RetrogeneDB ID: retro_tcac_2

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 7:1833374..1834538(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_030891
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_000745
• Aliases: None
• Description: None

Sequence

>retro_tcac_2
ATGTTTCCATGGTTGGCAAGGATAGCTCCCGCTTGTTGGAGACCAGTGAGTCGATGTGCCTGTATGAACGAGGACAATAA
TAATAGTAATAATGACGAAGCACTTTGGTGTAGAGACCTTGAAAAACACTCTTATGGTGATTTCTCCTTTGCTGTTGTTC
AAGGCAATGAGGTCATTGAAGATCATAGTCAAGTCGAGACTGGAAAAGAAGCCACTTTTGTTGGTGTCTATGATGGACAT
GGCGGCCCTGATGCTTCTCGCTTTATCTCTCATCATCTCTTTCAAAATCTAATCAGGCTTGCTCGAGCAAATGGAGCCAC
CATTTCTGACGATATTCTCAGAAGTGCTGTTTCCGCAACTGAAGATGGGTTTCTTACTCTTGTACGTAGGACATGTGGAA
TAAAACCATTAATGGCCGCAATTGGATCTTGTTGTCTGGTTGGAGTTATGTGGAAGGGAACATTATACATTGCTAATTTG
GGTGATTCTCGAGCTGTAATTGGTCATTTAGTTAGATCAAATAAGATAGGTAGATCAAATACGATAGTTGCTGAGCAGTT
GACTAGAGATCATAACGTTAGTATAGAGGAGGTCAGACAGGAACTCAGGTCATTGCATCCAGATGATTCTGATATTGTTG
TTATGAAGTATGGAGTATGGCGTGTTAAGGGCGTCATTCAGGTATCCAGATCTATCGGAGATGCATACCTGAAGCGACCA
GAGCTTTCTCCTCATCCTTCTTACCCACGATTTCTCCTCTCTGAACCTATTCGTCGACCTGTGCTAACAGCAGAACCATC
CATGTGCACCAGGGTTTTACAACCTAGTGATAAGTTTGTAATCTTCGCATCTGATGGACTTTGGAAATGTTTGACAAACC
AGCAGGCTGTGGAGATTGTGTATAAGTATCCACGAGCAGGAATTGCAAAGAGGCTTATCAAAACAGCTTTAAACAAGGCA
GCTAGGAAAAGCAAGATGAGATATGATGATGTTAAGAAGGTTAAAAAGGGGATCATCTGGCGGTTGTTCCATGATGACAT
TACAGTTGTTGTCATCTTTATAGACCATGAGTCGCCGCCGCTGGGTGCAAAGATGTCTGTGCCAGAGCAGTCTGTACGTG
GGTTTGTCGACACCGCCGGACCATCAAACTTTAACATTATGTAA

Alignment

ORF - retro_tcac_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.92 %
• Parental protein coverage: 84.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DELLWHIDLKPHAAGDYSIAVVQANSSLEDQGQVFTSPSATYIGVYDGHGGPEASRFITHHLFPFLHKFA
          DE.LW..DL..H..GD.S.AVVQ.N...ED..QV.T...AT..GVYDGHGGP.ASRFI.HHLF..L...A
Retrocopy DEALWCRDLEKHSYGDFSFAVVQGNEVIEDHSQVETGKEATFVGVYDGHGGPDASRFISHHLFQNLIRLA

Parental  SEHGG-VSAEVIRKAFEATEEEFLRLVKRSWPSRPQIASVGSCCLVGAIANGVLYVANLGDSRAVLGRGG
          ...G...S....R.A..ATE..FL.LV.R.....P..A..GSCCLVG....G.LY.ANLGDSRAV.G...
Retrocopy RANGATISDDILRSAVSATEDGFLTLVRRTCGIKPLMAAIGSCCLVGVMWKGTLYIANLGDSRAVIGHLV

Parental  SPN--GTNNQLVAERLSTDHNVGVEEVRKEVVALHPDDSHIVVNNRGVWRIKGIIQVSRSIGDIYLKKPE
          ..N..G..N..VAE.L..DHNV..EEVR.E...LHPDDS.IVV...GVWR.KG.IQVSRSIGD.YLK.PE
Retrocopy RSNKIGRSNTIVAEQLTRDHNVSIEEVRQELRSLHPDDSDIVVMKYGVWRVKGVIQVSRSIGDAYLKRPE

Parental  FNRDPLFQQFGLPIPLKRPVMTAEPSILIRKLKPEDLFLIFASDGLWEQLSDQAACEIVLKSPRAGIAKR
          ....P....F.L..P..RPV.TAEPS...R.L.P.D.F.IFASDGLW..L..Q.A.EIV.K.PRAGIAKR
Retrocopy LSPHPSYPRFLLSEPIRRPVLTAEPSMCTRVLQPSDKFVIFASDGLWKCLTNQQAVEIVYKYPRAGIAKR

Parental  LVRAALKEAAKKREMRYQDIKRIEKG-VRRHFHDDITVIVMYLDH
          L...AL..AA.K..MRY.D.K...KG...R.FHDDITV.V...DH
Retrocopy LIKTALNKAARKSKMRYDDVKKVKKGIIWRLFHDDITVVVIFIDH

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_2 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_000745	1 retrocopy	retro_tcac_2 ,