RetrogeneDB ID: retro_tsyr_1519

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_476296:413..1076(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000002742
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PEX3
• Ensembl ID: ENSTSYG00000000277
• Aliases: None
• Description: peroxisomal biogenesis factor 3 [Source:HGNC Symbol;Acc:8858]

Sequence

>retro_tsyr_1519
ACAATTCTTGCTCCCCCAAATGTTCAACAGCAATATTTATCAAGTATTCAGCATCTCCTTGGAGATGGCCTGACAGAATT
AATCACTGTCATTAAACAAGCTGTGCAGAAAATTTTAGGAAGTGTTTCTCTTAAACATTCTTTGTCCCTTCTGGACTTGG
AGCAAAAACTAAAAGAAATCAGAAATCTCGTTGAGCAGCATAAATCTTCTTCCTGGATTAATAAAGATGGATCCAAATCT
TTATTATGCCATTATATGATGCCAGATGAAGAGACCCCATTAGCAGTTCAGGCCTGTGGGCTTTCTCCACAAGATATTAC
CACTATTAAACTTCTCAATGAAACTAAAGACATGTTAGAAAGCCCAGATGTTAGTACAATTTTGAATACCTGTTTAAACC
GAGGTTTTAGCAGACTTCTAGACAATATGGCTGAGTTCTTTCGATCTACTGAACAGGACCTGCAACATAGTAATTCTATG
GATAGTCTTTCCAGTGTCAGCCTGCCTTTAGCTAAGATAATCCCGATAGTAAATGGACAGATCCATTCAGTCTGCTGCAA
AACACCCAGTCATTTTGTTCAGGATCTGTTGACGATAGAGCAAGTGAAGGACTTTGCTGCTAATGTATACGAGGTTTTCA
GTACCCCTCAGAAACCGGAGAAA

Alignment

ORF - retro_tsyr_1519 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 59.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TILAPPDVQQQYLSSIQHLLGDGLTELITVIKQAVQKILGSVSLKHSLSLLDLEQSLKEIRNLVEQHKSS
          TILAPP.VQQQYLSSIQHLLGDGLTELITVIKQAVQKILGSVSLKHSLSLLDLEQ.LKEIRNLVEQHKSS
Retrocopy TILAPPNVQQQYLSSIQHLLGDGLTELITVIKQAVQKILGSVSLKHSLSLLDLEQKLKEIRNLVEQHKSS

Parental  SWINKDGSKSLLCHYMMPDEETPLAVQACGLSPRDITTIKLLNETRDMLESPDFSTVLNTCLNRGFSRLL
          SWINKDGSKSLLCHYMMPDEETPLAVQACGLSP.DITTIKLLNET.DMLESPD.ST.LNTCLNRGFSRLL
Retrocopy SWINKDGSKSLLCHYMMPDEETPLAVQACGLSPQDITTIKLLNETKDMLESPDVSTILNTCLNRGFSRLL

Parental  DNMAEFFRPTEQDLQHSNSMDSLSSVSLPLAKIIPIVNGQIHSVCSETPSHFVQDLLTMEQVKDFAANVY
          DNMAEFFR.TEQDLQHSNSMDSLSSVSLPLAKIIPIVNGQIHSVC..TPSHFVQDLLT.EQVKDFAANVY
Retrocopy DNMAEFFRSTEQDLQHSNSMDSLSSVSLPLAKIIPIVNGQIHSVCCKTPSHFVQDLLTIEQVKDFAANVY

Parental  EAFSTPQQLEK
          E.FSTPQ..EK
Retrocopy EVFSTPQKPEK

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_1519 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Tarsius syrichta	ENSTSYG00000000277	2 retrocopies	retro_tsyr_1519 , retro_tsyr_850,