RetrogeneDB ID: retro_sbic_4

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 10:58369465..58370331(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb10g028570
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb06g027670
• Aliases: None
• Description: None

Sequence

>retro_sbic_4
ATGGCCTCTTCCGCCGCTCCCATGAAGACGTTGGTTCTGGCGGCGGCGATGCTGCTACTGCTGGTGCACGGGGGAGTCGC
CGGCGGCGGCAACTTCTACCAGGACGTGGACATCACGTGGGGCGACGGCCGTGGCAAGATCCTGAACAACGGGCAGCTCC
TGACGCTGTCCATGGACAGGTCCTCCGGGTCGGGGTTCCAGTCCAAGTCCCAGTACCTCTACGGCCGCTTCGACATGCAG
CTGAAGCTGGTGCCAGGCAACTCCGCCGGCACCGTCACCACCTTCTACCTCTCCTCGCAGGGCAGCGCCCACGACGAGAT
CGACTTCGAGTTCCTCGGCAACGCGAGCGGAGAGCCCTACACGGTGCACACCAACGTGTACAGCCAGGGGAAAGGCGGGC
GGGAGCAGCAGTTCCGGATGTGGTTCGACCCCACCGCGGACTTCCACGCCTACTCGGTGCTCTGGAACCCTTCCCACATC
GTCTTCTACGTCGACGGCGTCCCCATCCGCGAGTTCCGCCGCCGAAACGACGGCGCGGTGCCGTTCCCGACGTCGCAGCC
GATGCGGGTGTACGCCAGCGTGTGGGACGCCGAGGAGTGGGCCACGCAGGGCGGGCGTGTCAAGACGGACTGGTCCAAGG
CGCCCTTCGTCGCGTCGTACCAGGGGTACGCCGCCGCCGGCTGCACCGCGCCCGACGCCGCCGCGTGCGCCAGGTCCAAC
GGCGCCTGGATGTCGCAGGAGCTCGACAGCGCCGCGCAGGGGCAGCTCCGCCGGGCGCAGGCCAGCTACATGATCTACAA
CTACTGCACCGATAAGTACCGCTTCCCGCAGGGACCGCCGCCCGAGTGCTCGTCGCCGGCCAAGTA

Alignment

ORF - retro_sbic_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASAFSSSGACVLLALLLVLFATGAPTAAAAGRVDDGLEVTWGDGRGSVSPDGQVLSLSLDHTSGSGFRS
          MAS........VL.A..L.L...G....A..G........TWGDGRG.....GQ.L.LS.D..SGSGF.S
Retrocopy MASSAAPMKTLVLAAAMLLLLVHGG--VAGGGNFYQDVDITWGDGRGKILNNGQLLTLSMDRSSGSGFQS

Parental  KDTYLFARADAQIKLVPNNSAGTVTTFYFISEGPWDVHDEVDLEFLGNVSGQPYTLHTNVYANGNGGREQ
          K..YL..R.D.Q.KLVP.NSAGTVTTFY..S.G....HDE.D.EFLGN.SG.PYT.HTNVY..G.GGREQ
Retrocopy KSQYLYGRFDMQLKLVPGNSAGTVTTFYLSSQG--SAHDEIDFEFLGNASGEPYTVHTNVYSQGKGGREQ

Parental  QFHLWFDPTADFHTYSIEWTQQHILVLVDGTPIREFKNHADRGVPYPSSQRMRLYGSLWDAEDWATQGGR
          QF..WFDPTADFH.YS..W...HI...VDG.PIREF....D..VP.P.SQ.MR.Y.S.WDAE.WATQGGR
Retrocopy QFRMWFDPTADFHAYSVLWNPSHIVFYVDGVPIREFRRRNDGAVPFPTSQPMRVYASVWDAEEWATQGGR

Parental  VKTDWSQAPFVAQYRSFTAT--ATPPAAATTAGYGQQM----DAAAQQSMKWARDNYMVYDYCADTKRFP
          VKTDWS.APFVA.Y....A.....P.AAA.....G..M....D.AAQ.....A...YM.Y.YC.D..RFP
Retrocopy VKTDWSKAPFVASYQGYAAAGCTAPDAAACARSNGAWMSQELDSAAQGQLRRAQASYMIYNYCTDKYRFP

Parental  QGVPPECSMP
          QG.PPECS.P
Retrocopy QGPPPECSSP

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_4 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Physcomitrella patens	PP1S4_43V6	1 retrocopy	retro_ppat_17,
Sorghum bicolor	Sb06g027670	1 retrocopy	retro_sbic_4 ,