RetrogeneDB ID: retro_tsyr_1823

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_607806:4..557(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM49A
• Ensembl ID: ENSTSYG00000010693
• Aliases: None
• Description: family with sequence similarity 49, member A [Source:HGNC Symbol;Acc:25373]

Sequence

>retro_tsyr_1823
AAGCAGGTGTCCGAGTATAATATTTTCGTCCTTCGCCTATCCATCTCTCCTCCAATAGAGCTTGAGAAGGAAATTTATAA
TCAGGTGAATATAGCATTAAAAGATGCAGAAGGCATCTTGGAGGACTTGCAGTCATATGAGGAGCTGGCCATGAAATACG
AGAGGCAATCCAGCATCCCGTAGATGAGAAGTTGAAGGAGAAGGCGTGGGGTGCAGTTGTACCACTAGTAGGCAAATTAA
AAAAATTTAATGATTTTTTTCTGAGATTGAAAGAAGCATTAAGAAATATTCTACGATCCTGAAAAATACCCTATATTCTC
CCACCCAACATCTAGATTGAGAGTAGACTCTTGCAAAACAGTTTGCAGAAATTATTTATTTCACACTCCAGTTTGATGAA
ATCAAGATGACAAATCTTGCCATACAGAATGATCGCAGTTATTATAGAAGAACATTGAGTCATATGAAAATTAATAATGT
ACCAACAGAAGGAGAAAATTAAATAAATAATGAGTTGGCAAATAAAATGTCTTTGTTTTATGCTGAGGCAACT

Alignment

ORF - retro_tsyr_1823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.15 %
• Parental protein coverage: 57.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  REIENYPHFFLDFENAQPTEGEREIWNQISAVLQDSESILADLQAYK-GAGPEIRDAIQNPNDIHLQEKA
          .....Y..F.L......P.E.E.EI.NQ....L.D.E.IL.DLQ.Y..GAG.EIR.AIQ.P.D..L.EKA
Retrocopy KQVSEYNIFVLRLSISPPIELEKEIYNQVNIALKDAEGILEDLQSYE<GAGHEIREAIQHPVDEKLKEKA

Parental  WNAVCPLVVRLKRFYEFSIRLEKALQSLLESLTCPP-YTPTQHLEREQALAKEFAEILHFTLRFDELKMR
          W.AV.PLV..LK.F..F..RL..AL...L.S...P..Y.PTQHL..E..LAK.FAEI..FTL.FDE.KM.
Retrocopy WGAVVPLVGKLKKFNDFFLRLKEALRNILRS*KIPY<YSPTQHLD*E*TLAKQFAEIIYFTLQFDEIKMT

Parental  NPAIQNDFSYYRRTISRNRINNMHLDIENEVNNEMANRMSLFYAEAT
          N.AIQND.SYYRRT.S...INN.....EN..NNE.AN.MSLFYAEAT
Retrocopy NLAIQNDRSYYRRTLSHMKINNVPTEGEN*INNELANKMSLFYAEAT

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_1823 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012839	1 retrocopy	retro_cpor_68,
Microcebus murinus	ENSMICG00000013924	1 retrocopy	retro_mmur_898,
Tarsius syrichta	ENSTSYG00000010693	4 retrocopies	retro_tsyr_1129, retro_tsyr_1823 , retro_tsyr_2111, retro_tsyr_827,