RetrogeneDB ID: retro_tsyr_103

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_2859:32045..32440(-)
• Located in intron of: ENSTSYG00000000999

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM254
• Ensembl ID: ENSTSYG00000006920
• Aliases: None
• Description: transmembrane protein 254 [Source:HGNC Symbol;Acc:25804]

Sequence

>retro_tsyr_103
AGCTCCAATGTGGTGGAATTCAAGTCGGAGGCTGGCAGCACAGCCACCACTTACCTCCTTACAAACAGACCCTTGCCCAC
ACTGGTTACTGTCCTGGGGCTGGTATACTTCACGTGGGTTGTCTTCTGGCCTCAGAGTGTCCCTTATCAAAGTCTTGGGC
CCTGGGCACCTTCACTCAGTACTTGGTGGACCACCATCACATCCTTCTGTGCAATGGGTATTAGCTTGCCTGGCTGAGTC
ATATGGGAGAATCCTTATATGCCATGGTATTGTGCAAGTATAAAGGTATCACAAATGGTCAGGCTCGGCTATTCTGGCTC
CTACAGACTTTTCTCTTTGGGATAGCTTCTCTATCTTGATTGCTTACAGGCAGACCAAAGCGCCAAAAACAAACT

Alignment

ORF - retro_tsyr_103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.44 %
• Parental protein coverage: 92.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFNMVVAKSEAGGAATTYFRRSRPLPALVTVLGLAYFA-VVFWPQSVPYQSHGP-LGTFTQYLADHHHTL
          S.N.V..KSEAG..ATTY....RPLP.LVTVLGL.YF..VVFWPQSVPYQS.GP.LGTFTQYL.DHHH.L
Retrocopy SSNVVEFKSEAGSTATTYLLTNRPLPTLVTVLGLVYFTWVVFWPQSVPYQSLGP<LGTFTQYLVDHHHIL

Parental  LRNGYWLAWLIHVGESLYAMVLCKHKGITNGQAQLLWFLQTFLFGIASLSILIAYRPKRQKQT
          L.NGY.LAWL.H.GESLYAMVLCK.KGITNGQA.L.W.LQTFLFGIASLS.L...RPKRQKQT
Retrocopy LCNGY*LAWLSHMGESLYAMVLCKYKGITNGQARLFWLLQTFLFGIASLS*LLTGRPKRQKQT

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_103 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 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635, retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103 ,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454,