RetrogeneDB ID: retro_sbic_8

Retrocopy location

• Organism: Sorghum (Sorghum bicolor)
• Coordinates: 6:55815071..55816718(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Sb06g026810
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Sb10g022090
• Aliases: None
• Description: None

Sequence

>retro_sbic_8
ATGGCCATGGCTTCTTCCCAGCCGAAGCAGCAGATGTTCGGCGAGCCCATCTCTCTGGTTGGCCCGACGCCGGCCGACCT
CGAGGCCACGGCGGAGCTGGAGAAGGTCCTGCGCGAAGCGGGAATGTACGAGAGCCCCCAGGAGTCGGCTGTCCGCGCCG
AGGTGCTGCGCGACCTCCAGGGCATCGTCGACCGCTGGGTGAAGCAGCTCACGCTCAAGCATGGGTACCCCGACGCCATG
GTCGACGAGGCCACCGCCCTGCTGCTCCCCTTCGGATCCTACCGCCTCGGCGTCCACGGCGGCGGCTCCGACATCGACGC
GCTCGTCGTCGGTCCCTCCTTCGTGGACCGCGACCAAGACTTCTTCGGTGTGCTGGCCGGCGCGCTGGCCGAGGCGACGG
AGGCCGTGACGGACCTGCAGCCCGTGCCCGGCGCGCACGTCCCCGTCATGAAGCTTAGGTTCCGCGGCGTGCAGGTGGAC
CTCGTCTACGCCAGCGTCAACCTCCCCGTGGTGCCCCGGGACCTGGATCTGAGCGACCGCGCCGTGCTCCGCGGCCTGGA
CCACGTCACCGCCCGCAGCATGAACGGCGTGCGCGTGGCCGACGAGATCCTGCGGCTGGTCCCCGACGCCGCCGCGTTCC
GCACGGCGCTGCGGTGCGTGAAGCTGTGGGCCAAGGCGCGGGGCGTCTACTCCAACGTGTCCGGCTTCCTCGGCGGCGTG
GCCTGGGCCATCCTGGTGGCGCGCGTGTGCCAGCTCTACCCCAACGCCGCGCCCAGCATGCTGGTGTCGCGCTTCTTCAA
GGTGCTCAGCCAGTGGAAGTGGCCCACCCCGGTGATGCTCTGCGACATCGAGCACGACGACGAGCTTGGCCTCCCCGTCT
GGGACGGGCGGAGGAACCCGCGCGACCGGACGCACCTCATGCCTGTCATCACGCCGGCGTACCCGTGCATGAACTGCACC
TACAACGTCTCGCAGGCCACCCAGCGGATCATCAAGGAGCAGATCCAGGCCGGCCACGTCGCGTGCCAGGAGATCGCCGC
CGGCGGCGACCGCGGCTGGGGCGCGCTGTTCCAGCCGTTCCCGTTCTTCAGGACGCACAAGAGCTACCTGCAGGTGGACG
CGACGGTGGCGGGCGGCGAAGAAGAGCTCCGGGAGTGGAAGGGGTGGGTGGAGTCGCGGCTGCGGCAGCTGGTGGCCAAG
GTCGAGAGGGACACGTTCGGCGAGCTGCTGTGCCATCAGAACCCGCGCGCCTACGACGCCGAGCCACACGGCTTGCGGTG
CGCGTCGTCCTTCTTCGTGGGCTTGTCGAAGCCACAGCAGCAGCGACAGCAGCCATCCCCGCCGCAAGGGCAGCAGCCGC
AGTTTGACCTCCGTGCGACGGCGGACGAGTTCCTGCAGGACGTCTACACGTACAGGTTCTGGAGGCCCGGCTTGGAGTTG
GCCGTCAAGCACGTCCGGCGGAAGGACCTGCCGCCATACGTGATGCACAAGATTCGTGGTCCGAATATCCATGAGCTCAA
GAGGAAGCGCGACGACGACGATTCTTCACCTTCGTCGCCGACGTTGTGTTCGTCGTCATCCGCCTCCTCTTGTGACGATG
ACTCCGTCCGAAGACCTAGCAGCAGGGCAAGGCTGCATCCAACATAG

Alignment

ORF - retro_sbic_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.87 %
• Parental protein coverage: 92.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGSDPPKQYGITKPLSLLGPVEADLQRTAELEKFLVEAGLYESPDESARREEVLGKLDQIVKDWVKQL
          MA..S..PKQ.....P.SL.GP..ADL..TAELEK.L.EAG.YESP.ESA.R.EVL..L..IV..WVKQL
Retrocopy MAMASSQPKQQMFGEPISLVGPTPADLEATAELEKVLREAGMYESPQESAVRAEVLRDLQGIVDRWVKQL

Parental  TSQRGYTDQMVEEANAVLFTFGSYRLGVHGPGADIDTLCVGPSYVNREEDFFIVLHGILAQ-TEDVTELQ
          T...GY.D.MV.EA.A.L..FGSYRLGVHG.G.DID.L.VGPS.V.R..DFF.VL.G.LA..TE.VT.LQ
Retrocopy TLKHGYPDAMVDEATALLLPFGSYRLGVHGGGSDIDALVVGPSFVDRDQDFFGVLAGALAEATEAVTDLQ

Parental  PVPDAHVPVMKFKFHGISIDLLYASVSLLVVPADLDISQGSVLYDVDEATVRSLNGCRVADQIIRLVPNI
          PVP.AHVPVMK..F.G...DL.YASV.L.VVP.DLD.S...VL...D..T.RS.NG.RVAD.I.RLVP..
Retrocopy PVPGAHVPVMKLRFRGVQVDLVYASVNLPVVPRDLDLSDRAVLRGLDHVTARSMNGVRVADEILRLVPDA

Parental  ENFRTTLRCLKYWAKRRGVYSNVTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVFTQWQWPNPVML
          ..FRT.LRC.K.WAK.RGVYSNV.GFLGGV.WA.LVARVCQLYPNA.PSMLVSRFF.V..QW.WP.PVML
Retrocopy AAFRTALRCVKLWAKARGVYSNVSGFLGGVAWAILVARVCQLYPNAAPSMLVSRFFKVLSQWKWPTPVML

Parental  CSIE-EDEVGFPVWDPRKNPRDRCHHMPIITPAYPCMNSSYNVSTSTLRVMVEQFQFGNKICQEIEM-NK
          C.IE..DE.G.PVWD.R.NPRDR.H.MP.ITPAYPCMN..YNVS..T.R...EQ.Q.G...CQEI.....
Retrocopy CDIEHDDELGLPVWDGRRNPRDRTHLMPVITPAYPCMNCTYNVSQATQRIIKEQIQAGHVACQEIAAGGD

Parental  ASWSALFEPFQFFEAYKNYLQVD-IIAEDDEDLRLWKGWVESRLRQLTLKIERDTYGMLQCHPYPHEY-A
          ..W.ALF.PF.FF...K.YLQVD...A...E.LR.WKGWVESRLRQL..K.ERDT.G.L.CH..P..Y.A
Retrocopy RGWGALFQPFPFFRTHKSYLQVDATVAGGEEELREWKGWVESRLRQLVAKVERDTFGELLCHQNPRAYDA

Parental  DPSRQCAHCAFFMGLSRKE
          .P........FF.GLS...
Retrocopy EPHGLRCASSFFVGLSKPQ

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_8 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G109009	1 retrocopy	retro_zmay_18,
Hordeum vulgare	MLOC_32341	1 retrocopy	retro_hvul_46,
Sorghum bicolor	Sb10g022090	1 retrocopy	retro_sbic_8 ,