RetrogeneDB ID: retro_sbic_27

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:11199020..11200358(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g010340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb04g028050
• Aliases: None
• Description: None

Sequence

>retro_sbic_27
ATGGCCGCCGCCTGCTACTACCCAGCGCGCATCATGATCTCCTGCTCAGCCACCACCACCACCACCTCGTCGTCGCCGTC
AGCGCGCCCGCTGCGCGTGGCCGTAGTGGGGGGCGGCCCCGCGGGCGCGTCGGCCGCCGAGGCGCTGGCCTCGGCGGGGG
CCCGGACGTTCCTCCTCGAGCGCAGCCCCGCGGGTGCCAAGCCCTGCGGCGGCGCCATTCCGCTGTGCATGCTCGACGAG
TTCGCCATCCCGCGGGACCTCGTGGACCGCCGCGTCACCCGGATGCGCGTCGTCTCCCCCTCCAACCTCGCCGCCGACTT
CTCCCGCGCGCTGCCCCCCGGGGCGCACATCCCCATGCTCCGCCGCGAGGTGCTCGACTCCTTCCTCCGCCGCCGCGCCG
CCGAGGCCGGCGCCGAGCTAGTCCCGGGTCTCGTCACCTCGCTCTCGCTCCCCGCGGGGCCCGCCGACCCCTACCTCGTC
CACTACATCTCGTCCTCCTCCCCAGAGGGCGCGGGGCGGGGGGTGCTGGAGGTGGACGCCATCGTCGGCGCGGACGGCGC
CAACAGCCGCGTGGCGCGCGAGGTCGGGGCCGGGGACTACACGACGGCCATCGCGTTCCAGGAGCGCATCCGCCTTCCCG
ACGCCGCCATGGGGTACTACGACGACCTCGCCGAGATGTACGTGGGCGGGGACGTGTCCCCGGACTTCTATGGCTGGGTG
TTCCCCAAGTGCGACCACGTCGCCGTCGGGACGGGGACCGTCGCCGCCAAGCCGGAGATCAAACGCCTCCAGTCGGGCAT
CCGGGCGCGCGCGGGCCCCAAGATCGCCGGCGGCCGCGTGGTCAAGGTGGAGGCTCACCCGATCCCGGAGCACCCGCGCC
CGCGCCGCGTCGTGGGGCGCGTGGCCCTGGTCGGCGACGCGGCGGGGTACGTCACGCGGTGCTCCGGCGAGGGCATCTAC
TTCGCGGCCAAGTCCGGGCGGCTGTGCGGGCAGGCCATGGCGGAGGAGTGGGCGCGCACGGGCGCCGTGACGGAGGCCGG
GCTGAGGCGCGGCTACCTGCGGCGTTGGGACGACGAGTTCCTGCTCATGTTCCGGTTCCTCGACCTGTTGCAGCGCGTGT
TCTACGGCGGGAACGCCGGCCGCGAGGCGCTGGTGGAGATGTGCGCCGACGAGTACGTGCAGCGGCGGACCTTCGAAAGC
TACCTGTACAAGCGGATGGTGCCCGGCGAGCCGTGGGGCGACCTCCGGCTGCTGTGGCGGACGGTGGCCAGTATGGTGCG
CTGCGGCGTCATCGGCAGGGAGGTGGAGCGCCTGCGACGCCTGGAGCTGCAAGGCTAG

Alignment

ORF - retro_sbic_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.97 %
• Parental protein coverage: 94.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARMVVTRAAASSP--KLPNGRRLRVAVVGGGPAGGAAAEALAKGGVETVLIERKMDNCKPCGGAIPLCMV
          AR......A........P..R.LRVAVVGGGPAG..AAEALA..G..T.L.ER.....KPCGGAIPLCM.
Retrocopy ARIMISCSATTTTTSSSPSARPLRVAVVGGGPAGASAAEALASAGARTFLLERSPAGAKPCGGAIPLCML

Parental  SEFDLPLDLVDRKVRKMKMISPSNVAVDIGRTLAPHEYIGMVRREVLDAYLRSRAQSAGAEVVNGLFLRY
          .EF..P.DLVDR.V..M...SPSN.A.D..R.L.P...I.M.RREVLD..LR.RA..AGAE.V.GL....
Retrocopy DEFAIPRDLVDRRVTRMRVVSPSNLAADFSRALPPGAHIPMLRREVLDSFLRRRAAEAGAELVPGLVTSL

Parental  EAPKEPNGSYVVHYNHYDSSNGKIGGEKRSFEVDAIVGADGANSRVAKDMGAGDYEYAIAFQERVKIPDD
          ..P..P...Y.V...HY.SS....G......EVDAIVGADGANSRVA...GAGDY..AIAFQER...PD.
Retrocopy SLPAGPADPYLV---HYISSSSPEGAGRGVLEVDAIVGADGANSRVAREVGAGDYTTAIAFQERIRLPDA

Parental  KMVYYEERAEMYVGDDVSPDFYGWVFPKCDHVAVGTGTVTHKADIKKFQAATRLRAKDKIEGGKIIRVEA
          .M.YY...AEMYVG.DVSPDFYGWVFPKCDHVAVGTGTV..K..IK..Q...R.RA..KI.GG....VEA
Retrocopy AMGYYDDLAEMYVGGDVSPDFYGWVFPKCDHVAVGTGTVAAKPEIKRLQSGIRARAGPKIAGGRVVKVEA

Parental  HPIPEHPRPKRVSGRVTLVGDAAGYVTKCSGEGIYFAAKSGRMCAEAIVAGSANGTRMVEESDLRKYLAE
          HPIPEHPRP.RV.GRV.LVGDAAGYVT.CSGEGIYFAAKSGR.C..A.....A......E....R.YL..
Retrocopy HPIPEHPRPRRVVGRVALVGDAAGYVTRCSGEGIYFAAKSGRLCGQAMAEEWARTGAVTEAGLRRGYLRR

Parental  FDRLYWPTYKVLDILQKVFYRSNAAREAFVEMCADDYVQKMTFDSYLYKRVVPGNPLDDIKLAVNTIGSL
          .D.........LD.LQ.VFY..NA.REA.VEMCAD.YVQ..TF.SYLYKR.VPG.P..D..L...T..S.
Retrocopy WDDEFLLMFRFLDLLQRVFYGGNAGREALVEMCADEYVQRRTFESYLYKRMVPGEPWGDLRLLWRTVASM

Parental  VRATALRREMEKV
          VR.....RE.E..
Retrocopy VRCGVIGREVERL

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_27 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G59430	1 retrocopy	retro_bdis_46,
Zea mays	GRMZM2G105644	1 retrocopy	retro_zmay_29,
Oryza meridionalis	OMERI02G30980	1 retrocopy	retro_omer_17,
Oryza nivara	ONIVA06G04710	1 retrocopy	retro_oniv_24,
Oryza punctata	OPUNC02G29860	1 retrocopy	retro_opun_22,
Oryza rufipogon	ORUFI02G34000	1 retrocopy	retro_oruf_42,
Oryza sativa japonica	OS02G0744900	1 retrocopy	retro_osat_44,
Sorghum bicolor	Sb04g028050	1 retrocopy	retro_sbic_27 ,
Triticum aestivum	Traes_6DL_0FF72D765	1 retrocopy	retro_taes_28,