RetrogeneDB ID: retro_tsyr_1870

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_631565:117..742(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF115
• Ensembl ID: ENSTSYG00000004867
• Aliases: None
• Description: ring finger protein 115 [Source:HGNC Symbol;Acc:18154]

Sequence

>retro_tsyr_1870
TTAGGTGATGGCAGCAGCCGGGTAGGCAATAGCACGCCAACACATTTTGCAGAGCTCTGGGACCATTTTGGATCACACGT
TTTTTCAAGATTTTAGGCCATTTTTAAGTAGTAGTCCACTGGACCAAGATAACAGAGCCAATGAGAGGAGTCACCAAACT
CACACTGACTTCTGGGGACCAAGTCGGCCTCCACGGCTGCCAATGACTCGGAGATACAGATCTCAAGGAAGTTCTCGACC
TGACAGGTCTCCAGCTATTGAAGGAATAATACAACAGATCTTTGCAGGATTCTCTGCAAATTCTGCAATTCCTGGATCCC
CACACCCCTTTTCGTGGAGCGGGTTGCTGCACTCTAACCCTGGGGACTATGCCTGGGGTCAGACAGGACTTGATGCCATT
GTAACCCAGCCTTTAGGACAACTGGAAAACACAGGGCCTCCCCCAGCTGACAAAGAAAAGATCATATCTCTTCCAGCAGT
GACAGTAACTTAGGAACAAGTTGATATGGGTTTAGAGTGTCCAGTATGCAAAAGAAGATTACACAGTTAAAAGAGGAAGT
CTTGCAGTTACCTTGCAATCACTTTCTTTCACAGCAGTTGTATTGTGCCATGGTTAGAGCTGCAT

Alignment

ORF - retro_tsyr_1870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.42 %
• Parental protein coverage: 68.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LGGGSSRIDNSTSTHFAELWDH-LDHTFFQDFRPFLSSSPLDQDHRANERSHQTHTDFWGPSRPPRLPMT
          LG.GSSR..NST.THFAELWDH.LDHTFFQDFRPFLSSSPLDQD.RANERSHQTHTDFWGPSRPPRLPMT
Retrocopy LGDGSSRVGNSTPTHFAELWDH>LDHTFFQDFRPFLSSSPLDQDNRANERSHQTHTDFWGPSRPPRLPMT

Parental  RRYRSQGSSRPDRSPAIEGIIQQIFAGFFANSAIPGSPHPFSWSGMLHSNPGDYAWGQTGLDAIVTQLLG
          RRYRSQGSSRPDRSPAIEGIIQQIFAGF.ANSAIPGSPHPFSWSG.LHSNPGDYAWGQTGLDAIVTQ.LG
Retrocopy RRYRSQGSSRPDRSPAIEGIIQQIFAGFSANSAIPGSPHPFSWSGLLHSNPGDYAWGQTGLDAIVTQPLG

Parental  QLENTGPPPADKEKILSLPTVTVTQEQVDMGLECPVC-KEDYTV-KEEVRQLPCNH-FFHSSCIVPWLEL
          QLENTGPPPADKEKI.SLP.VTVT.EQVDMGLECPVC.KEDYTV.KEEV.QLPCNH.FFHSSCIVPWLEL
Retrocopy QLENTGPPPADKEKIISLPAVTVT*EQVDMGLECPVC>KEDYTV>KEEVLQLPCNH>FFHSSCIVPWLEL

Parental  H
          H
Retrocopy H

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_1870 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 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009030	1 retrocopy	retro_ecab_459,
Macropus eugenii	ENSMEUG00000002500	1 retrocopy	retro_meug_1546,
Oryctolagus cuniculus	ENSOCUG00000003055	1 retrocopy	retro_ocun_1138,
Pteropus vampyrus	ENSPVAG00000014487	13 retrocopies	retro_pvam_1039, retro_pvam_1096, retro_pvam_1111, retro_pvam_1293, retro_pvam_1295, retro_pvam_1442, retro_pvam_730, retro_pvam_733, retro_pvam_759, retro_pvam_796, retro_pvam_806, retro_pvam_849, retro_pvam_964,
Tarsius syrichta	ENSTSYG00000004867	2 retrocopies	retro_tsyr_1734, retro_tsyr_1870 ,