RetrogeneDB ID: retro_tcac_22

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 10:4122505..4124725(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_046956
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_004565
• Aliases: None
• Description: None

Sequence

>retro_tcac_22
ATGAATCGCAAGATTATTGGATTAGAAGAGGGATTGGGTTATATGCAGGATGGGATCACAAAGATTGAGAGGATTTTGGA
AGGTCGGCCAGAGCCGCCATTTAACTCAGAAGAATACATGAAGCTTTACACGACTATCTACAACATGTGTCTTCAAACGC
CTCCTGATGATCATACTCAGCAGCTTTACGACAAGTACCGACAGGCAATACAAGGGTATATTACTTCGACGGTATTGCCA
TCTATAAGAGCGAAGCACGATGAGTTCATGCTGAAGGAGCTTGTTAAGAGATGGGCCAACCATAAAGTAATGCTCAGGTG
GCTATCACACCTCTTCTATTACCTTGATCGCCACTTGATTGCCTGTAGATCACTTCCTTCTCTTAAAGAAGTTGGGCTGC
TCTACTTCCGTGATCTGGTATATCGGGACGTGCATGTCAAAGTCAGAGATGCTGTAATTACTCTTATTGATAAAGAACGT
GAGGGAGAGCAGGTAGACCGAGCGTTATTGAAGAATGTGTTGGATTTTTTTGTTGAGATTGGGATGGGACAGATGAACCG
TTATGAAGAAGATTTTGAAGCACACATGCTTCAGGACACTGGTGCTTACTATTCACGTAAGGCATCAAACTGGATTCTGG
AAGATTCTTGTCCAGATTACATGTTGAAGTCTGAAGAGTGCTTGAAGAAGGAAAGGGACAGAGTGGGTCATTACCTGCAT
TCAAGTAGTGAGACAAAATTGTCAGAGAGAGCGCAACATGAGTTGTTGGTGACGCATGTTAATCAGCTACTTGATAAGGA
GCATTCTGGATGCAGGGTCTTGCTTAGAGATGACAAGGTGGAGGATCTTTCCAGGATGTACAGGCTTTATAGTAAAATAC
CTCTAGGCTTGAAACTTGTTGCTGATATATTCAAGCAGCATATTACTGCTGAGGGTATAGCTTTGGTTCAACAGGCGGAA
GATGCTGCAAGTAGCAAAGCCTCAAATGCTGCAGCTGGAGTGCAGGAACAGGTCCTTATCAGGAAAATAATCGAGCTGCA
CGACAAGTATGTGGAGTACGTGACTGATTGTTTTGAAAACCATGCTCTGTTCCACAAGGCCTTGGAAGAGGCTTTCGAGG
TAGTTTGCAACGAAACTGTTGCTGGCAGCTCAAGTGCGGAGCTTTTGACAACTTTCTGTGATAATGTCCTCAAGAAGAGT
GGAAGTGAGAAATTAAGTGATGAAGCCATTGAAGAAACACTTGAGAAGGTAGTTAAGCTGCTTGCCTATATCAGTGATAA
AGACCTCTTTGCCGAATTCTACAGAAAGACGCTTGCTCGGCGTCTGCTTTTTGACCGCAGTGCTAATGACGATCGCGAAA
GGAGTATTCTGACTAAGCTAAAGCAGCAACGTGGTGGACAGTTCACTTCGAAGATGGAGGGCATGGTCACAGATTTGACA
TTGGCAAGAGAAAACCAGGCCAACTTTGAGGACTATCTTAGGAGTAACTCAGCTGCACGTCCTGGGATTGATTTAACAGT
TACTGTTCTTACCACAGGATTCTGGCCAAGTTACAAATCATCTGATCTCAATCTCCCTGCTGAGATGGTCAAGTGCGTAG
AAGTTTTCAAAGGGTTTTATGAAACAAAAACAAAACACAGAAAGCTGACATGGATATACTCACTGGGAACCTGCCACATT
AGTGGCAAGTTCGAGCAAAAAACTATTGAACTGATTGTCTCAACTTACCAGGCTGCTGTCCTCCTGCTTTTCAATGCTTC
TGATCGTCTGAGCTATTCTGAGATCATGGCTCAGTTGAACTTGACCCATGATGACTTGGTCAGATTACTACATTCGCTGT
CATGTGCCAAGTACCAGATTCTAAGTAAAGAGCCGAACACAAAAACCATCTCCCAAAGTGACTACTTTGAGTTCAACTCT
AAGTTCACGGACAAGCTGAGGAGGATTAAGATCCCTCTCCCTCCGGTGGATGAAAGGAAGCAAGTTGTGGATGATGTCGG
TAAACAACGGCGTTACGCTATCGATGCTGCAATTGTGCGCGTAATGAAGAGTCGGAAAGTTCTGGGCTACCAACAGTTGG
TCTCAGAGTGTGTTGAGCAGTTGAGTCGGATGTTCAAGCCTGACATTAAAGCCATCAAGAAGCAGATTGAAGACCTCATC
ACACAAGAATATCTGGAGAGAGACAAGGAGAACGCAAACATGTTTAAGTACTTAGCCTAA

Alignment

ORF - retro_tcac_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERKTIDLDQGWDYMQKGITKLKRILEGLPEPPFSSEEYMMLYTTIYNMCTQKPPHDYSQQLYDKYREAF
          M.RK.I.L..G..YMQ.GITK..RILEG.PEPPF.SEEYM.LYTTIYNMC.Q.PP.D..QQLYDKYR.A.
Retrocopy MNRKIIGLEEGLGYMQDGITKIERILEGRPEPPFNSEEYMKLYTTIYNMCLQTPPDDHTQQLYDKYRQAI

Parental  EEYITSTVLPSLRERHDEFMLRELVKRWANHKIMVRWLSRFFHYLDRYFIARRSLPALNEVGLTCFRDLV
          ..YITSTVLPS.R..HDEFML.ELVKRWANHK.M.RWLS..F.YLDR..IA.RSLP.L.EVGL..FRDLV
Retrocopy QGYITSTVLPSIRAKHDEFMLKELVKRWANHKVMLRWLSHLFYYLDRHLIACRSLPSLKEVGLLYFRDLV

Parental  YNDVHVKVRDAVITLIDKEREGEQIDRALLKNVLDIFVEIGMGLMDRYEEDFEAHMLQDTGAYYSRKASN
          Y.DVHVKVRDAVITLIDKEREGEQ.DRALLKNVLD.FVEIGMG.M.RYEEDFEAHMLQDTGAYYSRKASN
Retrocopy YRDVHVKVRDAVITLIDKEREGEQVDRALLKNVLDFFVEIGMGQMNRYEEDFEAHMLQDTGAYYSRKASN

Parental  WILEDSCPDYMLKSEECLKKERDRVSHYLHSSSETKLSEKVQHELLVMHANQLLDKEHSGCRALLRDDKV
          WILEDSCPDYMLKSEECLKKERDRV.HYLHSSSETKLSE..QHELLV.H.NQLLDKEHSGCR.LLRDDKV
Retrocopy WILEDSCPDYMLKSEECLKKERDRVGHYLHSSSETKLSERAQHELLVTHVNQLLDKEHSGCRVLLRDDKV

Parental  EDLSRMYRLYCKIPRGLDPVANIFKQHITAEGTALVQQAEDAASNQASNAA-GVQEQVLIRKIIELHDKY
          EDLSRMYRLY.KIP.GL..VA.IFKQHITAEG.ALVQQAEDAAS..ASNAA.GVQEQVLIRKIIELHDKY
Retrocopy EDLSRMYRLYSKIPLGLKLVADIFKQHITAEGIALVQQAEDAASSKASNAAAGVQEQVLIRKIIELHDKY

Parental  MTYVTDCFQNHTLFHKALKEAFEVFCNKTVAGSSSAELLATFCDNILKKGGSEKLSDEAIEETLEKVVKL
          ..YVTDCF.NH.LFHKAL.EAFEV.CN.TVAGSSSAELL.TFCDN.LKK.GSEKLSDEAIEETLEKVVKL
Retrocopy VEYVTDCFENHALFHKALEEAFEVVCNETVAGSSSAELLTTFCDNVLKKSGSEKLSDEAIEETLEKVVKL

Parental  LAYISDKDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTSKMEGMVTDLTLARENQASFE
          LAYISDKDLFAEFYRK.LARRLLFDRSANDD.ERSILTKLKQQ.GGQFTSKMEGMVTDLTLARENQA.FE
Retrocopy LAYISDKDLFAEFYRKTLARRLLFDRSANDDRERSILTKLKQQRGGQFTSKMEGMVTDLTLARENQANFE

Parental  DYLRSNSAAHPGIDLTVTVLTTGFWPSYKSFDLNLPAEMVKCVEVFKGFYETKTKHRKLTWIYSLGTCHI
          DYLRSNSAA.PGIDLTVTVLTTGFWPSYKS.DLNLPAEMVKCVEVFKGFYETKTKHRKLTWIYSLGTCHI
Retrocopy DYLRSNSAARPGIDLTVTVLTTGFWPSYKSSDLNLPAEMVKCVEVFKGFYETKTKHRKLTWIYSLGTCHI

Parental  NGKFEQKTIELIVSTYQAAVLLLFNASDRLSYSEIMAQLNLTHDDLVRLLHSLSCAKYKILSKEPNTKTI
          .GKFEQKTIELIVSTYQAAVLLLFNASDRLSYSEIMAQLNLTHDDLVRLLHSLSCAKY.ILSKEPNTKTI
Retrocopy SGKFEQKTIELIVSTYQAAVLLLFNASDRLSYSEIMAQLNLTHDDLVRLLHSLSCAKYQILSKEPNTKTI

Parental  SQSDYFEFNSKFTDKLRRIKIPLPPVDERKKVVEDVDKDRRYAIDAAIVRIMKSRKVLGHQQLVSECVEQ
          SQSDYFEFNSKFTDKLRRIKIPLPPVDERK.VV.DV.K.RRYAIDAAIVR.MKSRKVLG.QQLVSECVEQ
Retrocopy SQSDYFEFNSKFTDKLRRIKIPLPPVDERKQVVDDVGKQRRYAIDAAIVRVMKSRKVLGYQQLVSECVEQ

Parental  LSRMFKPDIKAIKKRMEDLITRDYLERDKDNANMFRYLA
          LSRMFKPDIKAIKK..EDLIT..YLERDK.NANMF.YLA
Retrocopy LSRMFKPDIKAIKKQIEDLITQEYLERDKENANMFKYLA

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_22 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo01031s010	1 retrocopy	retro_bole_8,
Prunus persica	PRUPE_ppa001948mg	1 retrocopy	retro_pper_19,
Theobroma cacao	TCM_004565	1 retrocopy	retro_tcac_22 ,