RetrogeneDB ID: retro_tcac_21

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 5:4113190..4114303(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_022360
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_025327
• Aliases: None
• Description: None

Sequence

>retro_tcac_21
ATGAAGATTCTTCAACAGAATCTCGCTCTTAACCAACCAGGATCAGTGAAGATCATCCTGGAAGAAGAAGACGATCTATG
GCTTGCCTACAACCTTTTTGCCAAGGGTGACACAATCGTCGCCGACACCACCAGGAAAGTTATTCACAACAAAAGCTCTG
CCAATGGCAAGAGGAAGGACTCAACTCGTGTCAAAACCAAACTCGAAATCAGAATCACGGACGTTGATTATGAGAAAGAC
TCGTCCAAAGTGCGCGTGCGGGGTAGGAACCTCGTGGCCAATGAACTCATGGCGTACGGTGCGTACCATACCCTGGAGAT
TGAGATGAACAAAGAGTTTGATCTTTCAAAGAAACACTGGGACTCGGATGCCATTGACACTTTGCATGAAGGTTCTGAAA
AAGCATCAGGAGCCGACCTAGCCGTGGTGCTCTTTCAACAATGGTCGGCTCAAGTGTTTCTGATTGGACACAAGGTCACA
ACCCTTGCAAAGGTTGAGGCTTCAAAAACCAACAATAAGACCGCCTCAAACAAGTTTTTTGAAAAGGTTTTTCAGGCTTT
TGTAAAGCATGTGGATTTCAACACCGTTCGTTGTGTTGTGTTAGGAAGCCCGGATTCTACAAAAGAAGAGTTTCGAGGTT
ATTTGTTCCAGGAAGCACAAAGATTGAAGATGAAACGGGTCGAAGAAAACAAGTCACGATTTGTAATGGTAAATATAGGG
AACAAGAATAGTTTGAAGGAGGTTTTGCATGACAACGAAGTGATGGGATTGATTAAAGATACGAAAGCCGTGATGGAAAT
CAGGGCTTACAAGCAGTTTTCGGACTTGTTATTGACTGATTCGGATCGTGCATGTTATGGGCCACGGAGCGTGGAAACTG
CACAGGAGATGATGGCCATTGAGACCCTTTTGATTATGGATGAGTTGCTTAGGAATAAAGAGATTGCATTGAGGAAAAAG
TACATGGAGTTGGTGAAATCTGTGAAGAAAGCAGGAGGGAAAGCGTTTCTGTTCTCGTCTATGCATGTTTCAGGAGAGCA
GTTGGCGCAGTTGACCGGTATTGCCGCCATTCTGAGGTTTCCATTGCCTCAACTTGATGAACTTGTACTTTGA

Alignment

ORF - retro_tcac_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.08 %
• Parental protein coverage: 52.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAALKKFFENVLQAFMKHIDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSG
          ..A..KFFE.V.QAF.KH.DFN.VRC.V..SP..TK..F...L..EA.R.......ENKSR...V....G
Retrocopy KTASNKFFEKVFQAFVKHVDFNTVRCVVLGSPDSTKEEFRGYLFQEAQRLKMKRVEENKSRFVMVNI--G

Parental  YKHSLREVLDAPNVMNMIKDTKAAQEVRALKDFFSMLSNDPARACYGPKHVEIAHERMAVQTLLITDDLF
          .K.SL.EVL....VM..IKDTKA..E.RA.K.F...L..D..RACYGP..VE.A.E.MA..TLLI.D.L.
Retrocopy NKNSLKEVLHDNEVMGLIKDTKAVMEIRAYKQFSDLLLTDSDRACYGPRSVETAQEMMAIETLLIMDELL

Parental  RNSDIATRQKYVNLVNSVKDSGGTAHIFSSMHVSGEQLAQLTGIAAILRFPLPDLEDI
          RN..IA.R.KY..LV.SVK..GG.A..FSSMHVSGEQLAQLTGIAAILRFPLP.L...
Retrocopy RNKEIALRKKYMELVKSVKKAGGKAFLFSSMHVSGEQLAQLTGIAAILRFPLPQLDEL

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_21 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G27650	1 retrocopy	retro_atha_7,
Brassica oleracea	Bo7g111550	1 retrocopy	retro_bole_15,
Brassica rapa	Bra019037	1 retrocopy	retro_brap_29,
Aegilops tauschii	F775_08238	1 retrocopy	retro_atau_9,
Hordeum vulgare	MLOC_5075	1 retrocopy	retro_hvul_86,
Hordeum vulgare	MLOC_54416	1 retrocopy	retro_hvul_87,
Theobroma cacao	TCM_025327	1 retrocopy	retro_tcac_21 ,
Vitis vinifera	VIT_04s0023g00140	1 retrocopy	retro_vvin_2,