RetrogeneDB ID: retro_tsyr_1489

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_46186:10313..10680(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD3
• Ensembl ID: ENSTSYG00000007649
• Aliases: None
• Description: small nuclear ribonucleoprotein D3 polypeptide 18kDa [Source:HGNC Symbol;Acc:11160]

Sequence

>retro_tsyr_1489
ATCAAAGTCCTACATGAGGCCGAGAGCCGCAGAGCGCCATGTGAGACAAACACCAGCAAAGTATATCAGGTGAAGCTCAC
TGAAGCAGAGGACAACGTGAATGGCCAGATGTCCAACATCACAGTCACGTTCACGCACAGAGATGGCCGAGTGGCACAAC
TGGAGCGAGTATACATCCATGGCAACAAGATCCGCATTCTGATTTTGTTTGACTTTCTGAAAAAATGTACCCATGTTAAA
GAACACAGAGAATGAAAACCAGGGCTTAGAGACCAGCCGAGGAAAAGCTACTATTCTGAAGGCCCAAGTGACTGAAAGAG
GAAGAGGGCATGGAATGGGACGTGGAAACATCTTCTAGAAGTGAAGA

Alignment

ORF - retro_tsyr_1489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTY--RDGRVAQLEQVYIRGSKIRFLILP
          IKVLHEAE.....CETNT..VY..KL.EAEDN.N.QMSNITVT...RDGRVAQLE.VYI.G.KIR.LIL.
Retrocopy IKVLHEAESRRAPCETNTSKVYQVKLTEAEDNVNGQMSNITVTFTHRDGRVAQLERVYIHGNKIRILILF

Parental  DMLK-NAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR
          D.LK.N.PMLK...N.NQG....RGKA.ILKAQV..RGRG.GMGRGNIF.K.R
Retrocopy DFLK>NVPMLKNTENENQGLETSRGKATILKAQVTERGRGHGMGRGNIF*K*R

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_1489 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Rattus norvegicus	ENSRNOG00000050410	1 retrocopy	retro_rnor_232,
Tarsius syrichta	ENSTSYG00000007649	1 retrocopy	retro_tsyr_1489 ,