RetrogeneDB ID: retro_tcac_8

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 5:4533332..4534007(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_022426
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_028816
• Aliases: None
• Description: None

Sequence

>retro_tcac_8
ATGGCAGCTTCCTTAACAGTCTCAAGGTTTCTCTCGCCAACCGTCCTCTCTTTTTCCGCTACCACCACCAAACTTTACCC
TAAATCCTTTTCGTCGAAACTCTCCTTTTCTCCCCGTTCCCTCAACCTCCACCGCCGCCCTTCAAAACCCATTTCCTTTT
CCACCAAAACAACCCAAATCTCCGCCTCAATCTCCGTCGGAGACAAGCTTCCCGACGCAACCCTCTCCTACTTCGACGCC
GACGGAGAACTCCAAACCACCTCAGTCTCCTCCCTAACCGCTGGCAAAAAAGTCGTCCTCTTCGCCGTTCCGGGCGCTTT
CACTCCCACCTGTTCCCAAAAGCACCTCCCGGGCTTCGTCGAAAAATCGGGGGAGCTCAAAGCCAAAGGGGTCGATACCA
TTGCCTGCGTGTCGGTGAACGACTCGTTTGTGATGCGTGCGTGGAAGGAGAATCTGGGGATTAACGACGAGGTTCTGTTG
TTATCTGATGGGAATGGGGAGTTCACGAAGAAAATTGGGTGTGAATTGGATTTGAGTGATAAGCCCGTTGGGCTCGGAGT
CCGCTCCCGAAGATACGCGCTTTTGGCTGAAAATGGAGTCGTTAAGGTTCTTAATTTGGAGGAAGGTGGTGCTTTTACTT
TCAGCGGGGCTGAAGACATTCTCAAAGTGCTCTGA

Alignment

ORF - retro_tcac_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.5 %
• Parental protein coverage: 97.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVGDTIPDGTLSYADEDDQILNVSVHSLAACKQVILVGVPGAFTPTCSLKHVPGFIEKAEELKSKGISEI
          .VGD..PD.TLSY.D.D......SV.SL.A.K.V.L..VPGAFTPTCS.KH.PGF.EK..ELK.KG...I
Retrocopy SVGDKLPDATLSYFDADGELQTTSVSSLTAGKKVVLFAVPGAFTPTCSQKHLPGFVEKSGELKAKGVDTI

Parental  FLISVNDPYVMKAWAKSYPENKHVKFFSDSSAAYIKTLGLDLDVSDR--GFGVRSQRFALLIDDLKVKVV
          ...SVND..VM.AW......N..V...SD......K..G..LD.SD...G.GVRS.R.ALL.....VKV.
Retrocopy ACVSVNDSFVMRAWKENLGINDEVLLLSDGNGEFTKKIGCELDLSDKPVGLGVRSRRYALLAENGVVKVL

Parental  NVESGGQFKVSSAEDMLKSL
          N.E.GG.F..S.AED.LK.L
Retrocopy NLEEGGAFTFSGAEDILKVL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Theobroma cacao was not studied using RNA-Seq expression data.

ChIP-Seq

Theobroma cacao was not studied using ChIP-Seq data.

EST

Theobroma cacao was not studied using EST data.

TSS

Theobroma cacao was not studied using FANTOM5 data.

Lab

retro_tcac_8 was not experimentally validated.

Homology

Retrocopy orthology:

Theobroma cacao 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8 ,