RetrogeneDB ID: retro_sbic_39

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:69293016..69295019(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g041830
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb04g001140
• Aliases: None
• Description: None

Sequence

>retro_sbic_39
ATGGCGGCTCGAGGAGGGTGGACGAAGTTGCTGTTTGCGCTGCTGGTCGCCGGGCTGCTTCCCGTCGTGGCTCCGACGAG
GACCTACGCAGCAGCGGCCGCTGAAGGAGGAGGTGCTCGCGGCACCGTGATCGGCATCGACCTGGGCACCACCTACTCGT
GCGTCGGCGTCTACCGGAACGGCCGCGTCGAGATCATCGCCAACGACCAGGGCAACCGGATCACGCCCTCATGGGTCGCC
TTCACCGACGGCGGCGAGCGCCTCATCGGCGAGGCCGCCAAGAACCAGGCGGCGGCCAACCCAGAGCGCACCATCTACGA
CGCCAAGCGGCTTATCGGTCGCCAGTTCGACGACGCCGTGGTGCAGCGGGACATGAAGCTGCTCTCCTACGACGTCGTCG
AGAGGAACGGGAAGCCGCACGTGCGGGTCCAGGTGAGGGAAGGCGACGTGCGCGAGTTGAGCCCCGAGGAGGTCAGCGCC
ATGGTGCTCACCAAGATGAAGGAGACGGCCGAGGCCTACCTCGGCGAGAAGGTCACGGACGCCGTCGTCACCGTCCCGGC
CTACTTCGACGACGCGCAGCGCCAGGCCACCAAGGACGCTGGCACCATCGCCGGGCTCAACGTGCGCCGCATAATCAACG
AGCCCACCGCGGCAGCCATCGCCTACGGCATCGACGACAAGGGCCCGGAGAAGAAGGTGCTCGTGTTCGACCTCGGCGGC
GGCACGTTCGACGTCAGCATCCTTGCCATCGACAACGGCGTCTTCGAGGTGCTCGCCACCAACGGCGACACCCACCTCGG
AGGCGAGGACTTCGACCAGCGCGTCATGGATTACTTCATCAAGCTCATCAAGCGCAGGCACGGCCGGGATATCTCCGGCG
ACGCCCGCGCGCTAGGGAAGCTCCGGCGCGAGTGCGAGCGCGCCAAGCGCGCGCTCAGCAACCAGCACCAGGTGCGCGTG
GAGATCGAGGCGCTCTTCGACGGCGTCGACATCTCGGAGCAGCTCACCAGGGCGCGCTTCGAGGAGCTCAACAGCGACCT
GTTCCGGAAGACGATGGTGCCGGTGAAGAAGGCCATGGCGGACGCCCGGCTGCAGAAGAGCGACATCGACGAGATCGTGC
TCGTCGGCGGTAGCACCAGGATCCCCAAGGTCCAGCAGCTGCTCAAGGACTATTTCAACGGCAAGGAGCCCAGTAGGGGA
ATCAACCCCGACGAGGCCGTCGCGTACGGCGCCGCCGTCCAGGGTGGTATCCTCAGTGGGCACGGCGAAAGTATGCTTGT
CATCGACGTTACGCCACTGACTCTGGGCATAGAGACCGTGGGTGGGGTGATGACCAAGCTGATCCCGAGGAACACGGTGA
TTCCGACGAAGAAGACGCAGGTGTTCACCACGTACCAGGACAGGCAGACCACAGTGAGCATCATGGTGTTCCAGGGCGAG
CGCAGCATGACCAAGGACAACGAGCTGCTCGGCAAGTTTGACCTGTCTGGGATCCCACCGGCGCCAAAGGGCACGCCGCA
GATCGAGGTGACCTTCGAGGTGGACGTGAACGGCATCCTCCACGTGAAGGCGGCGGACAAGGGCACCGGCAGGTCGGAGA
AGGTCACCATCACGAGCGACGCCCGCCGGGTCAGCCAGGAGGAGATGGACCGGATGGTGCACGAGGCGGAGGAGTTCGCG
GAGGAGGACCGGAAGGCGAGGGAGCGGGTCGACGCGCGCAACAAGCTGGAGACGTACGTCTACCAGGTGAAGAGCGCGGT
GGTGGACGACAGCAACATGGCCGACAAGATGAACGCCGACGAGAAGGAGAAGGTGGAGGAGGCAGTCAGGGAGGCCAACG
AGTGGATCGAAGTGAACTCGGATGCCGACAAGGAGGACTACGAGGAGAAGCTCAAGGAGCTAGAGGACGTGTGCAGCCCT
GTCATCTCGGCGGTGTACCAGAGGTCCGGCGGTGGTGCACCGGCAGACGACACTTACGATGAGGATGACCATGATGAGCT
TTA

Alignment

ORF - retro_sbic_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.34 %
• Parental protein coverage: 95.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTVIGIDLGTTYSCVGVYKNGHVEIIANDQGNRITPSWVAFTDS-ERLIGEAAKNQAAVNPERTIFDVKR
          GTVIGIDLGTTYSCVGVY.NG.VEIIANDQGNRITPSWVAFTD..ERLIGEAAKNQAA.NPERTI.D.KR
Retrocopy GTVIGIDLGTTYSCVGVYRNGRVEIIANDQGNRITPSWVAFTDGGERLIGEAAKNQAAANPERTIYDAKR

Parental  LIGRKFEDKEVQRDMKLVPYKIINKDGKPYIQVKIKDGENKVFSPEEISAMILGKMKDTAEAYLGKKIND
          LIGR.F.D..VQRDMKL..Y......GKP...V....G.....SPEE.SAM.L.KMK.TAEAYLG.K..D
Retrocopy LIGRQFDDAVVQRDMKLLSYDVVERNGKPHVRVQVREGDVRELSPEEVSAMVLTKMKETAEAYLGEKVTD

Parental  AVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKGGEKNILVFDLGGGTFDVSILTI
          AVVTVPAYF.DAQRQATKDAG.IAGLNV.RIINEPTAAAIAYG.D.KG.EK..LVFDLGGGTFDVSIL.I
Retrocopy AVVTVPAYFDDAQRQATKDAGTIAGLNVRRIINEPTAAAIAYGIDDKGPEKKVLVFDLGGGTFDVSILAI

Parental  DNGVFEVLATNGDTHLGGEDFDQRIMEYFIKLIKKKYSKDISKDNRALGKLRREAERAKRALSNQHQVRV
          DNGVFEVLATNGDTHLGGEDFDQR.M.YFIKLIK.....DIS.D.RALGKLRRE.ERAKRALSNQHQVRV
Retrocopy DNGVFEVLATNGDTHLGGEDFDQRVMDYFIKLIKRRHGRDISGDARALGKLRRECERAKRALSNQHQVRV

Parental  EIESLFDGTDFSEPLTRARFEELNNDLFRKTMGPVKKAMEDAGLQKSQIHEIVLVGGSTRIPKVQQLLRD
          EIE.LFDG.D.SE.LTRARFEELN.DLFRKTM.PVKKAM.DA.LQKS.I.EIVLVGGSTRIPKVQQLL.D
Retrocopy EIEALFDGVDISEQLTRARFEELNSDLFRKTMVPVKKAMADARLQKSDIDEIVLVGGSTRIPKVQQLLKD

Parental  YFDGKEPNKGVNPDEAVAFGAAVQGSILSGEGGDETKDILLLDVAPLTLGIETVGGVMTKLIPRNTVIPT
          YF.GKEP..G.NPDEAVA.GAAVQG.ILSG.G.......L..DV.PLTLGIETVGGVMTKLIPRNTVIPT
Retrocopy YFNGKEPSRGINPDEAVAYGAAVQGGILSGHG----ESMLVIDVTPLTLGIETVGGVMTKLIPRNTVIPT

Parental  KKSQVFTTYQDQQTTVSIQVFEGERSMTKDCRLLGKFDLSGIPPAPRGTPQIEVTFEVDANGILNVKAED
          KK.QVFTTYQD.QTTVSI.VF.GERSMTKD..LLGKFDLSGIPPAP.GTPQIEVTFEVD.NGIL.VKA.D
Retrocopy KKTQVFTTYQDRQTTVSIMVFQGERSMTKDNELLGKFDLSGIPPAPKGTPQIEVTFEVDVNGILHVKAAD

Parental  KGTGKSEKITITNEKGRLSQEEIDRMVKEAEEFAEEDKKVKERIDARNQLETYVYNMKNTVGDKDKLADK
          KGTG.SEK.TIT....R.SQEE.DRMV.EAEEFAEED.K..ER.DARN.LETYVY..K..V.D....ADK
Retrocopy KGTGRSEKVTITSDARRVSQEEMDRMVHEAEEFAEEDRKARERVDARNKLETYVYQVKSAVVDDSNMADK

Parental  LEAEEKEKVEEALKEALEWLDDNQSAEKDEYVEKLKEVEAVCNPIVSAVYQRSGGAPGGGDDSEGGVDDD
          ..A.EKEKVEEA..EA.EW...N..A.K..Y.EKLKE.E.VC.P..SAVYQRSGG.....D.......DD
Retrocopy MNADEKEKVEEAVREANEWIEVNSDADKEDYEEKLKELEDVCSPVISAVYQRSGGGAPADDTYD---EDD

Parental  HDEL
          HDEL
Retrocopy HDEL

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_39 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G01477	1 retrocopy	retro_bdis_30,
Aegilops tauschii	F775_27431	1 retrocopy	retro_atau_11,
Oryza longistaminata	KN538684.1_FG046	1 retrocopy	retro_olon_13,
Hordeum vulgare	MLOC_55999	1 retrocopy	retro_hvul_1,
Oryza nivara	ONIVA01G37420	1 retrocopy	retro_oniv_8,
Oryza rufipogon	ORUFI02G01160	1 retrocopy	retro_oruf_18,
Sorghum bicolor	Sb04g001140	1 retrocopy	retro_sbic_39 ,
Triticum aestivum	Traes_6DS_A593093E1	1 retrocopy	retro_taes_72,