RetrogeneDB ID: retro_tcac_3

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 3:31840587..31841529(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_016205
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_032188
• Aliases: None
• Description: None

Sequence

>retro_tcac_3
ATGGTTAAACGGCTTCTTCCTGGCCATTTGAGATTTTCTCGGCGACCTCTCTATGGGTTCTTTCCCCATCTGCAAAGGGT
CTCCGGAAGGGTTGAAAAGAAAAAGTCGGACAGGGCAATTTTAAAGCTCTGTTCAAGACAAAGACCTGAATTGGAGGCAA
CAGGTAAAGGGATTAACGCAGTTGAAGCAAAGGACAAGACATTAGAGTTGGTGAATAAGGGAAGAAATCAGTTGGTGAGG
AACGAAACGATATCTGAGGTCGCAGCATTTGAGCTCCCTGGTATTCCCTTGGCACATTCAGAACCAGACAGAAAATCCGG
AGTAACCTTTGTTCTCGAGCAAGCCTCATTGGTTTGTGCTAAGGTTGGAAGGAGATACCCGATTTTAAACTCCAATGAAC
ATGCGGCCTTCTTGCGGAAAAAGAATAAGAATCCTTATAAATACAGACCTGACATCATTCATGAGGTGCTAAGTAGAATT
ATAGATAGCCGACTCTGCAAGTCGGGTAGGATACAAGCTATATATGTGAAGACTGACGAAGGGGTCTTGATTAAAGTTGA
ACCAAATACTCACATACCAAGGACACCACGACGTTTTAGGAATATGATGGCTGAGTTATTGCAAAAGTTGAGTGTCAAAG
CTGCGAATAAACATGGGAAGCTTTTACGCTTGGTTCAGAATCCTGTGACTCAACACCTTCCAGCCAACTCGCGTAAAATA
GGTCTTTCTTATAGCTCAAACCAATTGGTTCGCCTAAAGGACTACGTTGGTGGTATTAGTGACAACGAGAACCTTGTTTT
TGTGGTTGGTGCAATGGCTCACGGGAAAATTGATGCTGACTACGTAGATGATCTCATATCAATTTATGGAGGTCGGATGA
GTGCTAGAATGTGTTTGGAAGAAATATTCGAAGCTGTGGAGAGTAAATGGAAGATCTTATGA

Alignment

ORF - retro_tcac_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.51 %
• Parental protein coverage: 71.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEKESGAHELVGIPIAPSDQNTKKAGVIFVLEKASLEVAKVGKSFQLLNSDDHANFLRKNKKNPADYRP
          E...E..A.EL.GIP.A.S.....K.GV.FVLE.ASL..AKVG.....LNS..HA.FLRK..KNP..YRP
Retrocopy ETISEVAAFELPGIPLAHSEPD-RKSGVTFVLEQASLVCAKVGRRYPILNSNEHAAFLRKKNKNPYKYRP

Parental  DIAHQALLAILDSPINKAGRLQAVYVKTEKGVLFEVKPHVRIPRTYKRFSGIILQLLQQHKITAVGKRES
          DI.H..L..I.DS...K.GR.QA.YVKT..GVL..V.P...IPRT..RF......LLQ.....A..K...
Retrocopy DIIHEVLSRIIDSRLCKSGRIQAIYVKTDEGVLIKVEPNTHIPRTPRRFRNMMAELLQKLSVKAANKHGK

Parental  LLRLIKNPVTQYFPVNSRKIGFSYSSEKLVKMSKYVDAVGDDVNLVFMVGAMAHGKIETEYVDDFIAISG
          LLRL..NPVTQ..P.NSRKIG.SYSS..LV....YV....D..NLVF.VGAMAHGKI...YVDD.I.I.G
Retrocopy LLRLVQNPVTQHLPANSRKIGLSYSSNQLVRLKDYVGGISDNENLVFVVGAMAHGKIDADYVDDLISIYG

Parental  YPLSAAMCIARITEALAEKWNIL
          ...SA.MC...I.EA...KW.IL
Retrocopy GRMSARMCLEEIFEAVESKWKIL

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_3 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_032188	1 retrocopy	retro_tcac_3 ,