RetrogeneDB ID: retro_sita_11

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 9:36929791..36931228(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si038716m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si021921m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_11
ATGGTGCTCGCGCAGCTGGGCGGTAGCATCGCCAGCACGCTGGCGCGGATGAGCCAGGCCACCGTCGTGGACGACAAGGC
GCTCGCGGACTGCCTCAACGAGGTCTCCCGCGCGCTCCTGCAGGCCGACGTCCGCTTCGAGACGGTCCGCGACGTCAAGG
CCGCCATTAAGAGCGCCGCCAACCTCGCCGCGCTCGCCCCGGGCACCGACAGGCGCCGCGTCATACGGAAGGCCGTCGTG
GGCGAGCTCTGCAGGATGCTGGATCCGGGGAAGCAGTCCTTCACCCCCAGCAAAGGGAAGCCCGGCGTCGTCATGTTCGT
CGGCCTGCAGGGTTCCGGAAAAACCACCACCTGCACCAAGTACGCGGATTACTACCGGCGCAAGGGGTTCAGCCCTGCAC
TTGTCTGCGCCGATACATTCCGAGCCGGTGCTTTTGATCAGCTGAAACAGAACGCGTCGAAGGCCAAGATCCCGTTCTAC
GGGAGCTACACCGAGTCAGATCCTGTGAAAATTGCCGTCGAGGGTGTGGACAGATTCAAAAAAGAAAAGTGCGATCTCAT
TATCGTTGATACAAGCGGACGCCACAAGCAGGAAGCTGCTCTCTTTGAAGAGATGCGCCAGGTTTTGGAAGCTACGAAAC
CGGACCTGGTGATATTCGTGATGGATGGCAGCATTGGTCAGGGTGCGTTTGATCAGGCGCAAGCGTTCAAGCAGAGTGCT
TCAGTTGGCGCTGTGATTGTTACGAAGATGGATGGCCATGCGAGAGGCGGGGGCGCACTCAGCGCGGTTGCAGCTACGAA
AAGCCCGGTCATATTCATCGGAACCGGAGAGCATGTTCAGGACTTTGAGGCTTTCGATGTGAGACCGTTTGTTAATCGCC
TGCTTGGCATGGGAGACTTGTCTGGCCTGATGGACAAGATCCAGGATGTTGTGCCTGCTGATGACATTACGCCGGACCTG
ATTGGAGGACCCTTCACTCTCAAAGTTATGTACCAGTTGTTCCAGAGTATCCAGAATATGGGTCCTCTTGGGCAGCTCGT
TTCTATGATACCTGGGTTTAGTGCCCAGTTCATCGAAAAGGGGATGGAAAAGGAAGGCCAAGCGAAGATTAAGAGGTACA
TGACGACCATGGACTCCATGACTGAAAAGGAGCTTGAAAGCACGAACCCGAAGCTGATGAACGAGTCGCGGATCACCCGT
ATCGCTCGTGGATCTGGCAGGCTCGCGAAGGAGGTGGTGGACATGCTGGAGGAGCACAAGCGAATGGCCAAAATGTGGAG
CAAATTGCCGCTCGATAAGAGGAGACTAAATACGAACAACCGTGACTCAATAAAGAATTTAGTCAATGTTATCCCTCCGA
ATATGCTGAATCAGCTGGGTGGCCTGAATGGGCTGCAGAATATGCTGAAACAGATGGGGGGACTCGAAAGAAGATGA

Alignment

ORF - retro_sita_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.76 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLAQLGGSIAGALARMGKATVVDEKVLAECLNEISRALLQADVRFETVRDVKANIKTTANLDALAAGTD
          MVLAQLGGSIA..LARM..ATVVD.K.LA.CLNE.SRALLQADVRFETVRDVKA.IK..ANL.ALA.GTD
Retrocopy MVLAQLGGSIASTLARMSQATVVDDKALADCLNEVSRALLQADVRFETVRDVKAAIKSAANLAALAPGTD

Parental  KRRVIQKAVVGELCRMLDPGKPSFTPSKGKPSVVMFVGLQGSGKTTTCTKYADYYRRKGFSPALVCADTF
          .RRVI.KAVVGELCRMLDPGK.SFTPSKGKP.VVMFVGLQGSGKTTTCTKYADYYRRKGFSPALVCADTF
Retrocopy RRRVIRKAVVGELCRMLDPGKQSFTPSKGKPGVVMFVGLQGSGKTTTCTKYADYYRRKGFSPALVCADTF

Parental  RAGAFDQLKQNASKAKIPFYGSYIESDPVKIAVEGVDRFRKEKCDLIIVDTSGRHKQEAALFEEMRQVSE
          RAGAFDQLKQNASKAKIPFYGSY.ESDPVKIAVEGVDRF.KEKCDLIIVDTSGRHKQEAALFEEMRQV.E
Retrocopy RAGAFDQLKQNASKAKIPFYGSYTESDPVKIAVEGVDRFKKEKCDLIIVDTSGRHKQEAALFEEMRQVLE

Parental  ATKPNLVIFVMDGSIGQAAFDQAQAFKQSASVGAVIVTKMDGHAKGGGALSAVAATKSPVIFIGTGEHIP
          ATKP.LVIFVMDGSIGQ.AFDQAQAFKQSASVGAVIVTKMDGHA.GGGALSAVAATKSPVIFIGTGEH..
Retrocopy ATKPDLVIFVMDGSIGQGAFDQAQAFKQSASVGAVIVTKMDGHARGGGALSAVAATKSPVIFIGTGEHVQ

Parental  DFEVFDVKPFVSRLLGMGDLSGLMDKIQDVMPADQLPELVDNLTGGFTLRLLYQMFQNLHSMGPLGQLFS
          DFE.FDV.PFV.RLLGMGDLSGLMDKIQDV.PAD......D...G.FTL...YQ.FQ....MGPLGQL.S
Retrocopy DFEAFDVRPFVNRLLGMGDLSGLMDKIQDVVPADDITP--DLIGGPFTLKVMYQLFQSIQNMGPLGQLVS

Parental  MIPGLSAQFIEKGKEKEGQAKIKRYMTIMDSMTEKELDNTNPKLMNESRINRIARGSGRLVKEVVDMLEE
          MIPG.SAQFIEKG.EKEGQAKIKRYMT.MDSMTEKEL..TNPKLMNESRI.RIARGSGRL.KEVVDMLEE
Retrocopy MIPGFSAQFIEKGMEKEGQAKIKRYMTTMDSMTEKELESTNPKLMNESRITRIARGSGRLAKEVVDMLEE

Parental  HKRIAKMWNKLPINNKRLNMNNRNSLKPLLNALPANMLNQLGGLNGLQNMVKQMGAQRR
          HKR.AKMW.KLP....RLN.NNR.S.K.L.N..P.NMLNQLGGLNGLQNM.KQMG...R
Retrocopy HKRMAKMWSKLPLDKRRLNTNNRDSIKNLVNVIPPNMLNQLGGLNGLQNMLKQMGGLER

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Setaria italica was not studied using RNA-Seq expression data.

ChIP-Seq

Setaria italica was not studied using ChIP-Seq data.

EST

Setaria italica was not studied using EST data.

TSS

Setaria italica was not studied using FANTOM5 data.

Lab

retro_sita_11 was not experimentally validated.

Homology

Retrocopy orthology:

Setaria italica 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Setaria italica	Si021921m.g	1 retrocopy	retro_sita_11 ,
Setaria italica	Si034718m.g	1 retrocopy	retro_sita_46,