RetrogeneDB ID: retro_sbic_20

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 6:1337286..1339478(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb06g000930
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g037140
• Aliases: None
• Description: None

Sequence

>retro_sbic_20
ATGGGAGAGAGCCGCGGCAGCATCGCCTTTTTCGCCACGTACCGGCCGCCGATGCCGCTGGACATCTTCTCCGTGCCCAA
CCCGCCGTCTTCGATCCGCGACGAGGTACACCTCACCGACGGCGTCTCCTACAACTACAACTGCCGCCCCATCCCCAAGG
ACGCGCTCAAGTCCCTGCTCAAGCGCCCGAAGCTCGTCGCCGAGGGCGGCGCCACCGACGCCGACGTCGACAGCGGCCGC
GTCTCCGGCCTGCTCTTCGTCTCCGAGCGGGACGGCGGGCTGGAGACGCTCCGCGTTGCCCTCCGTTTCGACGACTCCGG
CGGCAAGCAGACCTGCAAGGTGTTCTCCCTTGCTGACGTCTTCGGCGCCGCCGACTTCACCGGCGCTCGCCTCGAGGACA
GCGGCTGCATCGGCGGCGGCTATAAGATGGGCTCTCGCTCCGTCGACCACTCGCTCATCTACGTCTCCACCAAGGAGCCG
GTGGAAGAGCGGCGGAGCCCATGGACCGTCGTGTACAAGACCAACCTCAGGACCGGCAAGACCGAGCGCCTGACTCCCAA
AGGTCAATTTGACCTGAGCCCAGCCGTGTCGCCGTCGGGGAAGAAGGTGGCGATGGCGACGTTCCGGCCGGAAGGCTGGG
AAGGCGAGATCGAGGACCTTCAGACGGACATCTTCGTGATGAACGTCGAGAGGCCGCCGATGAGGAAACGGCTGATCAAG
AACGGCGGGTGGCCGTCGTGGGCCAGCGACGACGTCATCTTCTTCCACCGGAAGGTGGGCGACACCTGGGGCGTGTTCCG
CCACGACACGAGGACGAACGAGACGGTGCGAGTGACGCCGGAGGCCTTCGACGCGGTGACGCCGGCGGCCATCAGCGAGA
CCAAGGTGGCGGTGGCGACGATCCGTCAGAAATCCAAGTTCACCGACGTCCGCGTGGAGGCGCAGTACCGCCACATCGAG
ATCTTCGACACGGCGGCGGGGGCGGGGCAGCCGCCGCTGCAAATCACCCAGAAGACGAGGCCCAAGACGGACCACTTCAA
CCCTTTCGTCCTCGACGACGGCGGCCGCGTCGGGTACCACCGCGCCAGGAGCGACCTCCTGAAGCACGGCGACGACGTTC
CCCGGAACTTCCACAAGATGGAGTCGCCGGTGAAGGACGTGGGGACGTTCCGGGTCTCCGGCGTGTTCCCGACCATCTCC
AACGACGGGTCGAAGCTGGCGTTCGTCGACAACGAGTTCAAGGCGGTGTGGGTCGCCGACAGCCAAGGCCTGCGCGTGGT
GTACGAGACCAAGGGCCCCGACAACATCTTCGCGCCGATGTGGAACCAGAACCCCGACAAGGACATCCTGTACGTGTGCA
TGGGCCCCTCCTTCAACGCCGGCAAGCCGCTGGAGATCTGCGCCATCCCCAACGTGTCCAGCGGCACCCGGCAGCGGCGG
CAGCTGACCAAGGGCAAGTTCAACAACGCGTTCCCGTCGAGCAGCCCCGACGGGAGCAGGTTCGTGTTCCGGTCGACGAG
GGACGGCGGCGACAAGAAGCACAAGAACCTGTACATCGCCGAGGACGCGGAGGTCGGCGAGTACAGCGGCGGCACGGTGA
CGAGGCTCACCAACGGGGAGTGGACGGACACGCACTGCCAGTGGTCGCCGAGAGGGGACTGGATCGTCTTCTCGTCGACG
AGGGACAAGCCCAAGGACGCGCCGGAGCTGGACAACGGCCTGGACTCAGGCTACTACGCCGTGTTCATGGTGAAGGTGAG
CGACCCGACGGTGGTGATCCGGGTGGTACAGAGCGGCGACGACCTCGGCGGGCACGTGAACCACCCGGTGTTCAGCCCGG
ACGGCCGGAGCATCGCCATGACGGCGGACCTCGCCGCCGTGTCGGCGGATCCCATCTCGCTGCCGCTCTTCATCCACTCG
GTGAGGCCCTACGGCGACATCTTCGTGGTGGACATCGACCCGGACGACGCGAGGAAGAACAAGGACGTGAAGAAGTTCCA
CCGGGTGACGCACAGCCGGTACGAGTACTCGACGCCGGCGTGGACCATGTTCGCCACGGACGACCCCAACGCGCAGTGGA
ACATGCTGGTGAACAAGGACTCGTACACGCCGGCGTGCCCCTACGCGTACCCGGACGGCGGCGAGAGCTGGCACATGACC
GGACACCTCTGCATCCCCAGGAGGTGCTGCTG

Alignment

ORF - retro_sbic_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.83 %
• Parental protein coverage: 85.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KIFSLADIYGSDLFSGARLEDNGCIAGGYEVDGSTNDHYLVYVSTKEPVQERRSPWNVVYKTNLRTSETE
          K.FSLAD..G...F.GARLED.GCI.GGY.......DH.L.YVSTKEPV.ERRSPW.VVYKTNLRT..TE
Retrocopy KVFSLADVFGAADFTGARLEDSGCIGGGYKMGSRSVDHSLIYVSTKEPVEERRSPWTVVYKTNLRTGKTE

Parental  HLTPPGTFDLSPSVSPSGKKIAVASFQGKTWDGEIKDLKTNIYLTSLENPPLERRRVIENGGWPSWGSEN
          .LTP.G.FDLSP.VSPSGKK.A.A.F....W.GEI.DL.T.I.....E.PP..R.R.I.NGGWPSW.S..
Retrocopy RLTPKGQFDLSPAVSPSGKKVAMATFRPEGWEGEIEDLQTDIFVMNVERPPM-RKRLIKNGGWPSWASDD

Parental  VIFFHRKVGDIWGVFRYNLSTGETVRVTPEAFDAVTPAAIDETRVAVATIRQKSEFTDVRNEAQYRHIEI
          VIFFHRKVGD.WGVFR....T.ETVRVTPEAFDAVTPAAI.ET.VAVATIRQKS.FTDVR.EAQYRHIEI
Retrocopy VIFFHRKVGDTWGVFRHDTRTNETVRVTPEAFDAVTPAAISETKVAVATIRQKSKFTDVRVEAQYRHIEI

Parental  FDTSAQ--EQPLQITQNTRAKADHFNPFVMD-GGNTYYHRCKSDLLKHGDDVPRHFHKVQSPHEDVGVFR
          FDT.A.....PLQITQ.TR.K.DHFNPFV.D.GG...YHR..SDLLKHGDDVPR.FHK..SP..DVG.FR
Retrocopy FDTAAGAGQPPLQITQKTRPKTDHFNPFVLDDGGRVGYHRARSDLLKHGDDVPRNFHKMESPVKDVGTFR

Parental  VSGVFPTFSKDGSKLAFVDNEFKAVWLADSHGLRVVFETDGPDSIFSPVWNQK--KDILYVCMGPSFKAN
          VSGVFPT.S.DGSKLAFVDNEFKAVW.ADS.GLRVV.ET.GPD.IF.P.WNQ...KDILYVCMGPSF.A.
Retrocopy VSGVFPTISNDGSKLAFVDNEFKAVWVADSQGLRVVYETKGPDNIFAPMWNQNPDKDILYVCMGPSFNAG

Parental  ETLEIYAIPDVSRGARARRHTRQLTKGKFNNAFPFTNPDGTKFVFRSTRDGGDKNYKNLYIMEDAEFGEV
          ..LEI.AIP.VS.G.R.R...RQLTKGKFNNAFP...PDG..FVFRSTRDGGDK..KNLYI.EDAE.GE.
Retrocopy KPLEICAIPNVSSGTRQR---RQLTKGKFNNAFPSSSPDGSRFVFRSTRDGGDKKHKNLYIAEDAEVGEY

Parental  GGGKVTRLTEGSWIDTHCQWSPDGNLVVFASNRDKPADAPERDHGLDPGYFAVYLMNVSDRSVV-RVIRS
          .GG.VTRLT.G.W.DTHCQWSP.G...VF.S.RDKP.DAPE.D.GLD.GY.AV....VSD..VV.RV..S
Retrocopy SGGTVTRLTNGEWTDTHCQWSPRGDWIVFSSTRDKPKDAPELDNGLDSGYYAVFMVKVSDPTVVIRVVQS

Parental  GYDLSGHVNHPVFSPDGRSIAVTSDLAAVSADPMSLPTFLHSVRPYGDIFSVDIDPDDMEKNKDLDKFVR
          G.DL.GHVNHPVFSPDGRSIA.T.DLAAVSADP.SLP.F.HSVRPYGDIF.VDIDPDD..KNKD..KF.R
Retrocopy GDDLGGHVNHPVFSPDGRSIAMTADLAAVSADPISLPLFIHSVRPYGDIFVVDIDPDDARKNKDVKKFHR

Parental  VTHSRYENSTPAWTVFSTHDPHAQWNLLVMEDEYTPACPYAHPDGGESWHMTGQICIPKRHC
          VTHSRYE.STPAWT.F.T.DP.AQWN.LV..D.YTPACPYA.PDGGESWHMTG..CIP.R.C
Retrocopy VTHSRYEYSTPAWTMFATDDPNAQWNMLVNKDSYTPACPYAYPDGGESWHMTGHLCIPRRCC

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_20 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
Oryza punctata	OPUNC03G14590	1 retrocopy	retro_opun_27,
Sorghum bicolor	Sb01g037140	1 retrocopy	retro_sbic_20 ,