RetrogeneDB ID: retro_tsyr_1116

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_31056:12450..12929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D3
• Ensembl ID: ENSTSYG00000004536
• Aliases: None
• Description: TM2 domain containing 3 [Source:HGNC Symbol;Acc:24128]

Sequence

>retro_tsyr_1116
GTAGACCACATGACAGATTTCTCCTGAGTCTATGGGAAGTTTGTCACTTTTGACTGTACAGTAAAACCTTTTGTTACTTG
TATTGATTAAGGATTCATATCCTAAAATAACTTTATCATCAACATGCATGCAGATTTTGCTGGCAGCATCTAGAAACAGA
TTATGAATGTTTGAATTCCATCCGCTGCATGAGGTGTCCTGTCCTCAATACTATTAACATTGCCAACTGTGTGACAAACA
CATTCATGACTTGGGCAGCTGTACTTTTTTCAAAATATTGTACCGCAATTGGATTGGAGGCTATGAGAGTTCTGCTGCTC
TGTCCCTAAGCATCACCTTGGTGGGTTTGGAGCAGACTATTTCTACTTGGGCCAGTGGTTAAAAGGCCTCAGTGAGCTCT
TCATCTTTGATGGCCAGGGAACGTGACACCAATAGACATCTGCTTAATTAGAGTTGGCTATGTTGGACCTGCAGATGGC

Alignment

ORF - retro_tsyr_1116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.47 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IDCTTNFSCIYGKPVTFDCTVKPSVTCVDQDFKPQKNFIINM-TCRFCWQLPETDYECFNSTSCM-TVSC
          .D..T.FS..YGK.VTFDCTVKP.VTC.D..F....NFIINM..CRFCWQ..ETDYEC.NS..CM..VSC
Retrocopy VDHMTDFS*VYGKFVTFDCTVKPFVTCID*GFIS*NNFIINM<ACRFCWQHLETDYECLNSIRCM<EVSC

Parental  PRQRYIANCTVRD-HIHCLGNRTFPKMLYCNWTGGYKWSTALALSIT-LGGFGADRFYLGQWREGLGKLF
          P...Y...C...D.HIH.LG..TF.K.LY.NW.GGY..S.AL.LSIT.LGGFGAD.FYLGQW..GL..LF
Retrocopy P--QYY*HCQLCDKHIHDLGSCTFFKILYRNWIGGYESSAALSLSIT<LGGFGADYFYLGQWLKGLSELF

Parental  SFGGLGI-WTLIDVLLIGVGYVGPADG
          .F.G.G...T.ID..LI.VGYVGPADG
Retrocopy IFDGQGT<VTPIDICLIRVGYVGPADG

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_1116 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017340	1 retrocopy	retro_cjac_3233,
Homo sapiens	ENSG00000184277	1 retrocopy	retro_hsap_1138,
Gorilla gorilla	ENSGGOG00000011598	1 retrocopy	retro_ggor_887,
Macaca mulatta	ENSMMUG00000000277	1 retrocopy	retro_mmul_884,
Mustela putorius furo	ENSMPUG00000010985	1 retrocopy	retro_mputfur_313,
Nomascus leucogenys	ENSNLEG00000000529	1 retrocopy	retro_nleu_937,
Pan troglodytes	ENSPTRG00000007515	1 retrocopy	retro_ptro_775,
Tarsius syrichta	ENSTSYG00000004536	1 retrocopy	retro_tsyr_1116 ,