RetrogeneDB ID: retro_tsyr_145

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_3828:45088..45747(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM3
• Ensembl ID: ENSTSYG00000006736
• Aliases: None
• Description: glutathione S-transferase mu 3 (brain) [Source:HGNC Symbol;Acc:4635]

Sequence

>retro_tsyr_145
AGCACCATGCCAATGACACTGGGATACTGGGACATCCATGGGCTGGCCTACGCCATCCGCCTGCTCCTGGAATACACAGA
CTCAAGCTATGAGGAAAAGAAGTACACCATGGGGGATGCTCCTGACTATGACAAAAGCCAGTAGCTGAATGAAAAATTCA
AGCTGGGCCTGGACTTTCCCAATCTGCCCTACCTAATCGATGGGGCTCACAAGCTCACCCAGAGCAACACCATCCTGCGC
TACATTGCCCTCAAACACAACGTGTGGGGAGACAGAAGAGGAGAAGATTCGAGTGGACATTTTGGAGAACCAGGCTATGG
ACGTCTCTAATCAGCTGGCCAGAGTCTGCTATAGCCCTGATTTTGAAAAACTGAAAGCAGAGTACCTGGAGGGGTCTCCC
TGACATGATGAGGTTCTTCTCACAGTTCTTAGGGAAGTAGTCAGGGTTTGCAGAGGACAAGATCACCTTTGTGGATTTCC
TCGCTTACGATATCCTTGACCTGCACTGTATATTTGAGCCGAAGTGTTTAGATGCATTTCCAGACCTGAAGGATTTCATG
TACTGATTTGAGGGCTTAAAGAAAATCTCTGCCTACATGAAGTTCAGCCGTTTCCTCCCAACGCCTCTGTATACAAAGGT
GGCCATCTGGGGCAACAAA

Alignment

ORF - retro_tsyr_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.86 %
• Parental protein coverage: 98.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSKSMVLGYWDIRGLAHAIRLLLEFTDTAYEEKLYTCGEAPDYDRSQWLDVKFKLNLDFPNLPYLMDGKN
          S...M.LGYWDI.GLA.AIRLLLE.TD..YEEK.YT.G.APDYD.SQ.L..KFKL.LDFPNLPYL.DG..
Retrocopy STMPMTLGYWDIHGLAYAIRLLLEYTDSSYEEKKYTMGDAPDYDKSQ*LNEKFKLGLDFPNLPYLIDGAH

Parental  KITQSNAILRYIARKHNMCGD-TEEEKIRVDIMENQVMDFRMQLIRLCYNSDHEKLKPEYLE-QLPGQLK
          K.TQSN.ILRYIA.KHN..GD..EE.KIRVDI.ENQ.MD...QL.R.CY..D.EKLK.EYLE..LP....
Retrocopy KLTQSNTILRYIALKHNVWGD>EEE-KIRVDILENQAMDVSNQLARVCYSPDFEKLKAEYLE>GLPDMMR

Parental  QFSLFLGKFSWFAGEKLTFVDFLTYDVLDQNRMFEPKCLDEFPNLKAFMCRFEALEKIAAYIQSDRFFKM
          .FS.FLGK.S.FA..K.TFVDFL.YD.LD....FEPKCLD.FP.LK.FM..FE.L.KI.AY....RF...
Retrocopy FFSQFLGK*SGFAEDKITFVDFLAYDILDLHCIFEPKCLDAFPDLKDFMY*FEGLKKISAYMKFSRFLPT

Parental  PVNNKMAQWGNK
          P...K.A.WGNK
Retrocopy PLYTKVAIWGNK

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_145 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 16 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145 ,
Tarsius syrichta	ENSTSYG00000007276	1 retrocopy	retro_tsyr_793,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,