RetrogeneDB ID: retro_sbic_33

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 4:40894672..40896264(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb04g017460
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb03g038160
• Aliases: None
• Description: None

Sequence

>retro_sbic_33
ATGGCGGTGTCCGCGGCCAGGGTGGCCGTCGCCACGGCCGTCTCCTTAGCCGTGCACTGGCTCCTCCGGTCCTTCCTCCA
GGCGCAGCACCCCGCGCTGGGCCTGCTCCTCCTGGCCGCCGTCTTCCTCGGCATTGCCGCGACGGGCAACGCTGGCGCCG
CCAACGCGCCGCCGGGGCCGGCGGCCGTGCCGGTGTTCGGCAACTGGCTGCAGGTGGGCAACGACCTGAACCACCGCTTC
CTGGCGCGCCTGTCGGCGCGGTACGGGCCCGTCTTCCGCCTCCGCCTCGGCGTGCGCAACCTGGTGGTCGTCTCCGACCC
GCGGCTCGCCACGGAGGTGCTGCACACGCAGGGGGTGGAGTTCGGCTCCCGCCCCCGCAACGTCGTCTTCGACATCTTCA
CCGCCAACGGCGCCGACATGGTCTTCACCGAGTACGGCGACCACTGGCGCCGCATGCGCCGCGTGATGACGCTGCCCTTC
TTCACCGCGCGCGTGGTGCAGCAGTACAGGGACATGTGGGAGGCCGAGATGGACGCCGTCGTCTCCGACATCTCCGGGGA
CGGCGCGGCCCAGCAAGCCGGCTTCGTCGTGCGCCGCAGGCTGCAGCTCATGCTGTACAACATCATGTACCGGATGATGT
TCGACGCGCGCTTCGACTCGGTCGACGACCCCATGTTCGTGGAGGCCACCAGGTTCAACTCCGAGCGCAGCCGCCTCGCG
CAGAGCTTCGACTACAACTACGGCGACTTCATCCCCATCCTGCGCCCCTTCCTGCGCGGCTACCTCAACAAGTGCAAGGA
CCTGCAGACCAGGAGGCTCGCCTTCTTCAACAACAACTACGTCGAGAAGAGGAGAAAGGTGATGGACACGCCGGGGGACA
AGAACAAGCTCAGGTGCGCCATCGACCACATCCTCCAGGCGGAGAAGAGCGGCGAGATCACCTCGGAGAACGTCATCTAC
ATCGTCGAGAACATCAACGTCGCGGCCATCGAGACCACGCTCTGGTCCATCGAGTGGGCGCTCGCAGAGGTCGTCAACCA
CCCGGCGGTGCAGCGCAAGGTCCGCGACGAGATCAAGGCCGTCGTCGGCGACGACGAGCCCATCACGGAGTCCACCATCC
ACAGACTCCCTTACCTGCAGGCTGTCATCAAGGAGACGCTGCGCCTCCACTCGCCCATCCCGCTCCTCGTCCCGCACATG
AACCTCGAGGAGGCCAAGCTCGGCGGCTACACCATCCCCAAGGGCTCCAAGGTGGTGGTCAACGCGTGGTGGCTGGCCAA
CAACCCGGAGCTGTGGGAGAAGCCCGAGGAGTTCCGGCCGGAGCGGTTCCTAGGCGAGGAGAAGAGCGTGGACGCTACCG
TCGGCGGGAAGGTGGACTTCAGGTTCCTGCCGTTCGGCGTGGGCCGCCGCAGCTGCCCCGGGATCATCCTGGCGCTGCCC
ATCCTCGCGCTCATCGTCGGGAAGCTCGTGCGCAGCTTCGAGATGGTACCACCGCCCGGCGTGGAGAAGCTCGACGTCAG
CGAGAAAGGAGGACAGTTCAGCCTGCACATTGCCAAGCACTCTGTCATCGCCTTCCACCCTGTCTCTGCATG

Alignment

ORF - retro_sbic_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 97.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFASVVVAIAVSKMRGRKLRLPPGPVPVPIFGNWLQVGDDLNHRNLAALARKFGDIFLLRMGQRNLVVVS
          L.A.V...IA.....G.....PPGP..VP.FGNWLQVG.DLNHR.LA.L....G..F.LR.G.RNLVVVS
Retrocopy LLAAVFLGIAATGNAGAA-NAPPGPAAVPVFGNWLQVGNDLNHRFLARLSARYGPVFRLRLGVRNLVVVS

Parental  SPPLAREVLHTQGVEFGSRTRNVVFDIFTGEGQDMVFTVYGDHWRKMRRIMTVPFFTNKVVQQYRHGWEA
          .P.LA.EVLHTQGVEFGSR.RNVVFDIFT..G.DMVFT.YGDHWR.MRR.MT.PFFT..VVQQYR..WEA
Retrocopy DPRLATEVLHTQGVEFGSRPRNVVFDIFTANGADMVFTEYGDHWRRMRRVMTLPFFTARVVQQYRDMWEA

Parental  EAAAVVDDVRADPAAATEGVVLRRRLQLMMYNNMYRIMFDRRFESMDDPLFLRLRALNGERSRLAQSFEY
          E..AVV.D...D.AA...G.V.RRRLQLM.YN.MYR.MFD.RF.S.DDP.F......N.ERSRLAQSF.Y
Retrocopy EMDAVVSDISGDGAAQQAGFVVRRRLQLMLYNIMYRMMFDARFDSVDDPMFVEATRFNSERSRLAQSFDY

Parental  NYGDFIPILRPFLRGYLRICKEVKETRLKLFKDFFLEERKKLASTKAVDSNGLKCAIDHILEAQQKGEIN
          NYGDFIPILRPFLRGYL..CK.....RL..F.....E.R.K...T...D.N.L.CAIDHIL.A...GEI.
Retrocopy NYGDFIPILRPFLRGYLNKCKDLQTRRLAFFNNNYVEKRRKVMDTPG-DKNKLRCAIDHILQAEKSGEIT

Parental  EDNVLYIVENINVAAIETTLWSIEWAIAELVNHPEIQQKLRQELDTVLAPGQQITEPDTHNLPYLQAVIK
          ..NV.YIVENINVAAIETTLWSIEWA.AE.VNHP..Q.K.R.E...V......ITE...H.LPYLQAVIK
Retrocopy SENVIYIVENINVAAIETTLWSIEWALAEVVNHPAVQRKVRDEIKAVVGDDEPITESTIHRLPYLQAVIK

Parental  ETLRLRMAIPLLVPHMNLHDAKLGGYDIPAESKILVNAWYLANNPESWKRPEEFRPERFLEEEKHVEANG
          ETLRL...IPLLVPHMNL..AKLGGY.IP..SK..VNAW.LANNPE.W..PEEFRPERFL.EEK.V.A..
Retrocopy ETLRLHSPIPLLVPHMNLEEAKLGGYTIPKGSKVVVNAWWLANNPELWEKPEEFRPERFLGEEKSVDATV

Parental  N---DFRYLPFGVGRRSCPGIILALPILGITIGRLVQNFELLPPPGQDKLDTTEKGGQFSLHILKHSNIV
          ....DFR.LPFGVGRRSCPGIILALPIL....G.LV..FE..PPPG..KLD..EKGGQFSLHI.KHS.I.
Retrocopy GGKVDFRFLPFGVGRRSCPGIILALPILALIVGKLVRSFEMVPPPGVEKLDVSEKGGQFSLHIAKHSVIA

Parental  CKP
          ..P
Retrocopy FHP

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_33 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G010468	1 retrocopy	retro_zmay_26,
Hordeum vulgare	MLOC_4708	1 retrocopy	retro_hvul_35,
Sorghum bicolor	Sb03g038160	1 retrocopy	retro_sbic_33 ,