RetrogeneDB ID: retro_sbic_60

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 8:53647787..53648149(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb02g042765
• Aliases: None
• Description: None

Sequence

>retro_sbic_60
GTTTTTCTTGAGCCTAAGGGCTTTGATGATGTCAAACCAGAGATGGTAACAACGGGATTATTGTGATGGTTGTATGAACG
CGACCTGTGTGAGAACAAAACATGCTAGATCCTTGCAAGTTGCTGTTGATGTCATTAAGGAGGTATCATCAGACATTAAC
TTTGATGACTGGGACTGTCTGAAACGAGCGTCTTCTCTCAAGATGATGATATGTTTCCCTAAAGAAACATGACTCTAAGA
TGATGTTTTCTGATGATGACCTATCAAAATTGTTGGTTCTGGCGCCTAGCCTAGAGGGTAAGTTCTATAAGAATACTTGT
CTGCAAATCTACAAAGATATTGTATTGGCTTGTGAAGTTAGG

Alignment

ORF - retro_sbic_60 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.4 %
• Parental protein coverage: 82.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IFLERNGFA-VKPQMVNDRTIEMAYA--LCENK-HAKSLQDMEDISGVMKKVSGINFDDWDSLKRVFVVK
          .FLE..GF..VKP.MV........Y...LCENK.HA.SLQ...D........S.INFDDWD.LKR....K
Retrocopy VFLEPKGFDDVKPEMVTTGLL*WLYERDLCENK>HARSLQVAVDV--IKEVSSDINFDDWDCLKRASSLK

Parental  IIICYPEET-ENSKMFSDNELSKLLSIAPSLEGKLFIKNTCMEIYEDIVFARAVR
          ..IC.P.ET.....MFSD..LSKLL..APSLEGK.F.KNTC..IY.DIV.A..VR
Retrocopy MMICFPKET>DSKMMFSDDDLSKLLVLAPSLEGK-FYKNTCLQIYKDIVLACEVR

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_60 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sorghum bicolor	Sb02g042765	1 retrocopy	retro_sbic_60 ,