RetrogeneDB ID: retro_tcac_18

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 5:34299927..34301199(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_025721
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_030978
• Aliases: None
• Description: None

Sequence

>retro_tcac_18
ATGCATACTTCGAATCTCATATCATCCTCTCATGTCACTTTCTCCAAATCCACACATCAATATTATCCCACAAAAAGGAT
CGAAAACCCAAAAAACTTCAGTTACCCTCCTGGTTTTCTCAACAAATCCACCCCTCACAGCCCCAAACTTTGCAACTTTC
ACAAAATCCATTGTTACCCTTTTGGCAAGATCCAAGGCTTAGGCACCAAAAGAACTCCTTTCAGCTATATCCATGAAAAC
CCTTCTAGGAAACCTGGATCCCGTATTCCCAGATCAGCTGCAGCATCTGAATCTAATCCAGAAGGAGAAGCTGAAGCAGC
TGAAGTAGCAGCGAAGTCAAAGGCTAAAACTTTACAGCTTGCTCTTGTGTTCGGTTTTTGGTACTTTCAAAACATTGTCT
TTAACATTTACAACAAAAAAGCATTGAATGTCTTTCCATTCCCTTGGCTTCTTGCTTCTTTTCAACTCTTCGCTGGTTCC
ATTTGGATGTTCGTTCTCTGGTCTTTAAAGTTGCAACCTTGTCCCAAAATCACAAAGCCTTTTATTATTGCACTTCTTGG
ACCTGCATTGTTTCACACAATAGGCCATATTTCAGCTTGTGTATCGTTTTCTAAGGTTGCCGTTTCCTTCACTCATGTTA
TCAAATCATCAGAGCCTGTGTTTTCTGTTGTTTTCTCTTCATTTCTTGGTGATACATACCCTTTGAAAGTCTGGCTTTCC
ATTGTTCCCATTGTTTTGGGATGTTCTCTAGCTGCTATTACTGAGGTTTCCTTTAATTTTCAAGGCTTATGGGGTGCTTT
GATTAGCAATGTTGGTTTTGTGTTAAGGAACATTTACTCCAAGAAAAGTTTGCAGAACTTTAAGGAAGTGAATGGATTGA
ATTTGTATGGTTGGATCAGTATAATCTCACTGCTTTATCTGTTTCCAGTCGCGGTTATTGTTGAAGGGTCGCAATGGGTT
CAAGGGTATCACAAAGCAATCGAGACTGTTGGCAAAGCATCCACATTTTACATATGGGTCTTGCTTTCAGGAATATTTTA
CCATCTATACAACCAATCATCTTATCAGGCACTTGATGAAATTAGCCCTTTGACTTTTTCAGTTGGGAACACAATGAAGA
GGGTTGTGGTTATAGTGTCAACTGTTTTGGTGTTCAGAAATCCAGTCCGGCCTTTGAATGCACTTGGATCTGGGATTGCA
ATACTTGGAACTTTCTTGTATTCACAAGCAACAGCTAAGAAGAAGAGTGCTGGAGGTGAAAAGAAGAGCTAA

Alignment

ORF - retro_tcac_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.92 %
• Parental protein coverage: 98.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRESLADRSQP---IEAAGEVKSEAAKRVKIGIYFATWWALNVVFNIYNKKVLNAYPYPWLTSTLSLACG
          PR...A..S.P....EAA.......AK.......F..W...N.VFNIYNKK.LN..P.PWL.....L..G
Retrocopy PRSAAASESNPEGEAEAAEVAAKSKAKTLQLALVFGFWYFQNIVFNIYNKKALNVFPFPWLLASFQLFAG

Parental  SLMMLISWATRIAETPKTDFEFWKTLFPVAVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRLL
          S..M...W.......PK....F...L...A..HTIGH..A.VS.SKVAVSFTH.IKS.EP.FSV..S...
Retrocopy SIWMFVLWSLKLQPCPKITKPFIIALLGPALFHTIGHISACVSFSKVAVSFTHVIKSSEPVFSVVFSS-F

Parental  LGEAFPLSVYLSLVPIIGGCALAAVTELNFNMTGFMGAMISNLAFVFRNIFSKKGMKG-KSVSGMNYYAC
          LG...PL.V.LS.VPI..GC.LAA.TE..FN..G..GA.ISN..FV.RNI.SKK.....K.V.G.N.Y..
Retrocopy LGDTYPLKVWLSIVPIVLGCSLAAITEVSFNFQGLWGALISNVGFVLRNIYSKKSLQNFKEVNGLNLYGW

Parental  LSLMSLLILTPFAIAVEGPQMWAAGWEKALSQIG--PQFIWWVAAQSIFYHLYNQVSYMSLDEISPLTFS
          .S..SLL.L.P.A..VEG.Q.W..G..KA....G....F..WV....IFYHLYNQ.SY..LDEISPLTFS
Retrocopy ISIISLLYLFPVAVIVEGSQ-WVQGYHKAIETVGKASTFYIWVLLSGIFYHLYNQSSYQALDEISPLTFS

Parental  VGNTMKRISVIVSSIIIFHTPVQPINALGAAIAILGTFLYSQAKA
          VGNTMKR..VIVS....F..PV.P.NALG..IAILGTFLYSQA.A
Retrocopy VGNTMKRVVVIVSTVLVFRNPVRPLNALGSGIAILGTFLYSQATA

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_18 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Brassica oleracea	Bo9g118840	1 retrocopy	retro_bole_30,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Populus trichocarpa	POPTR_0001s44610	1 retrocopy	retro_ptri_19,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Arabidopsis lyrata	scaffold_802017.1	1 retrocopy	retro_alyr_24,
Theobroma cacao	TCM_030978	1 retrocopy	retro_tcac_18 ,