RetrogeneDB ID: retro_sbic_24

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 2:148970..150728(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb02g000260
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb03g006420
• Aliases: None
• Description: None

Sequence

>retro_sbic_24
ATGGCGGCCATGGCCAGTGGAGGAGATGAGACGACGACGACGACGCTTGACGGGACGACGGATCACTCCGGCAAGCCGGC
GGTGCGGAGCAAGACGGGGACGTGGCGCGCGTGCCCTTTCATCCTGGGCAACGAGTGCTGCGAGCGCCTGGCCTACTACG
GCATGAGCTCCAACCTCGTCAACTACATGATCGACCGCCTCCACCAGGGGAACGCCGCCGCCGCCAACAACGTCAGCAAC
TGGTCCGGCACCTGCTACGTCATGCCCCTCCTCGGCGCCTTCCTGGCCGACGCCTACCTCGGCAGGTACCGCACCATCGC
CGCCTTCATGGCGCTCTACATCCTCGGCCTCACGCTGCTCACCATGAGCGCCGCCGTCCCGGGCCTCAGGCCGCCGCCCG
ACGGAGCAGGCGCCGTGACCGCGGGCCAGAGCGCCGCCTTCTTCGTGGCGCTCTACCTCATCGCGGTGGGCACGGGAGGC
ATCAAGCCCTGCGTCTCATCCTTCGGCGCCGACCAGTTCGACGACGCCGACCCGCGCGAGCGCCAGAGCAAGAGCTCCTT
CTTCAACTGGTTCTACATGTCCATCAACGTCGGCGCACTCCTCGCCTCCTCCGTGCTCGTCTGGGTCCAGATGAACGTCG
GCTGGGGATGGGGCTTTGGCATCCCCGCCGCCGCCATGGCCGTCGCCGTCGCCAGCTTCCTGATGGGGAGCAAGCTGTAC
AGGCACCAGAAGCCGGGGGGCAGCCCGCTCACGCGGATGCTGCAGGTGGTGGTCGCCGCCTGGAGGAAGGGAAAGCAGCC
CGTGCCCGCGGACGCGTCCCTGCTCCACGAGGCGTCCTCCGCCTCCGCGTCCGCCATCCAGGGCAGCAGGAAGCTGGAGC
ACACGGAGCAGTTCCGGTGGCTGGACAGGGCGGCGGTGGTGACCTCCACCGATGAGGACGGCAAGAACAACCCCGACCCC
TGGCGGCTGTGCACGGTGACGCAGGTGGAGGAGCTCAAGAGTGTCATCCGTCTTCTGCCGGTGTGGGCGAGCGGCATCGT
CATGTCGGCGGTGTACAGCCAGATGAGCACCATGTTCGTGCTGCAGGGCAACACGCTGGACCCGCGCATGGGCTCCGGCG
CCGGCGCCTTCAAGATCCCCTCCGCCTCGCTCTCCATCTTCGACACCCTCAGCGTCATCGCCTGGGCGCCCGCCTACGAC
CGACTCGTCGTCCCCGCCGCGCGCCGCTGGACGGGGCACCCGCGCGGCTTCACGCAGCTCCAGCGCATGGGCATCGGCCT
CGCCGTCTCCGTCCTGTCCATGCTCGCCGCGGGGGCGCTGGAGGTGGCCAGGCTCCGCGTCGCCGCCTCGCACGGCATGC
TCGACGACTCCACCAACTACCTGCCCATCTCCATCTTCTGGCAGGTGCCGCAGTACTTCATCATCGGAGCCGCAGAGGTG
TTCACCTTCATCGGCCAGATCGAGTTCTTCTACGACCAGGCGCCGGACGCCATGAGGAGCATGGGCACCGCGCTCTCGCT
CACCTCGTCCGCGCTCGGCAGCTACCTCAGCGCGCTGCTGGTGTCCGTCGTCACCGCCATCACCACGAGGAACGGCGGCC
TCGGCTGGATCCCCGACAACCTCAACCGGGGCCACCTCGACTACTTCTTCTGGCTGCTCTCCGTGCTCAGCGTCATCAAC
TTCGTCGTCTACCTCTGGATTGCAAAGTGGTACAGGTACAAGCAGGCAACCACAAGTTATGAACTCAGCAGTGTATAG

Alignment

ORF - retro_sbic_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GEVADMYTQDGTVDRKGNPALKKDTGNWRACPYILANECCERLAYYGMSTNLVHYMKTRLGQVNSVASNN
          G......T.DGT.D..G.PA....TG.WRACP.IL.NECCERLAYYGMS.NLV.YM..RL.Q.N..A.NN
Retrocopy GDETTTTTLDGTTDHSGKPAVRSKTGTWRACPFILGNECCERLAYYGMSSNLVNYMIDRLHQGNAAAANN

Parental  VTNWSGTCYITPLIGAFFADAYLGRFWTIASFMVIYIFGLALLTMASSVKGLVPTSCDNDGVCHPTDAQS
          V.NWSGTCY..PL.GAF.ADAYLGR..TIA.FM..YI.GL.LLTM...V.GL.P.....DG....T..QS
Retrocopy VSNWSGTCYVMPLLGAFLADAYLGRYRTIAAFMALYILGLTLLTMSAAVPGLRPPP---DGAGAVTAGQS

Parental  AVVFVALYLIALGTGGIKPCVSSFGADQFDENDEREKKSKSSFFNWFYFSINIGALVASTVLVYVQTHIG
          A..FVALYLIA.GTGGIKPCVSSFGADQFD..D.RE..SKSSFFNWFY.SIN.GAL.AS.VLV.VQ...G
Retrocopy AAFFVALYLIAVGTGGIKPCVSSFGADQFDDADPRERQSKSSFFNWFYMSINVGALLASSVLVWVQMNVG

Parental  WGWGFGIPAVVMAIAVVSFFVGTPLYRHQKPGGSPLTRIAQVLVACARKWNVAVPADKSRLHETLD-KES
          WGWGFGIPA..MA.AV.SF..G..LYRHQKPGGSPLTR..QV.VA..RK....VPAD.S.LHE......S
Retrocopy WGWGFGIPAAAMAVAVASFLMGSKLYRHQKPGGSPLTRMLQVVVAAWRKGKQPVPADASLLHEASSASAS

Parental  GIEGSRKLEHTDQLACLDRAAVVTAEDSAAGAATATSPWRLCTVTQVEELKSVIRLLPIWASGIVFAAVY
          .I.GSRKLEHT.Q...LDRAAVVT..D..........PWRLCTVTQVEELKSVIRLLP.WASGIV..AVY
Retrocopy AIQGSRKLEHTEQFRWLDRAAVVTSTDE--DGKNNPDPWRLCTVTQVEELKSVIRLLPVWASGIVMSAVY

Parental  SQMSTMFILQGDTLDQRMGS---KFKIPSATLSMVDTISVIFWVPVYDRVIVPVVRSYTGRPRGFTQLQR
          SQMSTMF.LQG.TLD.RMGS....FKIPSA.LS..DT.SVI.W.P.YDR..VP..R..TG.PRGFTQLQR
Retrocopy SQMSTMFVLQGNTLDPRMGSGAGAFKIPSASLSIFDTLSVIAWAPAYDRLVVPAARRWTGHPRGFTQLQR

Parental  MGIGLVVSIFSMVAAGVLDIVRLNAVARHG-LYGKDDHVPISIFWQIPQYFIIGCAEVFTFVGQLEFFYD
          MGIGL.VS..SM.AAG.L...RL...A.HG.L.......PISIFWQ.PQYFIIG.AEVFTF.GQ.EFFYD
Retrocopy MGIGLAVSVLSMLAAGALEVARLRVAASHGMLDDSTNYLPISIFWQVPQYFIIGAAEVFTFIGQIEFFYD

Parental  QAPDAMRSMCSALSLTTVALGNYLSTVLVTIVTHITTRNGNIGWIPENLNRGHLDYFFWLLAVLSLLNFL
          QAPDAMRSM..ALSLT..ALG.YLS..LV..VT.ITTRNG..GWIP.NLNRGHLDYFFWLL.VLS..NF.
Retrocopy QAPDAMRSMGTALSLTSSALGSYLSALLVSVVTAITTRNGGLGWIPDNLNRGHLDYFFWLLSVLSVINFV

Parental  VYLVIATWYKYKK
          VYL.IA.WY.YK.
Retrocopy VYLWIAKWYRYKQ

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_24 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
Oryza punctata	OPUNC01G02400	1 retrocopy	retro_opun_3,
Sorghum bicolor	Sb03g006420	1 retrocopy	retro_sbic_24 ,
Setaria italica	Si000816m.g	1 retrocopy	retro_sita_38,