RetrogeneDB ID: retro_tsyr_1670

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_538918:1..561(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD12
• Ensembl ID: ENSTSYG00000013154
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [Source:HGNC Symbol;Acc:9557]

Sequence

>retro_tsyr_1670
AAAAAATGGGATTTCCTGAATGAAAATATTATGCTTTGTCCAAAAGGAGGAGTCGGTTAAAACAAGCTGTTGCAAAAATG
GTTCAACGGTGCTGTACCTATGCTGAAATAACAGACCTTCCAATTAAACTTTGATTAATTGATACTCTACGAATGGTTAC
AAAAGGAAAGATTGATGTTGAAATTGAGTGTGCTCAACTAACTAAAACCTTAGCAACTATAAGAGAGCAAAATGGCGATG
TGAAAGAGGCAGCTTCCATCTTACAAGAGTTATAGGTGGAAACTTATGGGTCAATGGAGAAGAAGGAGCCAGTGGAGTTC
TTTCTGGAGCAAATGAGGCTCTGCCTCACGGTGAAGGATTACATCTGGACACAAACCATCAACAAGAAGATTAACACCAA
ATTTTTCCAGGAAGAAAATACAGAGAAATTAAAGTTGAAATACTATAATTTGATGATCCAGCTGGATCAGCACGAGGGAT
CCTATTTGTCTATTTGTAAGCACTACAGAGCGATATATGACACTCCCTGTATACAGGCAGAAAGAGAAAAGTGGCAGCAG

Alignment

ORF - retro_tsyr_1670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 57.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEWDLLNENITL-LSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEIERARLT
          K.WD.LNENI.L.LSKRRS.LKQAVAKMVQ.CCTY.E.ITDLPIKL.LIDTLRMVT.GKI.VEIE.A.LT
Retrocopy KKWDFLNENIML<LSKRRSRLKQAVAKMVQRCCTYAE-ITDLPIKL*LIDTLRMVTKGKIDVEIECAQLT

Parental  KTLATIKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKINTKFFQE
          KTLATI.EQNGDVKEAASILQEL.VETYGSMEKKE.VEF.LEQMRLCL.VKDYI.TQ.I.KKINTKFFQE
Retrocopy KTLATIREQNGDVKEAASILQEL*VETYGSMEKKEPVEFFLEQMRLCLTVKDYIWTQTINKKINTKFFQE

Parental  ENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAEREKWQQ
          ENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAEREKWQQ
Retrocopy ENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAEREKWQQ

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_1670 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008691	2 retrocopies	retro_cjac_1400, retro_cjac_2793,
Homo sapiens	ENSG00000197170	1 retrocopy	retro_hsap_2801,
Gorilla gorilla	ENSGGOG00000014761	1 retrocopy	retro_ggor_1947,
Loxodonta africana	ENSLAFG00000010876	1 retrocopy	retro_lafr_467,
Nomascus leucogenys	ENSNLEG00000001265	1 retrocopy	retro_nleu_1541,
Pongo abelii	ENSPPYG00000008565	1 retrocopy	retro_pabe_2223,
Pan troglodytes	ENSPTRG00000022722	1 retrocopy	retro_ptro_1898,
Tupaia belangeri	ENSTBEG00000014760	1 retrocopy	retro_tbel_443,
Tarsius syrichta	ENSTSYG00000013154	1 retrocopy	retro_tsyr_1670 ,