RetrogeneDB ID: retro_sbic_21

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: GL005820.1:101..773(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb3247s002010
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb06g023650
• Aliases: None
• Description: None

Sequence

>retro_sbic_21
ATGGACGCGCGCACGCTGGTGGCGCACGTCCTGGCCGTGGCCGCCATCGTGCTGGTGCTCCTCTGGTGCATCCACTTCCG
CGGCGGCCTCGCCCTGCGCTCCCAGGACAAGCCGCTCATCTTCAACGTCCACCCCGTGCTCATGGTGCTCGGCCCCATCG
TCCTCGCCGGAGAAGCCATCCTCAGCTACCGCTCTCTCCCTCTCGCCCGCGACGCCAGGAAGAAGGTGCACCTGGCGCTG
CACGCCGCGGGCCTCGCCGGTGGCGTCCTCGGCGTCTACGCCGTCTTCAAGTTTCACGTCGAGAGCGGCATCCCCAACCT
CTACTCGCTCCACTCCTGGGTCGGCATCGCCACCGTCACCCTCTACGGGCTCCAGTGGACCGCCGGATTCCTCACCTACT
TCTTCCCCGGCGCCTCCCCCACCACCAGGCGCAGAACGCTGCCATGGCACGCCGTCTTCGGCCTCCTCATCTTCGTGCTC
GCCGTTGGAACCGCGCAGCTGGGCTTCCTCGAGAAGCTCACCTTCATGCAGGGCCAGCCCCTGCGCCTACCCAAGTACGG
CGCAGAGGCGCTGCTCATCAACTTCACCGCCGTGGTCGTGCTCCTCCTCGGCGTCGCCGTCGTGCTTGCCACCGTCAACA
TCGACGGGACCAGGTACAACACCATTATGTGA

Alignment

ORF - retro_sbic_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.29 %
• Parental protein coverage: 88.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TYAAHALAAAAAVLVLVWCVHFRGGLALEAQNKNLIFNVHPVLMLIGYIILGSEAIMIYKVFPKLNHDTA
          T..AH.LA.AA.VLVL.WC.HFRGGLAL..Q.K.LIFNVHPVLM..G.I.L..EAI..Y...P.L..D..
Retrocopy TLVAHVLAVAAIVLVLLWCIHFRGGLALRSQDKPLIFNVHPVLMVLGPIVLAGEAILSYRSLP-LARDAR

Parental  KLTHLILHAIATVLGAFGIYCAFKYHNDSGIANLYSLHSWLGIGTISLYAIQWVFGFVTFFFPGAAPSVR
          K..HL.LHA.....G..G.Y..FK.H..SGI.NLYSLHSW.GI.T..LY..QW..GF.T.FFPGA.P..R
Retrocopy KKVHLALHAAGLAGGVLGVYAVFKFHVESGIPNLYSLHSWVGIATVTLYGLQWTAGFLTYFFPGASPTTR

Parental  RSALPWHALFGLFVYVLALATAELGFLEKLTFLESG--GLDKYGAEAFLVNFTALVVVLFGASVVVAAV
          R..LPWHA.FGL...VLA..TA.LGFLEKLTF.......L.KYGAEA.L.NFTA.VV.L.G..VV.A.V
Retrocopy RRTLPWHAVFGLLIFVLAVGTAQLGFLEKLTFMQGQPLRLPKYGAEALLINFTAVVVLLLGVAVVLATV

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_21 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G034668	1 retrocopy	retro_zmay_23,
Leersia perrieri	LPERR04G16060	1 retrocopy	retro_lper_17,
Hordeum vulgare	MLOC_12641	1 retrocopy	retro_hvul_22,
Oryza sativa japonica	OS04G0533500	1 retrocopy	retro_osat_39,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,
Sorghum bicolor	Sb06g023650	1 retrocopy	retro_sbic_21 ,
Setaria italica	Si010957m.g	1 retrocopy	retro_sita_34,