RetrogeneDB ID: retro_tsyr_197

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_5069:71533..71780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSTSYG00000008670
• Aliases: None
• Description: RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]

Sequence

>retro_tsyr_197
CTGGTTGGTCGCCAGATCCATGTGGACCATACAGGTAAACCTACCCAGGGAACCAGAGGGAGTGATTTTGGGCCTGTGGT
TGTGGCTACTCTAGAGGTGCTGGGGACCAGGGCTGTGGGAGTGGCAGACACGACAGTCGATCTGGAGATATGGATATGGA
TGCAGACAGTCCAGAGACTATGATGGCAGAAACCAGGTAGGTTATGACTGCTACTCAAGAAGAAATTACAGAAGCAATTA
TCAAGAC

Alignment

ORF - retro_tsyr_197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 53.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDGRQIRVDHAGKSARGTRGGAFG-ARGRGYSRGGGDQGYGSGRYDSRPGG-YGYGYGRSRDYGGRNQGG
          L.GRQI.VDH.GK...GTRG..FG.A.G.GYSRG.GDQG.GSGR.DSR.G..YGYG...SRDY.GRNQ.G
Retrocopy LVGRQIHVDHTGKPTQGTRGSDFG<ACGCGYSRGAGDQGCGSGRHDSRSGD<YGYGCRQSRDYDGRNQVG

Parental  YDRYSGGNYRDNYDN
          YD.YS..NYR.NY..
Retrocopy YDCYSRRNYRSNYQD

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_197 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 21 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197 , retro_tsyr_2002, retro_tsyr_679,
Tarsius syrichta	ENSTSYG00000009555	1 retrocopy	retro_tsyr_15,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,