RetrogeneDB ID: retro_sbic_14

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 1:6551548..6552946(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb01g007620
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g007640
• Aliases: None
• Description: None

Sequence

>retro_sbic_14
ATGGCCATGGCGGCACCACGCGTCCTAGTCCTGCCTTACCCCGCGCAGGGCCATGTCACCCCAATGATGGAGCTCTCCCA
CTGCCTCGTCGAGCACGGCGTCAAGGTCACCTTCGTGAACACCGAGGCAAACCACGGTTTGATTCTTGGTGCCTTGGCGA
CCGGAGACAGCGAATTCGGCGGGGTCGACATGGTGTCCATACCGGACGGCCTGGGCTGCGGCGAAGACCGGAAGGATCTC
GCCCGTCTCACCGACTCCTTCTCCAAGTTCATGCCCGCCGAGCTGGAGAAGCTCATTGCCAGCATCAATGCCGACGAGCA
AGAGCGCGAGAAGGCCAGCTGGTTGATTGCCGATGTGAACATGGCGTGGGCCTTCCCCGTGGCGAAGAAGCACGGCCTCC
GGACCGCCGGGTTCTGCCCGTCGTCGGCGGCGATGTTCGCGATGAGGATCAAAATTCCTGAGATGATAAGCGACGGCGTT
CTCGACGAGAGAGGCTGGCCCAAGCGGCGCGGCACGTTCCGGCTGGCTCCGGCGATGCCGGCCATCGACACGTCGGAGTT
CTCGTGGAACCGCGCCGGCGACGCCAAGGGCCAGCCAATCATCTTCCAGCTGATCCTCCAGAACAACGCGGCCACGCACC
TGGCCGAGACCATCGTCTGCAACTCCGTCCAGGAGCTCGAGCCCGGGGCCTTTGCGCTCTTCCCCGGCGTCCTCCCCGTG
GGCCCGCTCTCGGTCTCCTCCGACAAGCCGGTCGGCGGCTTCTGGGCCGAGGACGCCTCCTGCGCCGCGTGGCTGGACGC
GCAGCCGGACAGCTCCGTCGTGTACGTCGCGTTCGGCAGCCTCGCCGCCTACGACGCAGCGCAGCTAGTCGAGCTCGCCG
AGGGGCTGCTGCTGACCTCACGGCCGTTCCTGTGGGTGGTCAGGCCGGGGTTGGCGGGCGAGCACCTCCTTGAGCAGCTC
CGCCGCCGCGCCGCGCCGCGCGGGCGCGTGGTGAGCTGGTGCCCGCAGCAGAGCGTGCTGGCGCACCCGGCGGTCGCCTG
CTTCCTGACGCACTGCGGCTGGAACTCGACGATGGAGGCGGTGCGGAGCGGCGTGCCGCTCCTGTGCTGGCCCTACTTCA
CCGACCAGTTCTTGAACCAGAGCTACATCTGCGACGTGTGGGGGACAGGGCTGAAGGTGCCATTGCCGCCCGCGGCGGCG
GCGGCGGCGGCACACGGAGCGGGGCTTGTGGGGAGAGACGTTGTTCGGGACAAGATCGAGGAGCTGCTCCGCGACAATGA
GACCAAGGCGAGGGCGCTCGCGCTGCGGGACCTCGCCGGTCGGGCAGTCGGCGATGGCGGCTCGTCGCGCCAGAATCTCA
GGCGGTTCTTGGATCTTGTGCGAGGAGTGAAGAGCTAG

Alignment

ORF - retro_sbic_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.61 %
• Parental protein coverage: 86.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKAHVLVLPMPCQGHVTPLMELSHRLVDQGFEVTFVNTDVDHALVVTALDATGGGVAALGGGIHLASIP
          MA...VLVLP.P.QGHVTP.MELSH.LV..G..VTFVNT...H.L...AL.ATG......GG.....SIP
Retrocopy MAAPRVLVLPYPAQGHVTPMMELSHCLVEHGVKVTFVNTEANHGLILGAL-ATGD--SEFGG-VDMVSIP

Parental  DGLADDEDRKDINKLVDAYSRHMPGYLESLLADMEA--AGRPRAKWLVGDVNMGWSFEVAKKFGIRVVSF
          DGL...EDRKD...L.D..S..MP..LE.L.A...A....R..A.WL..DVNM.W.F.VAKK.G.R...F
Retrocopy DGLGCGEDRKDLARLTDSFSKFMPAELEKLIASINADEQEREKASWLIADVNMAWAFPVAKKHGLRTAGF

Parental  WPAASACLAFMLKIPNLIEEGLINDKGLPVRQETFQLAPGMPPLHSSQLSWNNAGEPEGQHIIFDLVTLN
          .P...A..A...KIP..I..G.....G.P.R..TF.LAP.MP....S..SWN.AG...GQ.IIF.L...N
Retrocopy CPSSAAMFAMRIKIPEMISDGVLDERGWPKRRGTFRLAPAMPAIDTSEFSWNRAGDAKGQPIIFQLILQN

Parental  NKLNELAEMVVSNSFYEAEAGAFKLFPSILPIGPLFADPAFRKPVGHFLPEDERCIKWLDTQPDASVVYV
          N....LAE..V.NS..E.E.GAF.LFP..LP.GPL.......KPVG.F..ED..C..WLD.QPD.SVVYV
Retrocopy NAATHLAETIVCNSVQELEPGAFALFPGVLPVGPL--SVSSDKPVGGFWAEDASCAAWLDAQPDSSVVYV

Parental  AFGSITIFDPRQFEELAEGLELTGRPFLWVVRPDFTPGLSKAWLHE-FQQRVAGKGMIVSWCSQQQVLAH
          AFGS....D..Q..ELAEGL.LT.RPFLWVVRP....GL....L.E....R.A..G..VSWC.QQ.VLAH
Retrocopy AFGSLAAYDAAQLVELAEGLLLTSRPFLWVVRP----GLAGEHLLEQLRRRAAPRGRVVSWCPQQSVLAH

Parental  RAVACFVSHCGWNSTMEGVRNGVPFLCWPYFCDQYLNRSYIINVWRTGLAV
          .AVACF..HCGWNSTME.VR.GVP.LCWPYF.DQ.LN.SYI..VW.TGL.V
Retrocopy PAVACFLTHCGWNSTMEAVRSGVPLLCWPYFTDQFLNQSYICDVWGTGLKV

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_14 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
Zea mays	GRMZM2G031138	1 retrocopy	retro_zmay_13,
Sorghum bicolor	Sb01g007640	1 retrocopy	retro_sbic_14 ,