RetrogeneDB ID: retro_tsyr_965

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_25806:4949..5360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMNDC1
• Ensembl ID: ENSTSYG00000006636
• Aliases: None
• Description: survival motor neuron domain containing 1 [Source:HGNC Symbol;Acc:16900]

Sequence

>retro_tsyr_965
TGTTATGAAGCAGAGATCAAAAACATAGATGAAGAAAATGGCACCCCTGCAATCACTTTTGCTGGTTATGGCGATGCTGA
AGTGACTCCACTGTTGAACCTCAAGCCTGTAGAAGAAGGAGGAAAAGCAAAGGAGGACAGTGGCAACAAATCTATGTCAA
ATAATAATAATAATAATTGCCCAGCAGAGTGAATATAAAAAGAAGAAAGTTTTGGAAAAAAGCACAGAGAATAGAAGAAC
TTGAGCAAGAAAGACAGGACCAAAAGGTGAAATGGTAACAGTCCAACAACAGAGCCTATTCTAAAAACAAATAAAGGCCT
GCTGAAGAGGAGTATTTTTGCATCACGTGAGAATGTAACTGGCAAAGTTGGAGTATGAACTTGTGGAATTGCTGATAAGC
CTATGACACAA

Alignment

ORF - retro_tsyr_965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.58 %
• Parental protein coverage: 56.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CYEAEIEEIDEENGTAAITFAGYGNAEVTPLLNLKPVEEGRKAKEDSGNKPMSKKE-MIAQQR-EYKKKK
          CYEAEI..IDEENGT.AITFAGYG.AEVTPLLNLKPVEEG.KAKEDSGNK.MS.....I..Q..EYKKKK
Retrocopy CYEAEIKNIDEENGTPAITFAGYGDAEVTPLLNLKPVEEGGKAKEDSGNKSMSNNN>IIIAQQSEYKKKK

Parental  AL-KKAQRIKELEQEREDQKVKWQQFNNRAYSKNK-KGQVKRSIFASPESVTGKVGVGTCGIADKPMTQ
          .L.KKAQRI.ELEQER.DQKVKW.Q.NNRAYSKNK.KG..KRSIFAS.E.VTGKVGV.TCGIADKPMTQ
Retrocopy VL>KKAQRIEELEQERQDQKVKW*QSNNRAYSKNK>KGLLKRSIFASRENVTGKVGV*TCGIADKPMTQ

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_965 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006335	1 retrocopy	retro_cpor_408,
Macaca mulatta	ENSMMUG00000007775	2 retrocopies	retro_mmul_1972, retro_mmul_2419,
Mus musculus	ENSMUSG00000025024	1 retrocopy	retro_mmus_2685,
Tarsius syrichta	ENSTSYG00000006636	1 retrocopy	retro_tsyr_965 ,