RetrogeneDB ID: retro_tsyr_984

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_26273:21075..21638(-)
• 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_984
GGAAAGCCATCAGTGAGACAGGATCTTGATGCTGGTATAAGTGAGCATTCAGGTGATTGACTGGATCAGGATTCAGTTTC
AGATCAATTTAGCGTAGAATTTGAAGTTGAATCTTTTGATTCAGAAGATTACAGCCCCAGTGATGAAGGACAAGAACTCT
CCGATAAAGATGATGAGGTGTATCGGGTTACTGTGTACCAGGTGGGTGAGAGTGATACCGACTCCTTTGAAGAAGATCTG
GAAATTTCCTTAGCTGACTACTGGACATGCATCACTTGCAACAAGGTGGACCCTCCCCTGCCGTTGCACTGCAACAGGTG
CTGGGCCCTGCATGAGAACTAACTCCCTGAGGTCAAAGGGGAGGATGGAGGGATGCCCCTGAGAAGGCCATGCCGGAGCA
CTCAGTGCAGGCTGAGGAGGGCTTCGATGGTCCCAATTGTAGAAAGACTTCAGCGAGCGATTCCAAGGAGCCAAGTCCTG
AGAAAAGTGATGAGAAGGTTGCACCAGCCTCCCAGTCGCAGGACAGCGAGGACTACTACCAGTCATCCATTTCAAGTAGC
ATC

Alignment

ORF - retro_tsyr_984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.85 %
• Parental protein coverage: 50.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAPS-KLALDAGISEHSGDWLDQDSVSVYFSVELEVESLSSEGYSLSEE-QQLSDEDDEVY-ATVFE-GE
          G.PS....LDAGISEHSGD.LDQDSVS..FSVE.EVES..SE.YS.S.E.Q.LSD.DDEVY..TV...GE
Retrocopy GKPSVRQDLDAGISEHSGD*LDQDSVSDQFSVEFEVESFDSEDYSPSDEGQELSDKDDEVYRVTVYQVGE

Parental  SDTDS-EEDPEISLADCWKRTSCNETNRPLPPHCNR-WALPENWLPEDKAKDTG-EIPKKVKLE---TAE
          SDTDS.EED.EISLAD.W....CN....PLP.HCNR.WAL.EN.LPE.K..D.G...P.K...E....AE
Retrocopy SDTDSFEEDLEISLADYWTCITCNKVDPPLPLHCNRCWALHEN*LPEVKGEDGG<DAPEKAMPEHSVQAE

Parental  EGFDVPDCKKTTVNDSRESCVEENDDKFT-HSQSQESEDSSQSSAPSSI
          EGFD.P.C.KT...DS.E...E..D.K....SQSQ.SED..QSS..SSI
Retrocopy EGFDGPNCRKTSASDSKEPSPEKSDEKVAPASQSQDSEDYYQSSISSSI

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_984 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.

---

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 ,