RetrogeneDB ID: retro_sbic_29

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 8:44482004..44483186(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb08g016600
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb10g006910
• Aliases: None
• Description: None

Sequence

>retro_sbic_29
ATGTCCACCACGGAAGAAGCCGCTGGTGGCTACGACGACTACGACCGCCTGAGCGAGCTGAAGGCGTTCGACGACACCAA
GGCCGGCGTCAAGGGCCTCGTGGACGCCGGCGTCACGACCGTCCCCGCCATCTTCCGCCGCCACCGCCAGGACGTGCCGC
CGCAGGTATCGTCCTCTAGCAGCAGCAGCAGCAGCAGCACTGTTAGCTCGATCCCGGTCATCGACCTCTCGGCGGCGGAC
GCAGACGCAGCCACGCGGGAGCATGTGGTCGCGCAGGTGAAGGCCGCGGCGGAGACGGTGGGGTTCTTCCAGCTGGTGAA
CCACGGCGTCCCCGGCGAGCTCCTGTCGGAGATGCTGGCGTCGGTGAGGCGGTTCAACGAGGCGTCCCCAGTGACGAAGC
GTCCCTACTACACGCGGGACGCCCGGCGGAAGCTGCGGTTCAACTCCAACTTCGACCTGTTCCAGTCGCCGGCGGCCAAC
TGGCGCGACACGCTCTTCTGCGAGGCGGCGCCGGAGCCGCCGCGTGCCGAGGAGCTGCCGCCCGCCGTGAGGCGCGTGTT
CCTGGAGTACGGCGGCGCGGCGCGGGAGGTGGCGGCGCGGGTGCTGGCGCTGCTGTCGGAGGCCCTGGCGCTGGCGCCCG
GGCACCTCGCCGGGATGGGGTGCGCCGAGGGCCTCAGCCTGGTGTGCAACTACTACCCGCCGTGCCCGGAGCCGGACCTC
ACCATGGGGTGCAGCGCGCACTCGGACCCCAGCTTCCTGACCGTGCTGCTCCAGGACGCGCACGCGGGGGGAGGACTGCA
GGCGCTGCTCGAGGACAGGTGGGTGGACGTGCCTCCGGCGGTGCCCGGCGGCGCGCTACTGGTGAACGTCGGCGACCTCC
TCCAGCTGGTCAGCAACGGGCGGTTCAGGAGCGTGGAGCACCGGGTGGTGGCCAACCGGAGCAGGGACACGGCGAGGGTG
TCAGTGGCGTGCTTCTTCAACGCGGACATCGCGAGGTCCACGAGGCTGTATGGACCCATCGCGGAGCTCGTCACCTCGGA
CGACGGCGACGGCGACGGCGATGGCGCGGGAAGTGGAAGGGCGCTGTACAGGAGCGTGACGGTCCCGGAGTTCCTGGCGC
ACTACGACAAGAAAGGCCTCGACGGTCGCCCGGCGCTCCACCACTTCCTGCTGAAGCAATAA

Alignment

ORF - retro_sbic_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.93 %
• Parental protein coverage: 89.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSATEPAAGLASDGYDRRRELLQAFDDTKAGVKGLVDAGVTAIPAIFR-HPPESLEATSSPPPTDVVASA
          MS.TE.AAG...D.YDR..EL..AFDDTKAGVKGLVDAGVT..PAIFR.H........SS..........
Retrocopy MSTTEEAAG-GYDDYDRLSEL-KAFDDTKAGVKGLVDAGVTTVPAIFRRHRQDVPPQVSSSSSSSSSSTV

Parental  GTIPVIDLAA----AAPRGEVASQVKRAAETVGFFQVTNHGVPRELMAGVLAGVRRFNEQQPEVKRRFYT
          ..IPVIDL.A....AA.R..V..QVK.AAETVGFFQ..NHGVP.EL....LA.VRRFNE..P..KR..YT
Retrocopy SSIPVIDLSAADADAATREHVVAQVKAAAETVGFFQLVNHGVPGELLSEMLASVRRFNEASPVTKRPYYT

Parental  RDTARKARFCSNYDLFQSAAANWRDTLFCELAPDPPRPEELPEAVRGVMLEYGDAATKLALWVLELLSES
          RD..RK.RF.SN.DLFQS.AANWRDTLFCE.AP.PPR.EELP.AVR.V.LEYG.AA...A..VL.LLSE.
Retrocopy RDARRKLRFNSNFDLFQSPAANWRDTLFCEAAPEPPRAEELPPAVRRVFLEYGGAAREVAARVLALLSEA

Parental  LGLASDHLREMGCAQSLNVASHYYPPCPEPHLTLGTSRHADATFVTVLLQD--GTGGLQVLLDRGGWVDV
          L.LA..HL..MGCA..L.....YYPPCPEP.LT.G.S.H.D..F.TVLLQD....GGLQ.LL....WVDV
Retrocopy LALAPGHLAGMGCAEGLSLVCNYYPPCPEPDLTMGCSAHSDPSFLTVLLQDAHAGGGLQALLE-DRWVDV

Parental  PPL--PGALIVNIGDFLQLVSNGRFRSVEHRVLANKSRDTPRVSVACFFNADAKRSTRLYGPITD
          PP....GAL.VN.GD.LQLVSNGRFRSVEHRV.AN.SRDT.RVSVACFFNAD..RSTRLYGPI..
Retrocopy PPAVPGGALLVNVGDLLQLVSNGRFRSVEHRVVANRSRDTARVSVACFFNADIARSTRLYGPIAE

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_29 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	GRMZM2G066358	1 retrocopy	retro_zmay_15,
Sorghum bicolor	Sb10g006910	1 retrocopy	retro_sbic_29 ,