RetrogeneDB ID: retro_sbic_41

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 2:54515751..54516825(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb02g022090
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g039890
• Aliases: None
• Description: None

Sequence

>retro_sbic_41
ATGTCGATGGCGCAGGTGTGCTGCGACTCGGCCGCAGCGGCGACGGCGGCGGCGGCACAGGTGGTTGGGGCGGAGGCGGA
GGCCAGGGCCAGGGCGCGCGCCGAGAGGCGGCGTCGGGCTGGGGAGGCCGCCGGGAGGTGGAGGCACGCGGGCGCGGCCG
CTGGTGGCACGCCCGACGCTGCCACGAGGAAGCGGAGCCTCGAGGCCGGGGAGCTGCTCGTGGCGCGCAAGCACGGCGCC
GCGTCGGTGGCCGGCCGCAGGAGGGAGATGGAGGACGCCGTGTCCGTGCGCGAGGCGTTCGCGCTCGCGGAGGGCTCCCA
CGGCGGGAGGCGCGACTTCTACGGGGTGTTCGACGGCCACGGCTGCTCGCACGTCGCCGAGGCGTGCCGGGACCGGATGC
ACGAGCTGCTCGCCGAGGAGCTCGCTGTCGCCGCCGCCGCCGACGACGTCTCCTGGACCGCGGCGATGGAGCGCAGCTTC
GCCCGGATGGACAGCGAGGTGATGTCGGCCGGCGGGGCCAGCGGCGCCTGCGGCTGCGACGCGCACAAGTGCGACCACGT
GGGTTCCACCGCCGTGGTGGCCGTCGTGGAGGAGCGGCGCGTGGTGGTGGCCAACTGCGGCGACAGCCGCGCCGTGCTGT
GCCGCGGCGGGGACGGCGCGCCGCCGGTGCCGCTGTCGTCGGACCACAAGCCCGACCGGCCCGACGAGCTGGCGCGGATC
GAGGCCGCGGGCGGGCGCGTCATCTTCTGGGAGGGCGCGCGCGTGCTGGGCGTGCTCGCCATGTCCCGCGCCATCGGGGA
CGGCTACCTCAAGCCGTACGTGTCGTCGGTGCCGGAGGTGACGGTCACCGACCGGTCCGACGGCGACGAGTGCCTCATCC
TGGCCAGCGACGGGCTGTGGGACGTGGTCAGCAACGAGGCCGCGTGCGAGGTGGCGCGCGCCTGCCTCCGCAGGGGCCGC
GCCAAGTGGTGCGCCGAGGCCGCCGCGCTGCTCACCAAGCTGGCCCTCGCCAGGCGCAGCTCCGACAACGTCTCGGTCGT
CGTCGTCGACCTCCGCCGGAGGAATCATCACTAG

Alignment

ORF - retro_sbic_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.58 %
• Parental protein coverage: 52.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FFGVFDGHGCSHVATSCGQRMHQIVAEEATAAAGSSASDDAARWRDVMEKSYSRMDAEAVGSRDTAGPAP
          F.GVFDGHGCSHVA..C..RMH...AEE...AA...A.DD...W...ME.S..RMD.E........G...
Retrocopy FYGVFDGHGCSHVAEACRDRMHELLAEELAVAA---AADDVS-WTAAMERSFARMDSEVMSAGGASG---

Parental  TCRCEMQLPKCDHVGSTAVVAVVGPRHLVVANCGDSRAVLCSGGAA---IPLSDDHKPDRPDELERIHAA
          .C.C.....KCDHVGSTAVVAVV..R..VVANCGDSRAVLC.GG......PLS.DHKPDRPDEL.RI.AA
Retrocopy ACGCDAH--KCDHVGSTAVVAVVEERRVVVANCGDSRAVLCRGGDGAPPVPLSSDHKPDRPDELARIEAA

Parental  GGRVIFWDGARVFGMLAMSRAIGDSYLKPFVISDPEVRVVERKDGEDEFLILASDGLWDVVSNEVACKVV
          GGRVIFW.GARV.G.LAMSRAIGD.YLKP.V.S.PEV.V..R.DG.DE.LILASDGLWDVVSNE.AC.V.
Retrocopy GGRVIFWEGARVLGVLAMSRAIGDGYLKPYVSSVPEVTVTDRSDG-DECLILASDGLWDVVSNEAACEVA

Parental  RTCLR
          R.CLR
Retrocopy RACLR

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_41 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
Hordeum vulgare	MLOC_56081	1 retrocopy	retro_hvul_16,
Oryza punctata	OPUNC03G11550	1 retrocopy	retro_opun_31,
Oryza sativa japonica	OS03G0268600	1 retrocopy	retro_osat_49,
Sorghum bicolor	Sb01g039890	1 retrocopy	retro_sbic_41 ,
Setaria italica	Si036015m.g	1 retrocopy	retro_sita_14,