RetrogeneDB ID: retro_sbic_18

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 3:74216786..74217871(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb03g047340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb01g032670
• Aliases: None
• Description: None

Sequence

>retro_sbic_18
ATGATGATGGTGAGGATGAGGAGGAGGGCCTCCACGCTCCTTTGCACCCTGCTCCTCCTCTCCCTGCCGTGCTTCCATCT
GGCAAGCGCCCATGGCGGCATCGACGACGGTGACAACGACGGACATGCCACCACTCCGCCGGCCGACGCCGACCCGTCGT
CGGTTCATCAGCACCTGCGTTCCAAGGGCCTGATCGCCGTCAAGGTGTGGTGCCTCGTCATCCTGCTCATCTTCACCTTC
CTCGGCGGCGTGTCACCCTACTTCTACCGCTGGAACGAGGCCTTCCTCCTCCTGGGCACACAGTTCGCCGCCGGTGTCTT
CCTCGGGACAGCGCTCATGCACTTCCTTGCCGACTCCACCAGCACCTTCCACGGGCTCACCAAGAACCAGTACCCGTTCT
CCTACATGCTGGCCTGCGTCGGCTTCCTGCTCACCATGCTCGCCGACTGCGTCGTCGCCGCGGTCACCAAGAGAAGCGCC
GCCGGCGGCGGCGGCGGCCAGAGGGTGGTCAACGAGGCCGCCAGGGAAGAAGGTGACGCCCGTCATCAGACTCAGACCAA
GCAGGAGGATGCGGCGCACGCGCGCCACCCCATGTTGGTCACGGTCAGGACGGCGTCGTTTGAGGACGCCGTCCTGCTCA
TCTTCGCGCTCTGCTTCCACTCCATCTTCGAAGGCATCGCTATCGGCGTCTCGGCAACCAAGAGCGACGCGTGGCGCAAC
CTGTGGACGATCGGGCTGCACAAGGTGTTCGCGGCGGTGGCCATGGGTATCGCGCTGCTGCGCATGATCCCCAAGCGCCC
GTTCCTGATGACGGTGGCCTACTCGCTGGCGTTCGCCGTGTCCAGCCCCGTCGGCGTGGGCATCGGTATCGGCATCGACG
CCACGGCCGAGGGCAGGGCGGCGGACTGGACGTTCGCCATCTCCATGGGCTTCGCCACGGGGGTGTTCCTCTACGTGGCC
ATCAACCACCTCATCGCCAAGGGCTACCGACCCCAGGAGCCCACCCGCGTGGACAGCCCCTCCTTCAAGTTCCTCGGCGT
GCTCCTCGGCGTCGCTGTCATGGCCGTCGTCATGATCTGGGGCTA

Alignment

ORF - retro_sbic_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.1 %
• Parental protein coverage: 56.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAGSSSGSAAAGLEEGKMGATNGTISDPTPPETHGSDHSAASMLRNASTLG--DSVLLIVALCFHSVFEG
          T..S..G...............G.....T........H....ML....T....D.VLLI.ALCFHS.FEG
Retrocopy TKRSAAGGGGGQRVVNEAAREEGDARHQTQTKQEDAAHARHPMLVTVRTASFEDAVLLIFALCFHSIFEG

Parental  IAIGVAETKADAWKALWTISLHKIFAAIAMGIALLRMLPNRPLLSCFAYAFAFAISSPIGVGIGIVIDAT
          IAIGV..TK.DAW..LWTI.LHK.FAA.AMGIALLRM.P.RP.L...AY..AFA.SSP.GVGIGI.IDAT
Retrocopy IAIGVSATKSDAWRNLWTIGLHKVFAAVAMGIALLRMIPKRPFLMTVAYSLAFAVSSPVGVGIGIGIDAT

Parental  TQGRVADWIFAVSMGLATGVFVYVSISHLLSKGYKPRRPVAVDTPVGRWLAVVLGVAVIAVVMIW
          ..GR.ADW.FA.SMG.ATGVF.YV.I.HL..KGY.P..P..VD.P....L.V.LGVAV.AVVMIW
Retrocopy AEGRAADWTFAISMGFATGVFLYVAINHLIAKGYRPQEPTRVDSPSFKFLGVLLGVAVMAVVMIW

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_18 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S17_293V6	1 retrocopy	retro_ppat_13,
Sorghum bicolor	Sb01g032670	1 retrocopy	retro_sbic_18 ,