESENYSQPST*SSNIV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1343 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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,