RetrogeneDB ID: retro_sbic_5

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 2:74213280..74214447(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb02g040190
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb09g029240
• Aliases: None
• Description: None

Sequence

>retro_sbic_5
ATGGCAGCGGCTGCAATCGCGACCCTATCCTTCAGTTCAGTTCCTTGCAAAAAACGGCCCCGGCATGGCGCTAGTTCCTT
CGACGCACAACAGTTCAGTAACTCCAGTTCCTACTGTCACTCTCTCACTCTAAGACCAAGAGTGCCAAGGTCCCGAGCCG
TGAGCCGGGTCGTCGTCGCGCAGGCCGGCAGCGGCAGCTACAAGGTGGCCATCCTTGGCGCGGCGGGAGGGATCGGGCAG
CCTCTTTCTCTGCTGGCCAAGATGTCCCCGCTCGTCTCGGCGCTGCACCTGTACGACATCGCCAACGTGGAGCCCGTGAC
CGCCGACCTCAGCCACTGCAACACCCCGGCGCAGGTCGCCGGCTTCACAGGTAAAGACGCGCTCGCGGGGTGCCTATCGG
GCGCGGACGTCGTGGTCATCCCCGCCGGCGTGCCCCGGAAGCCCGGCATGACGCGGGACGACCTGTTCAGCGTCAACGCC
GGCATCGTGCGCGACCTCGTCGCGGCGGTGGCGGACCACGCGCCGGGCGCGCTGGTGCACGTGATCAGCAACCCGGTGAA
CTCCACGGTGCCGATCGCCGCCGAGGTGCTGAAGCAGAAGGGCGCGTACGACCCGCGGAGGCTGTTCGGCGTCACGACGC
TGGGCGTGGTCCGCGCCAACGCGTTCGTAGCGGCGAGGAAGGGCCTCCCCGTGGCGGAAGTGGATGTGCCGGTTGTGGGC
GGCCACGCGGCGGCTACCATCCTGCCGCTGCTGTCCAAGGCGCGGCCCAAGGCGGCGTTCACGGACGAGGAGGTGGAGGA
GCTCACCGCCAGGATCCGGGACGCCGGCACCGAGGTGGTGGAGGCCAAGGCCGGCGCCGGGTCCGCCACGCTGTCCATGG
CGTACGCCGCCGCGCGGTTCCTCGAGGCGTCGCTGCGTGGACTCGACGGCCACGACGACGTGTACGAGTGCACGTACGTG
CAGTCGCAGGTTGTGCCGGAGCTCCCGTTCTTCGCGTGCAGGGTGAAGCTTGGGAGGGACGGCGTGGAGGAGGTGCTGGG
TTCAGAGCTGAGGGGACTCACCGACTACGAGGCGCGCGAGCTGGAGGATCTCAAGCCCAAGCTCAAGGCCAGCATCGACA
AGGGCATCGCGTACGTGCAGCAGAACCAGGAGGCAGCGTTGAACTGA

Alignment

ORF - retro_sbic_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 94.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASAANPERKVAILGAAGGIGQPLSLLMKLNPLVSSLSLYDIAGTPGVAADVSHINSPALVKGFMGDDQLG
          A.A.....KVAILGAAGGIGQPLSLL.K..PLVS.L.LYDIA....V.AD.SH.N.PA.V.GF.G.D.L.
Retrocopy AQAGSGSYKVAILGAAGGIGQPLSLLAKMSPLVSALHLYDIANVEPVTADLSHCNTPAQVAGFTGKDALA

Parental  EALEGSDVVIIPAGVPRKPGMTRDDLFNINAGIVKGLCTAIAKHCPNALVNMISNPVNSTVPIAAEVFKK
          ..L.G.DVV.IPAGVPRKPGMTRDDLF..NAGIV..L..A.A.H.P.ALV..ISNPVNSTVPIAAEV.K.
Retrocopy GCLSGADVVVIPAGVPRKPGMTRDDLFSVNAGIVRDLVAAVADHAPGALVHVISNPVNSTVPIAAEVLKQ

Parental  AGTYDKKKLFGVTTLDVVRAKTFYAGKAGVPVTEVNVPVVGGHAGITILPLFSQATPASNSLSQEDIEAL
          .G.YD...LFGVTTL.VVRA..F.A...G.PV.EV.VPVVGGHA..TILPL.S.A.P.......E..E.L
Retrocopy KGAYDPRRLFGVTTLGVVRANAFVAARKGLPVAEVDVPVVGGHAAATILPLLSKARPKA-AFTDEEVEEL

Parental  TKRTQDGGTEVVEAKAGKGSATLSMAYAGAVFADACLKGLNGVPDVVECSFVQS-TVTELPFFASKVRLG
          T.R..D.GTEVVEAKAG.GSATLSMAYA.A.F..A.L.GL.G..DV.EC..VQS..V.ELPFFA..V.LG
Retrocopy TARIRDAGTEVVEAKAGAGSATLSMAYAAARFLEASLRGLDGHDDVYECTYVQSQVVPELPFFACRVKLG

Parental  KNGVEEVLG--LGELNDFEKKGLENLKGELMSSIEKGVKFAHSN
          ..GVEEVLG..L..L.D.E...LE.LK..L..SI.KG......N
Retrocopy RDGVEEVLGSELRGLTDYEARELEDLKPKLKASIDKGIAYVQQN

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_5 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
Arabidopsis lyrata	fgenesh2_kg.3__1630__AT3G15020.2	1 retrocopy	retro_alyr_12,
Sorghum bicolor	Sb09g029240	1 retrocopy	retro_sbic_5 ,