RetrogeneDB ID: retro_tcac_1

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 7:21941010..21941868(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_033463
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_016996
• Aliases: None
• Description: None

Sequence

>retro_tcac_1
ATGGAGATTGTTGACGTTAGTGTGGTTGTTTTGATCTTGAGTGTTGTGAGTGTGAAAAGTGTGGAGGGGAAGGACTTCAC
ACCCTACAATTTTAGATCAGTTTACAACTTTGGTGATCCTAATTCTGATACTGGCGGTGGATCAACTGGATTCTACCCTG
CAGGACCTCCATCCGGTGAGACTTTCTTCGGTAGGCCGGCTGAAAGGGGCTGCGACGGGCGTCTGATAATAGATTTCATT
GCTGAGCATCTTGATTTGCCTCACTTGAGTCCATACCTGGATTCCATTGGAACAAGCCATCGGCATGGTGCTAATTTCGC
CATTGGCGGATCAACCATCAGGCCACAAAATGAATCAATGTCTTTAAATGGAGTAAGCCCGTTCTCACTTGACATCCAGT
TTATACAATATAATCAGTTCAAGGCTCGCACCAGCTTTCTCTACAACCAAGCCAAGAAAAATTACCACAGAAAACATCTC
CCTAGACCTCAGGACCTCTCCCAGGCTCTTCATGTCATTGACATTGGTCAAAATGACATTGCTGCTGGTTTCAGGTTGAA
GAATGAGTCAGAATTTCATGCATCAATGCCAGACATAGTTGACCAGCTAGCTAAAGCAGTCCAAAATCTCTATGACCAAG
GGGCAAGGACATTTTGGATACATAATACAGGCCCAATTGGTTGCTTGCCTGTGAATCTACACCATCATCTTCAGCCTGAT
GAACTTGACAAGCAGGGCTGTCTTAAATCTCTAAATGACTTTGCTATAGAGTTTAATAGGCAGATTAAGGATAGAGTGAT
CAAACTTAGGACTAAGCTACCAAATGCTGCATTAACATATGTGTGTTGCAAAATATGA

Alignment

ORF - retro_tcac_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.26 %
• Parental protein coverage: 73.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEMVKASVVVLILAVLSVQIVEGKDFPPCNFRSVYNFGDSNSDTGGGSAAFYPAGPPSGETFFGRPAGRG
          ME.V..SVVVLIL.V.SV..VEGKDF.P.NFRSVYNFGD.NSDTGGGS..FYPAGPPSGETFFGRPA.RG
Retrocopy MEIVDVSVVVLILSVVSVKSVEGKDFTPYNFRSVYNFGDPNSDTGGGSTGFYPAGPPSGETFFGRPAERG

Parental  SDGRLIIDFIAEHLGLPHLSPYLDSIGTSYRHGANFAIGGSTIRPQNESMSLNGVSPFSLNIQFIQYNQF
          .DGRLIIDFIAEHL.LPHLSPYLDSIGTS.RHGANFAIGGSTIRPQNESMSLNGVSPFSL.IQFIQYNQF
Retrocopy CDGRLIIDFIAEHLDLPHLSPYLDSIGTSHRHGANFAIGGSTIRPQNESMSLNGVSPFSLDIQFIQYNQF

Parental  KARTSYLYNQAKKNYYRKHLPRPQDFSQALYVIDIGQNDMAAGFRLKNDSEFHASMPDIVEQLTKAVQNL
          KARTS.LYNQAKKNY.RKHLPRPQD.SQAL.VIDIGQND.AAGFRLKN.SEFHASMPDIV.QL.KAVQNL
Retrocopy KARTSFLYNQAKKNYHRKHLPRPQDLSQALHVIDIGQNDIAAGFRLKNESEFHASMPDIVDQLAKAVQNL

Parental  YDQGARTFWIHNTGPIGCLPVTLHYHLKPDELDKQGCLKSQNDFAIEFNRQLKVRVIKLRTELPDAALTY
          YDQGARTFWIHNTGPIGCLPV.LH.HL.PDELDKQGCLKS.NDFAIEFNRQ.K.RVIKLRT.LP.AALTY
Retrocopy YDQGARTFWIHNTGPIGCLPVNLHHHLQPDELDKQGCLKSLNDFAIEFNRQIKDRVIKLRTKLPNAALTY

Parental  V
          V
Retrocopy V

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_1 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_016996	1 retrocopy	retro_tcac_1 ,