XM_017364438.1

Resource Type: 
Polypeptide
Name: 
XM_017364438.1
Identifier: 
XM_017364438.1-protein
Sequence: 
MALKLLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGPNRRLLPYVDCQ
GLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTT
HGNRPKCP
Sequence Length: 
108
Sequence Checksum: 
adaf2a7011fa96dfef44843126bfa920
View location in JBrowse: 
DCARv2_Chr7:15414446..15415108+
Organism: 
Daucus carota subspecies sativus
Relationship: 
There is 1 relationship.
Relationships
The polypeptide, XM_017364438.1, derives from mRNA, XM_017364438.1.
Blast Results: 
The following BLAST results are available for this feature:
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Analysis Date: 2022-01-09
Analysis Name: NCBI peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 10
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2P5FDI7 ((Gibberellin regulated protein {ECO:0000313|EMBL:PON95860.1}))

HSP 1 Score: 159.073 bits (401), Expect = 1.787e-49
Identity = 74/108 (68.52%), Postives = 86/108 (79.63%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            MAL+L++L+ ++ F   Q+ S + I  QE     VVKGPNRRLLPY+DC GLC VRC  HSRPNVCTRACGTCCARCKCVPPGT GNR+ CGKCYT+M THGN+PKCP
Sbjct:    1 MALRLIILMAVLLFCLSQVSSESQIENQETHPAVVVKGPNRRLLPYLDCAGLCNVRCSKHSRPNVCTRACGTCCARCKCVPPGTAGNREVCGKCYTDMLTHGNKPKCP 108
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A5C7HHB5 ((Uncharacterized protein {ECO:0000313|EMBL:TXG56367.1}))

HSP 1 Score: 155.606 bits (392), Expect = 4.053e-48
Identity = 72/108 (66.67%), Postives = 87/108 (80.56%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            M+++L+LL++ + F  +Q+ S A I EQ+   + VVKG +RRLLP+VDC GLCK RC  HSRPNVCTRACGTCC RCKCVPPGT GNR  CG+CYT+MTTHGNRPKCP
Sbjct:    4 MSIRLVLLVSTLLFCIVQISSEAKI-EQDHQNIHVVKGSSRRLLPFVDCTGLCKARCSLHSRPNVCTRACGTCCVRCKCVPPGTSGNRHLCGRCYTDMTTHGNRPKCP 110
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2P5BCQ9 ((Gibberellin regulated protein {ECO:0000313|EMBL:PON46575.1}))

HSP 1 Score: 153.295 bits (386), Expect = 2.993e-47
Identity = 72/108 (66.67%), Postives = 84/108 (77.78%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            MAL+L++L+ ++ F   Q+ S      Q+     VVKGPNRRLLPY+DC GLC VRC  HSRPNVCTRACGTCCARCKCVPPGT GNR+ CGKCYT+M THGN+PKCP
Sbjct:    1 MALRLIILMAVLLFCLSQVSSEFQSENQKTHPAVVVKGPNRRLLPYLDCAGLCNVRCSKHSRPNVCTRACGTCCARCKCVPPGTAGNREVCGKCYTDMLTHGNKPKCP 108
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A2C9VUP1 ((Uncharacterized protein {ECO:0000313|EMBL:OAY49877.1}))

HSP 1 Score: 149.058 bits (375), Expect = 1.560e-45
Identity = 72/108 (66.67%), Postives = 84/108 (77.78%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            MAL+ LLL+ +  F   Q+ S   I EQ   + Q+VKGPNRRLLP++DC GLC+VRC  HSRPNVCTRACGTCC RCKCVPPGT G+R+ CGKCYT+MTTH NR KCP
Sbjct:    1 MALRSLLLVAIFLFCIAQVSSDMEIEEQ---STQLVKGPNRRLLPFLDCAGLCQVRCSLHSRPNVCTRACGTCCFRCKCVPPGTSGSRELCGKCYTDMTTHANRTKCP 105
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A6P6BG16 ((snakin-2-like {ECO:0000313|RefSeq:XP_022776048.1}))

HSP 1 Score: 147.902 bits (372), Expect = 3.936e-45
Identity = 69/104 (66.35%), Postives = 83/104 (79.81%), Query Frame = 0
 
Query:    5 LLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            L +LL ++FFS  Q+ +  +I +Q+    QVVKGP RRL P+VDC GLCKVRC  HSR N+CTRACGTCCARCKCVPPGT GNR+ CG+CYT+M THGN+PKCP
Sbjct:    6 LTILLLVLFFSIAQVSTETSIEDQQHT--QVVKGPRRRLFPFVDCGGLCKVRCSLHSRQNICTRACGTCCARCKCVPPGTSGNREMCGRCYTDMRTHGNKPKCP 107
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A1R3J518 ((Leucine-rich repeat, ribonuclease inhibitor subtype {ECO:0000313|EMBL:OMO89900.1}))

HSP 1 Score: 161.384 bits (407), Expect = 5.369e-45
Identity = 70/110 (63.64%), Postives = 80/110 (72.73%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSCAAIYEQE--QLALQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            M L+  LLL +MFF   Q+ S   I EQE  Q   QVVKGPNR+L  +VDC GLC+ RC  HSR NVC RACGTCCARC+CVPPGT GNR  CG+CYT+MTTHG + KCP
Sbjct:  664 MELRFTLLLLVMFFCITQVSSETKIEEQESTQSQSQVVKGPNRKLFSFVDCGGLCRTRCSLHSRQNVCMRACGTCCARCRCVPPGTSGNRHICGRCYTDMTTHGKKQKCP 773
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A438EHJ3 ((Snakin-2 {ECO:0000313|EMBL:RVW47193.1}))

HSP 1 Score: 146.362 bits (368), Expect = 1.623e-44
Identity = 71/109 (65.14%), Postives = 84/109 (77.06%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGP-NRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            M +++LLL+T++ F   +  S   I+E +    QVVKG   RRLLP++DC GLCK RC  HSRPNVCTRACGTCC RCKCVPPGTYGNR+ CG CYTEMTTHGN+PKCP
Sbjct:    1 MGIRVLLLVTILLFCIAEASSDNKIFEHQHN--QVVKGSAGRRLLPFLDCGGLCKERCSLHSRPNVCTRACGTCCVRCKCVPPGTYGNREMCGTCYTEMTTHGNKPKCP 107
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A438JNE2 ((Snakin-2 {ECO:0000313|EMBL:RVX10491.1}))

HSP 1 Score: 145.976 bits (367), Expect = 2.516e-44
Identity = 71/109 (65.14%), Postives = 84/109 (77.06%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSCAAIYEQEQLALQVVKGP-NRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            M +++LLL+T++ F   +  S   I+E +    QVVKG   RRLLP++DC GLCK RC  HSRPNVCTRACGTCC RCKCVPPGTYGNR+ CG CYTEMTTHGN+PKCP
Sbjct:    1 MGIRVLLLVTILLFCIAEASSDNKIFEHQHN--QVVKGSAGRRLLPFLDCGGLCKERCSLHSRPNVCTRACGTCCVRCKCVPPGTYGNREMCGICYTEMTTHGNKPKCP 107
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A1S2YTZ1 ((snakin-2-like {ECO:0000313|RefSeq:XP_004509878.1}))

HSP 1 Score: 145.591 bits (366), Expect = 3.960e-44
Identity = 69/110 (62.73%), Postives = 84/110 (76.36%), Query Frame = 0
 
Query:    1 MALKLLLLLTLMFFSTLQLRSC-AAIYEQEQLA-LQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            MAL LLL++T + F   Q  S  ++++ Q+Q    ++VKGPNRRLL +VDC   C VRC  HSRP VC RACGTCC RCKCVPPGTYGNR+ CG+CYT+MTTHGN+PKCP
Sbjct:    6 MALTLLLVMTFLLFCMAQASSVDSSVHIQDQFTNFELVKGPNRRLLAFVDCGRRCSVRCSMHSRPKVCMRACGTCCIRCKCVPPGTYGNREICGRCYTDMTTHGNKPKCP 115
[Close]
BLAST of XM_017364438.1 vs. ExPASy Swiss-Prot and TrEMBL without DCAR
Match: A0A1S3ZTP4 ((uncharacterized protein LOC107790377 {ECO:0000313|RefSeq:XP_016467785.1}))

HSP 1 Score: 146.747 bits (369), Expect = 1.253e-43
Identity = 67/86 (77.91%), Postives = 73/86 (84.88%), Query Frame = 0
 
Query:   23 AAIYEQEQLALQVVKGPNRRLLPYVDCQGLCKVRCGAHSRPNVCTRACGTCCARCKCVPPGTYGNRQACGKCYTEMTTHGNRPKCP 108
            ++  + E+   QVVKG NRRLLPYVDC GLCKVRC +HSRPNVCTRACGTCC RCKCVPPGT GNRQ CGKCYT+MTTHGNR KCP
Sbjct:   97 SSDIDIEEKQTQVVKGANRRLLPYVDCGGLCKVRCSSHSRPNVCTRACGTCCMRCKCVPPGTSGNRQVCGKCYTDMTTHGNRTKCP 182
Match NameStatsDescription
A0A2P5FDI7E-Value: 1.787e-49, PID: 68.52(Gibberellin regulated protein {ECO:0000313|EMBL:P... [more]
A0A5C7HHB5E-Value: 4.053e-48, PID: 66.67(Uncharacterized protein {ECO:0000313|EMBL:TXG5636... [more]
A0A2P5BCQ9E-Value: 2.993e-47, PID: 66.67(Gibberellin regulated protein {ECO:0000313|EMBL:P... [more]
A0A2C9VUP1E-Value: 1.560e-45, PID: 66.67(Uncharacterized protein {ECO:0000313|EMBL:OAY4987... [more]
A0A6P6BG16E-Value: 3.936e-45, PID: 66.35(snakin-2-like {ECO:0000313|RefSeq:XP_022776048.1}... [more]
A0A1R3J518E-Value: 5.369e-45, PID: 63.64(Leucine-rich repeat, ribonuclease inhibitor subty... [more]
A0A438EHJ3E-Value: 1.623e-44, PID: 65.14(Snakin-2 {ECO:0000313|EMBL:RVW47193.1})[more]
A0A438JNE2E-Value: 2.516e-44, PID: 65.14(Snakin-2 {ECO:0000313|EMBL:RVX10491.1})[more]
A0A1S2YTZ1E-Value: 3.960e-44, PID: 62.73(snakin-2-like {ECO:0000313|RefSeq:XP_004509878.1}... [more]
A0A1S3ZTP4E-Value: 1.253e-43, PID: 77.91(uncharacterized protein LOC107790377 {ECO:0000313... [more]
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Analysis: 
NameDescription
Carrot Genome Assembly DCARv2

An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4.

There are a few different naming schemes for this assembly. First there is the
Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.

Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0

LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926.

Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence.

RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records.

The NCBI Sequence report lists the correspondences between the various naming methods

Link to the LNRQ01000000.1 master record at NCBI

Raw Reads: Link to SRA accessions used for the genome assembly

This genome is available in the CarrotOmics Blast Search
NCBI Daucus carota subsp. sativus Annotation Release 100

The RefSeq genome records for Daucus carota subsp. sativus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

View the full report at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Daucus_carota_subsp._sativus/100/

Data from this analysis can be viewed in JBrowse here.
NCBI peptide blastp to SwissProt and TrEMBL without DCAR
This analysis is a blastp search of all of the NCBI Daucus carota subsp. sativus Annotation Release 100 polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the database was filtered to remove organisms not in the Viridiplantae, and also filtered to remove DCAR gene predictions from DCAR V1.0 Gene Prediction.