RetrogeneDB ID: retro_tcac_11

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 10:2672870..2674337(+)
• Located in intron of: TCM_042851

Retrocopy information

• Ensembl ID: TCM_042870
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_036702
• Aliases: None
• Description: None

Sequence

>retro_tcac_11
ATGGAGGATGGATTGGAAGCCCCAGGCCCGCTATGGAAGATTATAGTGGTTGCAGCCATAGCCGCCGGCGTACAGTTTGG
ATGGGCACTGCAGCTCTCTCTTCTAACCCCTTACGTTCAAACCCTTGGTGTCCCTCACATCTGGGCGGCTTTCATTTGGC
TTTGCGGCCCCATCTCTGGCCTCCTCGTGCAGCCTATTGTAGGCTACAACAGTGACCGTTGCACCTCTCGCTTCGGTCGT
CGCAGACCCTTTATTGCAGCTGGAGCCTGCTGTGTTGCTGCAGCTGTTTTCCTCATTGGTTTCGCCAAAGATATAGGACA
CAAAGCTGGTGATTCATTGGAAAAAAACACAAAACCTAGAGCCGTTGCTGTCTTTGTTGCAGGTTTTTGGATTCTCGACG
TGGCTAACAACATGTTACAAGGTCCATGTCGTGCTTTGCTTGCTGACCTTTCCGCAAATAATCATAAAAGAATGAGAGTT
GCAAATGAATGCTTCTCCTTTTTCATGGCTGTTGGAAACGTTTTGGGTTATGCGGCTGGTTCCTACTCAAATCTTCACAA
AATCTTCCCTTTCACAAGAACAACTGCCTGTGATGTATACTGCGCAAACCTCAAAACTTGCTTCATTATTCACATTGTTT
TCCTCTTGTTGGTGACAATAACCGCGATTATCAGCGTGAAAGAGACGCCACTAAGCATGAAGCAAGAAGAAGAGAAAGCG
TCTACGCCTTTTGTTGGGGAGTTATTGACAGCATTCAAGAGCTTGAAGAAACCGATGTGGATCTTGCTTCTTGTCACTTG
CCTTAACTGGATAGCCTGGTTCCCATTCTTGTTGTACGACACGGACTGGATGGGAAGGGAGATTTACGGAGGGTTTGTGG
ACGGAAATGCGACTCAACAGAAGCTGTATGATGATGGAGTACGGGCGGGTGCGTTGGGGTTGATGATTAACTCGATTGTT
TTGGGTTTTACTTCCTTGGGATTGGAGAATGTTGGGCGCTTGGTTGGTGGGGTTACAAACTTGTGGGGTGGGGTGAATTT
CATCTTGGCTGCATGCCTGGCTTCCACGGTGTGGATCACCAAGATAGTTGAGGCTTGGAGAGATAAACATGGACACTTGG
CCCCTCCAAACAACATCAAAGGCCCTGCCTTGGCTATTTTTGGATTGTTGGGTATTCCCCAAGCCGTTACTTACAGCATT
CCATTCGCTTTGACATCCATCTATTGCTCTACTTCTGGCGGTGGTCAAGGGCTTGCCCTGGGAGTGCTCAACATGTCAAT
AGTTATCCCACAAATGTTCATATCAGTGGTTAGCGGGCCGCTTGATGCAGCATTTGGGGGCGGTAACTTGCCAGCCTTTG
TATTGGGCTCCATCGTGGCTGCCGTTAGCGCTTTATTGGCAATTTTCGCCCTTCCAAATCCACCACAACAAGTGTCTCTC
AGTCCTGTAATGGGTGGAGGGCACTGA

Alignment

ORF - retro_tcac_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDGLEAPGPLWKIIVVAAIAAGVQFGWALQLSLLTPYVQTLGVPHTWAAFIWLCGPISGLLVQPIVGYN
          MEDGLEAPGPLWKIIVVAAIAAGVQFGWALQLSLLTPYVQTLGVPH.WAAFIWLCGPISGLLVQPIVGYN
Retrocopy MEDGLEAPGPLWKIIVVAAIAAGVQFGWALQLSLLTPYVQTLGVPHIWAAFIWLCGPISGLLVQPIVGYN

Parental  SDRCTSRFGRRRPFIAAGACCVAGAVFLIGFAKDIGHKAGDSLDKSTKPRAVAVFVTGFWILDVANNMLQ
          SDRCTSRFGRRRPFIAAGACCVA.AVFLIGFAKDIGHKAGDSL.K.TKPRAVAVFV.GFWILDVANNMLQ
Retrocopy SDRCTSRFGRRRPFIAAGACCVAAAVFLIGFAKDIGHKAGDSLEKNTKPRAVAVFVAGFWILDVANNMLQ

Parental  GPCRALLADLSANNHKRMRVANGWFSFFMAVGNVLGYAAGSYSNLHKIFPFTVTTACDVYCANLKTCFII
          GPCRALLADLSANNHKRMRVAN..FSFFMAVGNVLGYAAGSYSNLHKIFPFT.TTACDVYCANLKTCFII
Retrocopy GPCRALLADLSANNHKRMRVANECFSFFMAVGNVLGYAAGSYSNLHKIFPFTRTTACDVYCANLKTCFII

Parental  DILFLLLVTITAISCVKETPLSKKVMKQEEEKASTPLVGELLTAFKTLKKPMWILLLVTCLNWIAWFPFL
          .I.FLLLVTITAI..VKETPLS...MKQEEEKASTP.VGELLTAFK.LKKPMWILLLVTCLNWIAWFPFL
Retrocopy HIVFLLLVTITAIISVKETPLS---MKQEEEKASTPFVGELLTAFKSLKKPMWILLLVTCLNWIAWFPFL

Parental  LYDTDWMGREIYGGHVDGNDNQQKLYDNGVRAGALGLMINSIVLGFASLGLENIGRLVGGVKNLWGGVNF
          LYDTDWMGREIYGG.VDGN..QQKLYD.GVRAGALGLMINSIVLGF.SLGLEN.GRLVGGV.NLWGGVNF
Retrocopy LYDTDWMGREIYGGFVDGNATQQKLYDDGVRAGALGLMINSIVLGFTSLGLENVGRLVGGVTNLWGGVNF

Parental  ILAACLASTVWITKVVEAWRDTHGLLAPPSNIKGSALAVFGLLGIPLSVTFSIPFALASIYCSASGGGQG
          ILAACLASTVWITK.VEAWRD.HG.LAPP.NIKG.ALA.FGLLGIP..VT.SIPFAL.SIYCS.SGGGQG
Retrocopy ILAACLASTVWITKIVEAWRDKHGHLAPPNNIKGPALAIFGLLGIPQAVTYSIPFALTSIYCSTSGGGQG

Parental  LALGVLNMAIVIPQMFISVVSGPLDEAFGGGNLPAFVLGSIVAAISAVLAIVALPNPPKQVSLNPAMAGG
          LALGVLNM.IVIPQMFISVVSGPLD.AFGGGNLPAFVLGSIVAA.SA.LAI.ALPNPP.QVSL.P.M.GG
Retrocopy LALGVLNMSIVIPQMFISVVSGPLDAAFGGGNLPAFVLGSIVAAVSALLAIFALPNPPQQVSLSPVMGGG

Parental  H
          H
Retrocopy H

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_11 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_036702	1 retrocopy	retro_tcac_11 ,