Cotton_D_gene_10026369, Cotton_D_gene_10026369 (mRNA) Gossypium raimondii

Transcript Overview
NameCotton_D_gene_10026369
Unique NameCotton_D_gene_10026369-BGI-CGP_v1.0
TypemRNA
OrganismGossypium raimondii (Gossypium raimondii)
Sequence length408
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
scaffold194supercontigscaffold194:1988787..1989194 -Gossypium raimondii (D5) 'D5-3' genome BGI-CGP-draft_v1n/a
Analyses
This mRNA is derived from or has results from the following analyses
Analysis NameDate Performed
Gossypium raimondii (D5) 'D5-3' genome BGI-CGP-draft_v12012-01-11
BLASTx of BGI-CGP D genome v1.0 vs UniProt Swiss-Prot2019-06-28
BLASTx of BGI-CGP D genome v1.0 vs Uniprot TrEMBL2019-06-26
BLASTx of BGI-CGP D genome v1.0 vs Araport112019-06-26
BLASTx of BGI-CGP D genome v1.0 vs NCBI nr2019-06-28
Orthologs

Syntenic blocks
Syntentic blockAssemblySpecies
hbrbL0646Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1Gossypium hirsutum
hbrbL1531Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1Gossypium hirsutum
hbrbL2511Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1Gossypium hirsutum
abrbL0212Gossypium arboreum (A2) 'SXY1' genome CGP-BGI_v2_a1Gossypium arboreum
abrbL0213Gossypium arboreum (A2) 'SXY1' genome CGP-BGI_v2_a1Gossypium arboreum
rbrbL592Gossypium raimondii (D5) 'D5-3' genome BGI-CGP-draft_v1Gossypium raimondii
rbrbL593Gossypium raimondii (D5) 'D5-3' genome BGI-CGP-draft_v1Gossypium raimondii
rbrbL691Gossypium raimondii (D5) 'D5-3' genome BGI-CGP-draft_v1Gossypium raimondii
rbrbL748Gossypium raimondii (D5) 'D5-3' genome BGI-CGP-draft_v1Gossypium raimondii
acrbL1535Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1Gossypium arboreum
acrbL1729Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1Gossypium arboreum
acrbL1730Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1Gossypium arboreum
acrbL1889Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1Gossypium arboreum
hzrbL1590Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1Gossypium hirsutum
hzrbL1762Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1Gossypium hirsutum
hzrbL2034Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1Gossypium hirsutum
hzrbL3561Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1Gossypium hirsutum
hzrbL3750Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1Gossypium hirsutum
hzrbL3897Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1Gossypium hirsutum
bzrbL1581Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1Gossypium barbadense
bzrbL1747Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1Gossypium barbadense
bzrbL2016Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1Gossypium barbadense
bzrbL3548Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1Gossypium barbadense
bzrbL3741Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1Gossypium barbadense
bzrbL3887Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1Gossypium barbadense
ghzrbL1512Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1Gossypium hirsutum
ghzrbL1681Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1Gossypium hirsutum
ghzrbL1946Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1Gossypium hirsutum
ghzrbL3411Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1Gossypium hirsutum
ghzrbL3602Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1Gossypium hirsutum
ghzrbL3751Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1Gossypium hirsutum
ghtrbL1573Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1Gossypium hirsutum
ghtrbL1738Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1Gossypium hirsutum
ghtrbL2014Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1Gossypium hirsutum
ghtrbL3499Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1Gossypium hirsutum
ghtrbL3693Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1Gossypium hirsutum
ghtrbL3843Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1Gossypium hirsutum
fnrbL1419Gossypium longicalyx (F1) genome NSF_v1Gossypium longicalyx
fnrbL1596Gossypium longicalyx (F1) genome NSF_v1Gossypium longicalyx
fnrbL1597Gossypium longicalyx (F1) genome NSF_v1Gossypium longicalyx
fnrbL1748Gossypium longicalyx (F1) genome NSF_v1Gossypium longicalyx
hwrbL1463Gossypium herbaceum (A1) 'Mutema' genome WHU_v1Gossypium herbaceum
hwrbL1648Gossypium herbaceum (A1) 'Mutema' genome WHU_v1Gossypium herbaceum
hwrbL1649Gossypium herbaceum (A1) 'Mutema' genome WHU_v1Gossypium herbaceum
hwrbL1798Gossypium herbaceum (A1) 'Mutema' genome WHU_v1Gossypium herbaceum
rbtwR2113Gossypium hirsutum (AD1) 'TM-1' genome WHU_v1Gossypium hirsutum
rbtwR2114Gossypium hirsutum (AD1) 'TM-1' genome WHU_v1Gossypium hirsutum
rbtwR2115Gossypium hirsutum (AD1) 'TM-1' genome WHU_v1Gossypium hirsutum
rbtwR2116Gossypium hirsutum (AD1) 'TM-1' genome WHU_v1Gossypium hirsutum
rbtwR2119Gossypium hirsutum (AD1) 'TM-1' genome WHU_v1Gossypium hirsutum
rbtwR2120Gossypium hirsutum (AD1) 'TM-1' genome WHU_v1Gossypium hirsutum
grzrbL1319Gossypium raimondii (D5) 'GPD5lz' genome HAU_v1Gossypium raimondii
grzrbL1483Gossypium raimondii (D5) 'GPD5lz' genome HAU_v1Gossypium raimondii
grzrbL1628Gossypium raimondii (D5) 'GPD5lz' genome HAU_v1Gossypium raimondii
Relationships

The following CDS feature(s) are a part of this mRNA:

Feature NameUnique NameSpeciesType
Cotton_D_gene_10026369_CDS_1Cotton_D_gene_10026369_CDS_1-BGI-CGP_v1.0Gossypium raimondiiCDS


Homology
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BLAST of Cotton_D_gene_10026369 vs. ExPASy TrEMBL
Match: A0A1U8IJE6_GOSHI (NAD(P)H-quinone oxidoreductase subunit H, chloroplastic-like OS=Gossypium hirsutum OX=3635 GN=LOC107895763 PE=4 SV=1)

HSP 1 Score: 126.331 bits (316), Expect = 2.386e-34
Identity = 61/92 (66.30%), Postives = 70/92 (76.09%), Query Frame = 0 
Query:   14 PTLASDNPEFGTEALTWVVREVLEKVVEARLERTREMLQARCVDCGKKKDRNPPRLEPRSPKRVRTHLSGNKYVAKGASSGASTPFFEHCKK 105
            PT  SDNPEFGTEAL+W+VREVLEKV EAR+  T E  Q+RCVDC KK+DR+P RLEPRS K VRT+LSGN     G  SG S PF +HC+K
Sbjct:   76 PTSHSDNPEFGTEALSWIVREVLEKVFEARIRGTSETFQSRCVDCRKKRDRSPLRLEPRSTKHVRTYLSGNNSFTVGNGSGVSAPFCKHCRK 167
[Close]
BLAST of Cotton_D_gene_10026369 vs. ExPASy TrEMBL
Match: A0A0B0PKM6_GOSAR (Xylose operon regulatory OS=Gossypium arboreum OX=29729 GN=F383_32783 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.050e-9
Identity = 33/81 (40.74%), Postives = 50/81 (61.73%), Query Frame = 0 
Query:   14 PTLASDNPEFGTEALTWVVREVLEKVVEARLERTREMLQARCVDCGKKKDRNPPRLEPRSPKRVRTHLSGNKYVAKGASSG 94
            PT  S N + G EAL  ++R+V+E+V+E +++  RE LQ  C+ C K+KD +  + EPRS K V+T      + A  +SSG
Sbjct:   15 PTSGSGNSDLGIEALAELIRKVVEEVLETKVKEIRETLQTGCLQCKKRKDSSSQKTEPRSMKHVKTR---QNFPALASSSG 92
[Close]
BLAST of Cotton_D_gene_10026369 vs. ExPASy TrEMBL
Match: A0A2P5YUJ1_GOSBA (Uncharacterized protein OS=Gossypium barbadense OX=3634 GN=GOBAR_AA01319 PE=4 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 2.373e-7
Identity = 36/95 (37.89%), Postives = 50/95 (52.63%), Query Frame = 0 
Query:   16 LASDNPEFGTEALTWVVREVLEKVVEARLERTREMLQARCVDCGKKKDRNPPRLEPRSPKRVRTHLSGNKYVAKGASSGASTPFFEHCKKRHPKN 110
            +   N + G EALT +VREVLE V EARL +       RCV+CG K+  +P R      KR+++     K  A+G  SG+ T   EH     P++
Sbjct:    1 MGGGNSKVGVEALTQLVREVLEAVFEARLGKI------RCVECGNKRGCSPSRSVSLVVKRLKSQQKLEKGNAEG--SGSGTNIVEHVSDVCPRS 87
[Close]
BLAST of Cotton_D_gene_10026369 vs. NCBI nr
Match: gi|1029025225|ref|XP_016676478.1| (PREDICTED: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic-like [Gossypium hirsutum])

HSP 1 Score: 126.331 bits (316), Expect = 2.840e-34
Identity = 61/92 (66.30%), Postives = 70/92 (76.09%), Query Frame = 0 
Query:   14 PTLASDNPEFGTEALTWVVREVLEKVVEARLERTREMLQARCVDCGKKKDRNPPRLEPRSPKRVRTHLSGNKYVAKGASSGASTPFFEHCKK 105
            PT  SDNPEFGTEAL+W+VREVLEKV EAR+  T E  Q+RCVDC KK+DR+P RLEPRS K VRT+LSGN     G  SG S PF +HC+K
Sbjct:   76 PTSHSDNPEFGTEALSWIVREVLEKVFEARIRGTSETFQSRCVDCRKKRDRSPLRLEPRSTKHVRTYLSGNNSFTVGNGSGVSAPFCKHCRK 167
The following BLAST results are available for this feature:
BLAST of Cotton_D_gene_10026369 vs. ExPASy Swiss-Prot
Analysis Date: 2019-06-28 (BLASTx of BGI-CGP D genome v1.0 vs UniProt Swiss-Prot)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Cotton_D_gene_10026369 vs. ExPASy TrEMBL
Analysis Date: 2019-06-26 (BLASTx of BGI-CGP D genome v1.0 vs Uniprot TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A1U8IJE6_GOSHI2.386e-3466.30NAD(P)H-quinone oxidoreductase subunit H, chloropl... [more]
A0A0B0PKM6_GOSAR1.050e-940.74Xylose operon regulatory OS=Gossypium arboreum OX=... [more]
A0A2P5YUJ1_GOSBA2.373e-737.89Uncharacterized protein OS=Gossypium barbadense OX... [more]
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BLAST of Cotton_D_gene_10026369 vs. TAIR10
Analysis Date: 2019-06-26 (BLASTx of BGI-CGP D genome v1.0 vs Araport11)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Cotton_D_gene_10026369 vs. NCBI nr
Analysis Date: 2019-06-28 (BLASTx of BGI-CGP D genome v1.0 vs NCBI nr)
Total hits: 1
Match NameE-valueIdentityDescription
gi|1029025225|ref|XP_016676478.1|2.840e-3466.30PREDICTED: NAD(P)H-quinone oxidoreductase subunit ... [more]
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Sequences
The following sequences are available for this feature:

mRNA sequence

>Cotton_D_gene_10026369-BGI-CGP_v1.0 ID=Cotton_D_gene_10026369-BGI-CGP_v1.0; Name=Cotton_D_gene_10026369; organism=Gossypium raimondii; type=mRNA; length=408bp
ATGTGTGTCTATTCAAGAGTCAGAGGTCAATGCGATTCTCCAACTTTAGC
TAGCGATAACCCGGAGTTTGGTACTGAGGCATTGACTTGGGTAGTGAGGG
AAGTGCTAGAGAAAGTGGTTGAGGCTAGGTTAGAGAGGACTAGAGAAATG
CTTCAAGCTAGGTGCGTAGATTGTGGGAAGAAAAAAGATCGCAATCCTCC
GAGGTTGGAGCCTCGGTCTCCGAAGCGTGTTAGAACGCATTTGAGTGGAA
ATAAATATGTTGCAAAGGGTGCCAGTAGTGGTGCGAGCACTCCGTTTTTT
GAGCACTGTAAGAAACGTCATCCGAAAAATTACTGGAAAAAGGCAGGAGC
ATGTTTTCGAAACAGGTCCACAGAACATCAGATTCGAGAGTGTCCTCGAC
GACTTTGA
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mRNA from alignment at scaffold194:1988787..1989194-

Legend: CDS
Hold the cursor over a type above to highlight its positions in the sequence below.
>Cotton_D_gene_10026369-BGI-CGP_v1.0 ID=Cotton_D_gene_10026369-BGI-CGP_v1.0; Name=Cotton_D_gene_10026369; organism=Gossypium raimondii; type=mRNA; length=408bp; location=Sequence derived from: scaffold194:1988787..1989194- (Gossypium raimondii
ATGTGTGTCTATTCAAGAGTCAGAGGTCAATGCGATTCTCCAACTTTAGC
TAGCGATAACCCGGAGTTTGGTACTGAGGCATTGACTTGGGTAGTGAGGG
AAGTGCTAGAGAAAGTGGTTGAGGCTAGGTTAGAGAGGACTAGAGAAATG
CTTCAAGCTAGGTGCGTAGATTGTGGGAAGAAAAAAGATCGCAATCCTCC
GAGGTTGGAGCCTCGGTCTCCGAAGCGTGTTAGAACGCATTTGAGTGGAA
ATAAATATGTTGCAAAGGGTGCCAGTAGTGGTGCGAGCACTCCGTTTTTT
GAGCACTGTAAGAAACGTCATCCGAAAAATTACTGGAAAAAGGCAGGAGC
ATGTTTTCGAAACAGGTCCACAGAACATCAGATTCGAGAGTGTCCTCGAC
GACTTTGA
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Coding sequence (CDS) from alignment at scaffold194:1988787..1989194-

>Cotton_D_gene_10026369-BGI-CGP_v1.0 ID=Cotton_D_gene_10026369-BGI-CGP_v1.0; Name=Cotton_D_gene_10026369; organism=Gossypium raimondii; type=CDS; length=408bp; location=Sequence derived from: scaffold194:1988787..1989194- (Gossypium raimondii
ATGTGTGTCTATTCAAGAGTCAGAGGTCAATGCGATTCTCCAACTTTAGC
TAGCGATAACCCGGAGTTTGGTACTGAGGCATTGACTTGGGTAGTGAGGG
AAGTGCTAGAGAAAGTGGTTGAGGCTAGGTTAGAGAGGACTAGAGAAATG
CTTCAAGCTAGGTGCGTAGATTGTGGGAAGAAAAAAGATCGCAATCCTCC
GAGGTTGGAGCCTCGGTCTCCGAAGCGTGTTAGAACGCATTTGAGTGGAA
ATAAATATGTTGCAAAGGGTGCCAGTAGTGGTGCGAGCACTCCGTTTTTT
GAGCACTGTAAGAAACGTCATCCGAAAAATTACTGGAAAAAGGCAGGAGC
ATGTTTTCGAAACAGGTCCACAGAACATCAGATTCGAGAGTGTCCTCGAC
GACTTTGA
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