RetrogeneDB ID: retro_tcac_25

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 4:31754202..31754988(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_021124
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_027247
• Aliases: None
• Description: None

Sequence

>retro_tcac_25
ATGGCCGCGGTAGTGTGCGGGAGTAAGAGATCGTTCTTTGAGGATACCTCGTCGCCAGCAGCTTCTGTCTCTAAGAAGCT
CCGGCGTTGCTCGCCTTCATCTCCTTCGTCTGCTCGTTTCTCTTCGCCATCGTCTTCTCTCGCTCACCTCGAAGTCCTTT
TCCCTCATATGGACCCCGAGCTTCTGGAGAGAGCACTGCTAGAATGTGGCAAAGATGTAGACATTGCCATCAAGAGGCTG
CAGGAACTTTGCTTGGGAGCCGCAGGGGCTACAGAGGAAAAGGCAGGTCCTGTTGAAGAAGAGGGCTTAACTGCACAGCT
GGGAACATTGACCAATGATGGGGAAGCTGCTGCAGCTGCTACTGTGGCTGTTCAGAATCCAGCAGCCCCTGAGAATGTGC
CTGTTGATGGTGCAGAATGGGTGGACTTGTTTTTGAGGGAGATGACGAGTTGTACCAGTATGGATGATGCCAAAGCCCGT
GCCTCTAGGCTTTTGGAGGTTGTGGAGAAGTCCATTAGTAGATCGGCAGCACAAAGTTTTGAGAAAGAAAATATCATGTT
AAGAGAAGAAAATACAGTCCTCAAACGAGCGGTGGTAATGCAGCATGAGCGTCAGAAGGAGTATCAAGACAAAGTGCATG
AATTGCAACATCTGAGACACCAACTGTCTCAGTATCAGGAGCAGTTGCGAATTTTAGAGATAAATAACTACGCCTTAACC
ATGCATTTGAGACAGGCACAGCAAAATAGCTCCATTCCAGGGCGTTTCCACCCAGACGTCTTCTAA

Alignment

ORF - retro_tcac_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 84.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSAAVCGSKRSFFEDIPSSPSASVSKKLRRCSPSSPSSVRFPPPPSSLAHLEALFPHMDPELLERALLEC
          M.A.VCGSKRSFFED..SSP.ASVSKKLRRCSPSSPSS.RF..P.SSLAHLE.LFPHMDPELLERALLEC
Retrocopy MAAVVCGSKRSFFEDT-SSPAASVSKKLRRCSPSSPSSARFSSPSSSLAHLEVLFPHMDPELLERALLEC

Parental  GNDIDTAVKRLQELCLGAAEATGERSGPVEELGATAELCTLTNDGE--ATATVPVQNPSAPEKLPVDGAE
          G.D.D.A.KRLQELCLGAA.AT.E..GPVEE.G.TA.L.TLTNDGE..A.ATV.VQNP.APE..PVDGAE
Retrocopy GKDVDIAIKRLQELCLGAAGATEEKAGPVEEEGLTAQLGTLTNDGEAAAAATVAVQNPAAPENVPVDGAE

Parental  WVDLFVREMMSATSVDDAKARAFKLLEVLENSISRSAAEEAAQNFHKENIMLKEQIEVLIQENTVLKRAV
          WVDLF.REM.S.TS.DDAKARA..LLEV.E.SISRSAA......F.KENIML.E...VL...........
Retrocopy WVDLFLREMTSCTSMDDAKARASRLLEVVEKSISRSAAQ----SFEKENIMLREENTVLKRAVVMQHERQ

Parental  AIQHERQKEYQDKNHELQHLKQ
          ........E.Q...H.L.....
Retrocopy KEYQDKVHELQHLRHQLSQYQE

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_25 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Theobroma cacao	TCM_027247	1 retrocopy	retro_tcac_25 ,