RetrogeneDB ID: retro_sbic_3

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:10015983..10017065(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g009270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb03g042360
• Aliases: None
• Description: None

Sequence

>retro_sbic_3
ATGGCGACGACGACGGCGACGGCGACGAACCGGCGGGTGATCCTCAAGGAGTACGTGGAGGGGTACCCTCGGGAGGAGCA
CATGGAGCTGCTCCCCGGCTCCTCGGTGCCGCTCCGCCTGACGGGGACCGAGCCGGCGGGCTCCGTCCTCGTCCGGAACC
TCTACCTCTCCTGCGACCCCTACATGCGGCCCAAGATGTCGCGCCCGCTGCGTGAGTCCTACACGGCGGCGTTCGTCCCG
GGCGACGCCATCACGGGCTACGGCGTGTCGCGCGTGCTCGACTCCTCCGACCCGCGCTTCGCGCCGGGGGACCTCGTCTG
GGGCATCACCGGCTGGGAGGACTACAGCGTCGTGACCCCGCCCGTCTCCAAGTTCCTCGCCAAGATCTCCCACCACGGCG
AGGGCGTGCCGCTGTCCTACTACACCGGCATCCTCGGCATGCCGGGGCTCACCGCCTACGTGGGCTTCCACGAGATCTGC
GCGCCGAAGAAAGGCGAGACCGTGTTCGTGTCCGCGGCCTCGGGCGCCGTCGGCCAGCTGGTGGGACAGTTCGCGAGGCT
CGCCGGGTGCCACGTCGTCGGCAGCGCCGGGTCCAAGGAGAAGGTGGAGCTGCTCAAGACCAAGTTCGGCTTCCACGACG
CCTTCAACTACAAGGAGGAGCCCGACCTCGGCGCCGCGCTGAAGCGCTGCTTCCCGGACGGGATCGACATCTACTTCGAG
AACGTCGGGGGCGCCATGCTCGACGCCGTCCTGCTCAACATGCGCGTGCACGGCCGGATCGCCGTCTGCGGCTTCATCTC
GCAGTACAACCTGGCGGACGGGGAGAAGGACGCCGTGCGCAACCTGGCCGCCGTCATTGCCAAGCGACTCCGCCTGCAGG
GGTTCATCGAGCCCGACCACAAGCACCTGTACCCGCAGTACGAGGCGTGGGTGCTGCCTTACATCAGGGACGGCACGCTC
GCCTACGTCGAGGACGTCGCCGAGGGGCTCGAGAACGCGCCCAAGGCACTCATCGGACTCTTCCACGGACGCAACGTCGG
GAAGCAGCTCGTCCGCGTCGCCGACGACGAGTCGGCGGCGTG

Alignment

ORF - retro_sbic_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.66 %
• Parental protein coverage: 98.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVARNRKVVLRGYIDRAPREDDMELVDGGALELRVPECAGGGPAVLVKNLYLSCDPYMRGRM-RDFQGSY
          A.A.NR.V.L..Y....PRE..MEL..G....LR.......G..VLV.NLYLSCDPYMR..M.R....SY
Retrocopy ATATNRRVILKEYVEGYPREEHMELLPGSSVPLRLTGTEPAG-SVLVRNLYLSCDPYMRPKMSRPLRESY

Parental  IPPFKPGSPIEGFGVGRVVDSTYPGLSAGDIVSGMTGWEDYSLITKPEQ--LTKIQQ--SDIPLSYHLGL
          ...F.PG..I.G.GV.RV.DS..P....GD.V.G.TGWEDYS..T.P....L.KI.......PLSY..G.
Retrocopy TAAFVPGDAITGYGVSRVLDSSDPRFAPGDLVWGITGWEDYSVVTPPVSKFLAKISHHGEGVPLSYYTGI

Parental  LGMPGFTAYVGFYEICSPKKGEFVFVSAASGAVGQIVGQLAKLHGCYVVGSAGTNQKVELLKEKFGFDAA
          LGMPG.TAYVGF.EIC.PKKGE.VFVSAASGAVGQ.VGQ.A.L.GC.VVGSAG...KVELLK.KFGF..A
Retrocopy LGMPGLTAYVGFHEICAPKKGETVFVSAASGAVGQLVGQFARLAGCHVVGSAGSKEKVELLKTKFGFHDA

Parental  FNYKEEPDLTAALKRYFPEGIDIYFENVGGPMLDAVLLNMRVHGRIAVCGMVSQHGVT--APAGIHNLFS
          FNYKEEPDL.AALKR.FP.GIDIYFENVGG.MLDAVLLNMRVHGRIAVCG..SQ............NL..
Retrocopy FNYKEEPDLGAALKRCFPDGIDIYFENVGGAMLDAVLLNMRVHGRIAVCGFISQYNLADGEKDAVRNLAA

Parental  FISKRIEMKGFIQSDYVHLFPQFVDDITKHYRDGKIVYVEDVSIGLESGPAAFVGLFSGKNVGKQVVRVS
          .I.KR....GFI..D..HL.PQ.........RDG...YVEDV..GLE..P.A..GLF.G.NVGKQ.VRV.
Retrocopy VIAKRLRLQGFIEPDHKHLYPQYEAWVLPYIRDGTLAYVEDVAEGLENAPKALIGLFHGRNVGKQLVRVA

Parental  QD
          .D
Retrocopy DD

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_3 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	Sb03g042360	1 retrocopy	retro_sbic_3 ,