RetrogeneDB ID: retro_sbic_16

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 4:55123884..55125084(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb04g025350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb04g025300
• Aliases: None
• Description: None

Sequence

>retro_sbic_16
ATGGCTCGCATCCTGCTCGCCGCGTTCGTGGCGCTGCTTGTCGTCGTTAGCCCGTGCCACGAAAGACCAGCGCCGGCGCC
GCAACAGGCAGCGAAAGAGAAGGTGGTGGCGGTGGACGGCATCACTGCCATCTACAACTTCGGCGACTCCCTGTCGGACA
CCGGGAACCTGCTCCGCGAAGGCGCCACGGGCATGCTGCAGCACACCACGGGTCTTCCCTACGGGTCCGCCATCGGCGGC
GCCACCGGCCGATGCTCCGACGGGTACCTCATGATAGATTACCTCGCGAAGGATCTCGGCTTGCCTCTGCTGAACCCGTA
CCTCGACGATGGCGCCGACTTCTCGCACGGCGTCAACTTCGCCGTGGCCGGTGCCACGGCGCTCGACGCGGCGGCGCTCG
CCAGGAGAGGGGTCGCCGTCCCTCACACCAACAGCTCTCTAGGCGTCCAGCTGCAGCGGTTCAAGGACTTCATGAGCGCC
AACACACAGTCCCCGGAGGAGATCCGCGAGAAGCTGGCTCATTCCTTGGTCATGGTTGGGGAGATCGGCGGCAACGACTA
CAACTACGCCTTCTCGGCGAACAAGCCGGTGGCCGGCGGCGCGCGCAACATCTACAACTTCGGGCGCATGGCGACCGGCG
TGGCCGAGGCGATGGCGCTCGTCCCGGACGTAGTGCGTTCCGTCACGAGCGCGGCCAGAGAGCTCCTCGACATGGGCGCG
ACGCGGGTGGTGATCCCGGGCAACTTCCCGCTCGGGTGCGTGCCGAGCTACATGGCGGCGGTGAACGAGACGGACCCGGC
AGCGTACGACGCCAACGGCTGCCTGGCGGCGCTGAACCTGTTCGCCCAGATGCACAACGTGCTGCTGCAGCAGGGCATCC
GAGAGCTGCGCCGGTCCTACCCGTCGGCGACCATCTCGTACGCCGACTACTTCTACGCGTACGTGCGGATGCTGAGGGAC
GCCGGCAAGACGGGGTTCGACGAGGGGGCGCGGACCACGGCGTGCTGCGGCGCTGGCGGCGGCGCCTACAACTTCGACAT
GGACCGGATGTGCGGCGCGCCAGGCGCGTCGGTGTGCGCGAGGCCCGACGAGCGCATTAGCTGGGACGGCGTGCACCTGA
CGCAGCGCGCCAACAGCGTCATGAGCGACTTGCTCTACCACAAGGGATTCGCGTCCCCAGCGCCGGTGGAATTCCCGTGA

Alignment

ORF - retro_sbic_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.62 %
• Parental protein coverage: 95.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGRVLVVAF--LLVACSSSSSSCCPGAAAAP----TTVDGITAIYNFGDSITDTGNLIREGATGVLRYIG
          ..R.L..AF..LLV..S.......P....A.......VDGITAIYNFGDS..DTGNL.REGATG.L....
Retrocopy MARILLAAFVALLVVVSPCHERPAPAPQQAAKEKVVAVDGITAIYNFGDSLSDTGNLLREGATGMLQHTT

Parental  KLPYGIDLDLLHGPTGRCSNGYLMIDFLAKYLGLPLLNPYLDKAADFTHGVNFAVAGATALDTATLAERG
          .LPYG.......G.TGRCS.GYLMID.LAK.LGLPLLNPYLD..ADF.HGVNFAVAGATALD.A.LA.RG
Retrocopy GLPYG---SAIGGATGRCSDGYLMIDYLAKDLGLPLLNPYLDDGADFSHGVNFAVAGATALDAAALARRG

Parental  VTNALTNSSLDVQLAWFKDFMASATNS-NEIRRKLASSLVML-EIGGNDFNYAFQQQQTRPSDGAGYGLG
          V....TNSSL.VQL..FKDFM...T.S..EIR.KLA.SLVM..EIGGND.NYAF......P..G......
Retrocopy VAVPHTNSSLGVQLQRFKDFMSANTQSPEEIREKLAHSLVMVGEIGGNDYNYAF--SANKPVAGGARNIY

Parental  NVTRIVETLAQAGALVPPVVQSISNAAEELLEMGAVRVVIAGNFPIGCVPVYLAGANVTEPAAYDGDGCL
          N..R.....A.A.ALVP.VV.S...AA.ELL.MGA.RVVI.GNFP.GCVP.Y.A..N.T.PAAYD..GCL
Retrocopy NFGRMATGVAEAMALVPDVVRSVTSAARELLDMGATRVVIPGNFPLGCVPSYMAAVNETDPAAYDANGCL

Parental  GVLNAFAELYNARLRGAVAALQRAHPRAVVAYADYFAAYARVLREARARGFDPARTRTACCGAAAGAAYY
          ..LN.FA...N..L......L.R..P.A...YADYF.AY.R.LR.A...GFD.....TACCGA..GA..Y
Retrocopy AALNLFAQMHNVLLQQGIRELRRSYPSATISYADYFYAYVRMLRDAGKTGFDEGARTTACCGAGGGA--Y

Parental  GFDESRFCGAPGTAVCADRDRDRYVSWDGVHPTQHAYAEMAELLYRGGLAYPPPIKWP
          .FD..R.CGAPG..VCA....D...SWDGVH.TQ.A...M..LLY..G.A.P.P...P
Retrocopy NFDMDRMCGAPGASVCA--RPDERISWDGVHLTQRANSVMSDLLYHKGFASPAPVEFP

Legend:

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

Expression

RNA-Seq

Sorghum bicolor was not studied using RNA-Seq expression data.

ChIP-Seq

Sorghum bicolor was not studied using ChIP-Seq data.

EST

Sorghum bicolor was not studied using EST data.

TSS

Sorghum bicolor was not studied using FANTOM5 data.

Lab

retro_sbic_16 was not experimentally validated.

Homology

Retrocopy orthology:

Sorghum bicolor 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza nivara	ONIVA02G26140	1 retrocopy	retro_oniv_13,
Oryza glaberrima	ORGLA02G0200400	1 retrocopy	retro_ogla_1,
Oryza rufipogon	ORUFI02G24680	1 retrocopy	retro_oruf_12,
Oryza sativa japonica	OS02G0604000	1 retrocopy	retro_osat_12,
Sorghum bicolor	Sb04g025300	1 retrocopy	retro_sbic_16 ,