RetrogeneDB ID: retro_tsyr_70

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_1634:10476..10710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXYD4
• Ensembl ID: ENSTSYG00000014460
• Aliases: None
• Description: FXYD domain containing ion transport regulator 4 [Source:HGNC Symbol;Acc:4028]

Sequence

>retro_tsyr_70
AGAGTGACCTCAGTCCTTCTCCTACTGGCAGAACTGCCAGGCTCAGACACCCATGACCCATTTGCTGATAAAGACAGTAT
CTTCTGCTATGACTGGGAAGGCCTGTAGCTGAGCAGCAGGGTGGTTGTCCTGTGCATCGCCGGGATTGCTGTGACCCTGA
GTGGCAGATGCAAATACAAGGGCATTCAGAAGCACAGTCCCTTACCTGAGAAAGCCACCCCACTCCTCACTCCA

Alignment

ORF - retro_tsyr_70 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.5 %
• Parental protein coverage: 97.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVTSALLLLAGLPTLDANDSFADKDNPFYYDWEGLQLSGMIVGGLLCIAGIAVALSGKCKCKGNQKHSPL
          RVTS.LLLLA.LP..D..D.FADKD..F.YDWEGL.LS...V...LCIAGIAV.LSG.CK.KG.QKHSPL
Retrocopy RVTSVLLLLAELPGSDTHDPFADKDSIFCYDWEGL*LSSRVV--VLCIAGIAVTLSGRCKYKGIQKHSPL

Parental  PEKATPLITP
          PEKATPL.TP
Retrocopy PEKATPLLTP

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_70 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024923	1 retrocopy	retro_cfam_1820,
Dasypus novemcinctus	ENSDNOG00000017385	1 retrocopy	retro_dnov_643,
Erinaceus europaeus	ENSEEUG00000010030	4 retrocopies	retro_eeur_148, retro_eeur_264, retro_eeur_524, retro_eeur_559,
Felis catus	ENSFCAG00000022417	2 retrocopies	retro_fcat_284, retro_fcat_990,
Monodelphis domestica	ENSMODG00000027578	1 retrocopy	retro_mdom_976,
Oryctolagus cuniculus	ENSOCUG00000006722	1 retrocopy	retro_ocun_1050,
Tupaia belangeri	ENSTBEG00000016033	1 retrocopy	retro_tbel_1911,
Tarsius syrichta	ENSTSYG00000014460	3 retrocopies	retro_tsyr_1494, retro_tsyr_70 , retro_tsyr_875,