RetrogeneDB ID: retro_tsyr_1426

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_435749:592..1251(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HORMAD1
• Ensembl ID: ENSTSYG00000006025
• Aliases: None
• Description: HORMA domain containing 1 [Source:HGNC Symbol;Acc:25245]

Sequence

>retro_tsyr_1426
ATGGCCATTGCACAGTTGCAGAAGACTTCCATGAGTGCATTGATATTTCCCAGTAAGATATCAACTGAGCAGCAGTCTTT
GTTGCTAGTGAAGAGGCTCCTGGCAGTTTCAGTATCCTGCATCACATATTTGAGAGGACTACTTCCAGAATGTGCTTATG
GAACAAGATATCTAGATGATCTTTGTGTCAAAATTCTGAAAGAAGATAAAAATTGTCCAGGATCTATACAGTTAGTGAAG
TGGATGCAAGAGTGCTATGATGCTTTACAGAGAAAATATCTAAGGATGGTTGTTCTAGCTGTGTACACAAATCCAGAAGA
CCCTCAGACAATTTCAGAATGTTACCAGTTCAAATTCAAATACACCAATAATGGACCAATCTTGGACTTTATAAGTAAAA
ACCAAAGCAATGAGTCTAGCATGTCATCTGCTGACACCAAGAAAGCAAGTATACTCCTCATTCGCAAGATTTCTATTCTA
ATGCAAAACCTAGAGACCTTTACCTAATGATGTTTGTCTGACCATGGAACTTTTTTACTACAATGAAGTTACACCCCCAT
ATGACCAGCCTCCTGGTTTCAAAGAAATGATTGTGAAAGAGTAATATTTGAAAAGGAGCCTATGTATTTAAATGTGAGAA
AGTCCCAACACCTTTTCAC

Alignment

ORF - retro_tsyr_1426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.58 %
• Parental protein coverage: 59.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATAQLQKTSMSALIFPSKISTEQQSLLLVKRLLAVSVSCITYLRGLFPECAYGTRYLDDLCVKILKEDK
          MA.AQLQKTSMSALIFPSKISTEQQSLLLVKRLLAVSVSCITYLRGL.PECAYGTRYLDDLCVKILKEDK
Retrocopy MAIAQLQKTSMSALIFPSKISTEQQSLLLVKRLLAVSVSCITYLRGLLPECAYGTRYLDDLCVKILKEDK

Parental  NCPGSIQLVKWMRGCYDALQRKYLKLMVLMVYTNPEDPQTISECYQFKFKYTNNGPILDFISKNQSNESS
          NCPGSIQLVKWM..CYDALQRKYL...VL.VYTNPEDPQTISECYQFKFKYTNNGPILDFISKNQSNESS
Retrocopy NCPGSIQLVKWMQECYDALQRKYLRMVVLAVYTNPEDPQTISECYQFKFKYTNNGPILDFISKNQSNESS

Parental  MSSADTKKASILLIRKIYILMQNL-GPLPNDVCLTMKLFYYNEVTPPDYQPPGFKE-GDCEGVIFEGEPM
          MSSADTKKASILLIRKI.ILMQNL..PLPNDVCLTM.LFYYNEVTPP..QPPGFKE..DCE.VIFE.EPM
Retrocopy MSSADTKKASILLIRKISILMQNL>RPLPNDVCLTMELFYYNEVTPPYDQPPGFKE<NDCERVIFEKEPM

Parental  YLNV-GEVPTPFH
          YLNV...VPTPFH
Retrocopy YLNV<EKVPTPFH

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_1426 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000071	1 retrocopy	retro_dnov_2620,
Homo sapiens	ENSG00000143452	1 retrocopy	retro_hsap_3612,
Mus musculus	ENSMUSG00000028109	2 retrocopies	retro_mmus_1420, retro_mmus_2717,
Otolemur garnettii	ENSOGAG00000005640	1 retrocopy	retro_ogar_1908,
Rattus norvegicus	ENSRNOG00000021160	1 retrocopy	retro_rnor_1772,
Tarsius syrichta	ENSTSYG00000006025	1 retrocopy	retro_tsyr_1426 ,