RetrogeneDB ID: retro_sbic_23

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:52839792..52841271(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g026250
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb04g007470
• Aliases: None
• Description: None

Sequence

>retro_sbic_23
ATGGACACGAGCGGCAACTCGCTGCCGTCCCCGTCGTGCCCCGACGGCAAGAAGCGGGAGGTGTGCTACTACTACGACGC
CGGCATCGCCAGCGTCGACTACGGCGAGGACCACAGCATGGTGCCCCGCCGAGTCGACATGGCGCACGCGCTCGTCCGCT
CCTACGGCCTGCTCCACGACATGAGGCGTCTTCGCACGAGGCCCGCCACCGTCACGGAGATTACCGGAGACTTTCATGAG
CCCGACTACGTTCGTTTGCTGCAGAACCTCACCCCGGAGAGCTTCTACGCCGGCGGCGCCACCATGAGCGCAGCGAAGGC
GCACAATATAGGCGTGCTCAAGGAAGGCGAGACTTTCTACGACAACCCTCCCATCGCCGGCCTCTGGGACTACTGCCAGC
GCTACGCCGGCGGGTCGCTGGCCGCGGCGCGCGCGCTCGGCGAAGGCAAAGCCGACATCGCCATCAACTGGTCCGGCGGC
ATGCACCACGCGTGCAAAGCGGCGGCCAGCGGCTTCTGCTTCGTCAACGACATCGTGCTCGCCATCAAGGACCTCCTCCA
CCACTTCAGGCGCGTGCTGTACGTCGACATCGACGTCCACCACGGCGACGGCGTCGAGACGGCCTTCCTCGACTCCAACC
GTGTGATGACAGTGTCGTTCCACCAGCGCACCAAGAATTTCTTCCCGGAGGAAAGGGGACACGTCAACCACGTCGGCGAA
GGGGCCGGTCTGTACCGTGCTTTGAACGTGCCGTTCATGGAGGGCGTCGGCGACGAGGGGTACTGCGAGATGTTCAAGGC
CATCATGAAAAGGGTCGTCGACGTGTTCCAGCCGGAGGCCATCGTGATGCAGTGCGGCAGCGACTCGCTCTCCGGCGACA
GGCTCGGCCAGCTTAACCTGTCCATCGCCGGCCACGCCCAGTGCGTCAGCTACATGCGGAGCTTCAACTTGCCGCTGCTC
CTTCTCGGCGGCGGCGGATACACCGTCAACCACGTCGCCGCCTGCTGGTGCTACGAGACGGCGGTGGCCATCGGCAAGGA
GATCGACGACAACATACCGGTGCACTGCTACGACACCTACTACAGTGGCCAAGGCTACAAGCTCCATTACCCGGTGGACA
AGCAACTCAAGAACGAAAACAAGAGAAGCTACCTAGAACGCACGATGACCGCGGTCCTAGAGAACCTCTCCCATCTCGAG
GCGGCGCCGAGCGTGCAGTTCCAGGATCCGCCCGGGCCCGGCGGAAGCGGAAGCACCAATACCGAGCCGCTATTCTACGA
ACAGGCCCCGCGAGAAGACGACGACCCCATGGAGAGGCTGCATCGGCTTTGTGGCGAGAGGGACGAGCGCTGCTTCTTCA
GAGAGTTGGGAAAGAAGCGACAGGTAGCCAAGGATAGAGAAAATGGCGGTCATCACCAAACGTCTCGGCCCGAACCGGTC
AAAAAGTACCGACACGAAAAGTTCCATTTTAAATGTTGA

Alignment

ORF - retro_sbic_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.33 %
• Parental protein coverage: 57.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRLLKRFNVGEDCPVFDGLYSFCQTYAGASVGGAVKLNHGH-DIAINWSGGLHHAKKCEASGFCYVNDIV
          I..LK......D.P...GL...CQ.YAG.S...A..L..G..DIAINWSGG.HHA.K..ASGFC.VNDIV
Retrocopy IGVLKEGETFYDNPPIAGLWDYCQRYAGGSLAAARALGEGKADIAINWSGGMHHACKAAASGFCFVNDIV

Parental  LAILELLKHHERVLYVDIDIHHGDGVEEAFYTTDRVMTVSFH-KFGDYFPGT-GDIRDIGHSKGKYYSLN
          LAI..LL.H..RVLYVDID.HHGDGVE.AF....RVMTVSFH......FP...G.....G...G.Y..LN
Retrocopy LAIKDLLHHFRRVLYVDIDVHHGDGVETAFLDSNRVMTVSFHQRTKNFFPEERGHVNHVGEGAGLYRALN

Parental  VPLDDGIDDESYQSLFKPIMGKVMEVFRPGAVVLQCGADSLSGDRLGCFNLSIRGHAECVRYMRSFNVPL
          VP...G..DE.Y...FK.IM..V..VF.P.A.V.QCG.DSLSGDRLG..NLSI.GHA.CV.YMRSFN.PL
Retrocopy VPFMEGVGDEGYCEMFKAIMKRVVDVFQPEAIVMQCGSDSLSGDRLGQLNLSIAGHAQCVSYMRSFNLPL

Parental  LLLGGGGYTIRNVARCWCYETGVALGQELEDKMPVNEYYEYF-GPDYTLHV-APSNMENKNTRNQLDDIR
          LLLGGGGYT...VA.CWCYET.VA.G.E..D..PV..Y..Y..G..Y.LH........N.N.R..L....
Retrocopy LLLGGGGYTVNHVAACWCYETAVAIGKEIDDNIPVHCYDTYYSGQGYKLHYPVDKQLKNENKRSYLERTM

Parental  SKLLDNLSKLRHAPSVQFQE
          ...L.NLS.L..APSVQFQ.
Retrocopy TAVLENLSHLEAAPSVQFQD

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_23 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ostreococcus lucimarinus	OSTLU_119545	1 retrocopy	retro_oluc_1,
Sorghum bicolor	Sb04g007470	1 retrocopy	retro_sbic_23 ,