RetrogeneDB ID: retro_tsyr_2006

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_7836:294..777(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000000497
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRP15
• Ensembl ID: ENSTSYG00000012715
• Aliases: None
• Description: ribosomal RNA processing 15 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24255]

Sequence

>retro_tsyr_2006
GCTGTCCAGGATTCACATGTGAGTGTGGGGAAAAAGCTAAAAAAGCCCCCAAAGAAGAAGATGAAAATGGTAGCAAGAAC
CGTATCATCGGAGCTGGAAGACGAGGCCAAAGATGCTTCAGACGGCGAAGGTTCTATAGGAAGCTGTGGATTGGAAAAGG
ATTACTTTTCTTCCGATGATGAAGCAATAGAGGTTGACAATGAAGATGATGTTCAGCCCTGTGACAAAGAAAATAAAAAT
GCCGTAGAATCAAGTGTTGGGACTAATACAGGCTGGGCAGATGCCATGGCTAAAATTCTTAACAAAAAAACGCCTGAAAG
TAAATCCACCATTCTGGTAAAAAATAAAGAGCTGGAGAAGGAAAAAGAAAAGTTAAAACAAGAAAGAATAGAGAAAAGAA
AACAGCGTGATAAGAGGCTGGAGTGGGAAATGATGCACAGAGTAAAGCCAGATGTTGTCCAAGACAAAGAGACAGAAAGA
AAT

Alignment

ORF - retro_tsyr_2006 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.37 %
• Parental protein coverage: 56.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVQDSRVSAGKKLKKPPKKKMKMVAGAVSSELEDEAKDASDGE---GSCGLEKDYFSSDDEAIEADNEDD
          AVQDS.VS.GKKLKKPPKKKMKMVA..VSSELEDEAKDASDGE...GSCGLEKDYFSSDDEAIE.DNEDD
Retrocopy AVQDSHVSVGKKLKKPPKKKMKMVARTVSSELEDEAKDASDGEGSIGSCGLEKDYFSSDDEAIEVDNEDD

Parental  AEPYDIENKNAAESSVGTNTGWADAMAKILNKKTPESKSTILVKNKELEKEKEKLKQERIEKRKQRDKRL
          ..P.D.ENKNA.ESSVGTNTGWADAMAKILNKKTPESKSTILVKNKE.................QRDKRL
Retrocopy VQPCDKENKNAVESSVGTNTGWADAMAKILNKKTPESKSTILVKNKEXXXXXXXXXXXXXXXXXQRDKRL

Parental  EWEMMHRVKPDVVQDKETERN
          EWEMMHRVKPDVVQDKETERN
Retrocopy EWEMMHRVKPDVVQDKETERN

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_2006 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789, retro_cjac_455,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820, retro_ocun_962, retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006 ,