RetrogeneDB ID: retro_tsyr_259

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_655:17817..18147(-)
• Located in intron of: ENSTSYG00000002259

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHF5A
• Ensembl ID: ENSTSYG00000001082
• Aliases: None
• Description: PHD finger protein 5A [Source:HGNC Symbol;Acc:18000]

Sequence

>retro_tsyr_259
ATGGCTAAACATCACCCAGATTTGATTTTTTGCCACAAGCAGGCTGATGTTGCCATCGAAAGAGTGTGTGAAAAATGTGA
CAGCAAATGTGTGATCTGTTGACTCTATGTGTATCCCTGTACCCTGGTGCACATATGTGATGAGTATAATTATGGCTCTT
ACCAGGGGCGCTGTGTGATCTGTGGAGGCCCGGGAGTCTCCAATGCCTATTACTATAAAGAGTGCACCATCCAGGAGAAG
GATAGAGATGGCTGCCCAAAGATTGTCAATTTGGGGAACTCTAAGACAGACCTCTTCTATGAACGCAAAAAATACAGCTT
CAAGAAGAGG

Alignment

ORF - retro_tsyr_259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKHHPDLIFCRKQAGVXXXXXXXXXDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAY
          MAKHHPDLIFC.KQA.V.........D.KCVIC..YV.PCTLV.ICDE.NYGSYQGRCVICGGPGVS.AY
Retrocopy MAKHHPDLIFCHKQADVAIERVCEKCDSKCVIC*LYVYPCTLVHICDEYNYGSYQGRCVICGGPGVSNAY

Parental  YCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR
          Y.KECTIQEKDRDGCPKIVNLG.SKTDLFYERKKY.FKKR
Retrocopy YYKECTIQEKDRDGCPKIVNLGNSKTDLFYERKKYSFKKR

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_259 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 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015687	1 retrocopy	retro_amel_1674,
Canis familiaris	ENSCAFG00000001090	1 retrocopy	retro_cfam_369,
Callithrix jacchus	ENSCJAG00000004999	3 retrocopies	retro_cjac_1194, retro_cjac_1527, retro_cjac_906,
Echinops telfairi	ENSETEG00000010741	1 retrocopy	retro_etel_102,
Homo sapiens	ENSG00000100410	3 retrocopies	retro_hsap_2033, retro_hsap_2647, retro_hsap_2829,
Gorilla gorilla	ENSGGOG00000001104	2 retrocopies	retro_ggor_1848, retro_ggor_1965,
Latimeria chalumnae	ENSLACG00000012094	1 retrocopy	retro_lcha_25,
Microcebus murinus	ENSMICG00000013520	1 retrocopy	retro_mmur_758,
Macaca mulatta	ENSMMUG00000011354	3 retrocopies	retro_mmul_1390, retro_mmul_1471, retro_mmul_1503,
Mustela putorius furo	ENSMPUG00000016398	2 retrocopies	retro_mputfur_359, retro_mputfur_439,
Mus musculus	ENSMUSG00000061360	3 retrocopies	retro_mmus_1070, retro_mmus_1071, retro_mmus_1155,
Nomascus leucogenys	ENSNLEG00000015481	2 retrocopies	retro_nleu_1205, retro_nleu_653,
Oryctolagus cuniculus	ENSOCUG00000012705	1 retrocopy	retro_ocun_640,
Otolemur garnettii	ENSOGAG00000002839	1 retrocopy	retro_ogar_55,
Pongo abelii	ENSPPYG00000011870	2 retrocopies	retro_pabe_1661, retro_pabe_2324,
Pan troglodytes	ENSPTRG00000014427	3 retrocopies	retro_ptro_1352, retro_ptro_1917, retro_ptro_2479,
Pteropus vampyrus	ENSPVAG00000001162	1 retrocopy	retro_pvam_66,
Rattus norvegicus	ENSRNOG00000024170	3 retrocopies	retro_rnor_2660, retro_rnor_2704, retro_rnor_2712,
Tarsius syrichta	ENSTSYG00000001082	1 retrocopy	retro_tsyr_259 ,
Tursiops truncatus	ENSTTRG00000003369	1 retrocopy	retro_ttru_1483,