AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene035030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene035030.t1 MTR_1g063150 63.136 236 28 4 38 271 21 199 1.02e-89 265
MS.gene035030.t1 MTR_1g085590 52.098 286 84 12 6 269 15 269 3.74e-67 211
MS.gene035030.t1 MTR_1g063140 59.777 179 27 5 91 265 1 138 4.65e-54 173
MS.gene035030.t1 MTR_1g046810 44.255 235 68 10 53 242 94 310 5.52e-40 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGAAGGTGAAACAGAATT+AGG 0.205798 1.3:-45625118 MS.gene035030:CDS
AAAGAGAAAGAAGGGTATTT+AGG 0.220162 1.3:+45625712 None:intergenic
CTTAGCACTTGCCGTTTCTT+AGG 0.240976 1.3:+45625436 None:intergenic
CTCTTCAATACTTTGATTAG+AGG 0.294988 1.3:+45625150 None:intergenic
TGAATCACCGTGGTGCTAAA+AGG 0.300323 1.3:-45625315 MS.gene035030:CDS
ACTTCTAACAAAGCTTTGAA+TGG 0.400226 1.3:-45625529 MS.gene035030:CDS
ACGGTGATTCAAATTGATAT+TGG 0.408428 1.3:+45625327 None:intergenic
ATGAAGGTGAAACAGAATTA+GGG 0.423059 1.3:-45625117 MS.gene035030:CDS
GGAGCTATGGTCAACATGAT+TGG 0.423303 1.3:+45625744 None:intergenic
TATTCTGTTCCTAATGATGC+TGG 0.432407 1.3:-45625595 MS.gene035030:CDS
TCTTCAACAACTAATGATGC+TGG 0.461941 1.3:-45625646 MS.gene035030:CDS
CTGGAAAACAGAAGATCATA+TGG 0.475072 1.3:-45625627 MS.gene035030:CDS
ATATCTCGTGGCGGTTTCGA+CGG 0.494058 1.3:-45625358 MS.gene035030:CDS
ATACTTTGATTAGAGGCAGC+AGG 0.495332 1.3:+45625157 None:intergenic
GAAGAGAAGAAGATTAATGA+AGG 0.510676 1.3:-45625133 MS.gene035030:CDS
AATCAATGAAAGAGAAAGAA+GGG 0.516168 1.3:+45625704 None:intergenic
ATCTTCCTCTGCAAGCTATG+AGG 0.522500 1.3:-45625473 MS.gene035030:CDS
TATGATGGATGCTAATATGA+TGG 0.534594 1.3:-45625275 MS.gene035030:CDS
TGATATTGAGAAGACGAAGA+AGG 0.543732 1.3:-45625251 MS.gene035030:CDS
TAATCAATGAAAGAGAAAGA+AGG 0.544898 1.3:+45625703 None:intergenic
TCATAGCTTGCAGAGGAAGA+TGG 0.548781 1.3:+45625475 None:intergenic
ACTTCCTACCACCTAAGAAA+CGG 0.558147 1.3:-45625447 MS.gene035030:CDS
TCATCTTCAAAATCATCACT+TGG 0.561254 1.3:+45624989 None:intergenic
AAATTCTTCACATCATCACT+TGG 0.564670 1.3:+45625028 None:intergenic
AGCACTTGCCGTTTCTTAGG+TGG 0.568114 1.3:+45625439 None:intergenic
TTCATGTGATGTTTGCAACA+AGG 0.571040 1.3:-45625557 MS.gene035030:CDS
CTTGCCGTTTCTTAGGTGGT+AGG 0.575022 1.3:+45625443 None:intergenic
TATTGCAGCTGAAACTCTGT+TGG 0.580874 1.3:-45625383 MS.gene035030:CDS
AAATTCATCACATCATCACT+TGG 0.595232 1.3:+45625058 None:intergenic
GAGGAAGATGGTGCAACAGT+TGG 0.627306 1.3:+45625487 None:intergenic
ACGAAGAAGGAGAAAGAACA+AGG 0.647791 1.3:-45625238 MS.gene035030:CDS
CTGTTGGATATATCTCGTGG+CGG 0.650335 1.3:-45625367 MS.gene035030:CDS
GTGATCCTCATAGCTTGCAG+AGG 0.672732 1.3:+45625468 None:intergenic
ACTCTGTTGGATATATCTCG+TGG 0.678764 1.3:-45625370 MS.gene035030:CDS
AATATCAATTTGAATCACCG+TGG 0.727003 1.3:-45625325 MS.gene035030:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGGTTTTGTTATGATTA+GGG + chr1.3:45625080-45625099 None:intergenic 20.0%
!!! TTTTTGGTTTTGTTATGATT+AGG + chr1.3:45625081-45625100 None:intergenic 20.0%
! AATCAATGAAAGAGAAAGAA+GGG + chr1.3:45625050-45625069 None:intergenic 25.0%
! TAATCAATGAAAGAGAAAGA+AGG + chr1.3:45625051-45625070 None:intergenic 25.0%
!! AAAACTCTTTTGCAATATGA+TGG - chr1.3:45625461-45625480 MS.gene035030:CDS 25.0%
!! AGTTGTTGAAGAAAAGTTTT+TGG + chr1.3:45625097-45625116 None:intergenic 25.0%
AAATTCATCACATCATCACT+TGG + chr1.3:45625696-45625715 None:intergenic 30.0%
AAATTCTTCACATCATCACT+TGG + chr1.3:45625726-45625745 None:intergenic 30.0%
AATATCAATTTGAATCACCG+TGG - chr1.3:45625426-45625445 MS.gene035030:CDS 30.0%
AATGAAGGTGAAACAGAATT+AGG - chr1.3:45625633-45625652 MS.gene035030:CDS 30.0%
ACGGTGATTCAAATTGATAT+TGG + chr1.3:45625427-45625446 None:intergenic 30.0%
ATGAAGGTGAAACAGAATTA+GGG - chr1.3:45625634-45625653 MS.gene035030:CDS 30.0%
CTCTTCAATACTTTGATTAG+AGG + chr1.3:45625604-45625623 None:intergenic 30.0%
GAAGAGAAGAAGATTAATGA+AGG - chr1.3:45625618-45625637 MS.gene035030:CDS 30.0%
TCATCTTCAAAATCATCACT+TGG + chr1.3:45625765-45625784 None:intergenic 30.0%
!! AAAGAGAAAGAAGGGTATTT+AGG + chr1.3:45625042-45625061 None:intergenic 30.0%
!! ACTTCTAACAAAGCTTTGAA+TGG - chr1.3:45625222-45625241 MS.gene035030:CDS 30.0%
!! AGGGTATTTAGGTTTTTGAA+GGG + chr1.3:45625031-45625050 None:intergenic 30.0%
!! TATGATGGATGCTAATATGA+TGG - chr1.3:45625476-45625495 MS.gene035030:CDS 30.0%
!!! AAGGGTATTTAGGTTTTTGA+AGG + chr1.3:45625032-45625051 None:intergenic 30.0%
!!! TTTTGTTTTCCAGCATCATT+AGG + chr1.3:45625168-45625187 None:intergenic 30.0%
CTGGAAAACAGAAGATCATA+TGG - chr1.3:45625124-45625143 MS.gene035030:CDS 35.0%
TATTCTGTTCCTAATGATGC+TGG - chr1.3:45625156-45625175 MS.gene035030:CDS 35.0%
TCTTCAACAACTAATGATGC+TGG - chr1.3:45625105-45625124 MS.gene035030:CDS 35.0%
TGATATTGAGAAGACGAAGA+AGG - chr1.3:45625500-45625519 MS.gene035030:CDS 35.0%
TTCATGTGATGTTTGCAACA+AGG - chr1.3:45625194-45625213 MS.gene035030:CDS 35.0%
!!! TGGTCAACATGATTGGTTTT+TGG + chr1.3:45625003-45625022 None:intergenic 35.0%
ACGAAGAAGGAGAAAGAACA+AGG - chr1.3:45625513-45625532 MS.gene035030:CDS 40.0%
ACTCTGTTGGATATATCTCG+TGG - chr1.3:45625381-45625400 MS.gene035030:CDS 40.0%
ACTTCCTACCACCTAAGAAA+CGG - chr1.3:45625304-45625323 MS.gene035030:CDS 40.0%
ATACTTTGATTAGAGGCAGC+AGG + chr1.3:45625597-45625616 None:intergenic 40.0%
TATTGCAGCTGAAACTCTGT+TGG - chr1.3:45625368-45625387 MS.gene035030:CDS 40.0%
! GTTTTTGCCTTTTAGCACCA+CGG + chr1.3:45625446-45625465 None:intergenic 40.0%
!! TAGGTTTTTGAAGGGAGCTA+TGG + chr1.3:45625023-45625042 None:intergenic 40.0%
ATCTTCCTCTGCAAGCTATG+AGG - chr1.3:45625278-45625297 MS.gene035030:CDS 45.0%
CTGTTGGATATATCTCGTGG+CGG - chr1.3:45625384-45625403 MS.gene035030:CDS 45.0%
GGAGCTATGGTCAACATGAT+TGG + chr1.3:45625010-45625029 None:intergenic 45.0%
! CTTAGCACTTGCCGTTTCTT+AGG + chr1.3:45625318-45625337 None:intergenic 45.0%
! TCATAGCTTGCAGAGGAAGA+TGG + chr1.3:45625279-45625298 None:intergenic 45.0%
! TGAATCACCGTGGTGCTAAA+AGG - chr1.3:45625436-45625455 MS.gene035030:CDS 45.0%
ATATCTCGTGGCGGTTTCGA+CGG - chr1.3:45625393-45625412 MS.gene035030:CDS 50.0%
GAGGAAGATGGTGCAACAGT+TGG + chr1.3:45625267-45625286 None:intergenic 50.0%
! AGCACTTGCCGTTTCTTAGG+TGG + chr1.3:45625315-45625334 None:intergenic 50.0%
! CTTGCCGTTTCTTAGGTGGT+AGG + chr1.3:45625311-45625330 None:intergenic 50.0%
! GTGATCCTCATAGCTTGCAG+AGG + chr1.3:45625286-45625305 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 45624979 45625794 45624979 ID=MS.gene035030
chr1.3 mRNA 45624979 45625794 45624979 ID=MS.gene035030.t1;Parent=MS.gene035030
chr1.3 exon 45624979 45625794 45624979 ID=MS.gene035030.t1.exon1;Parent=MS.gene035030.t1
chr1.3 CDS 45624979 45625794 45624979 ID=cds.MS.gene035030.t1;Parent=MS.gene035030.t1
Gene Sequence

>MS.gene035030

ATGTCTTCTTTTGATCATAAACCAAAAACCAATCATGTTGACCATAGCTCCCTTCAAAAACCTAAATACCCTTCTTTCTCTTTCATTGATTATTCAAACCCTAATCATAACAAAACCAAAAACTTTTCTTCAACAACTAATGATGCTGGAAAACAGAAGATCATATGGTTTTTTTCTTATTCTGTTCCTAATGATGCTGGAAAACAAAAGAAACATTCATGTGATGTTTGCAACAAGGTTTTTACTTCTAACAAAGCTTTGAATGGACATATGATATGTCACTCACCAACTGTTGCACCATCTTCCTCTGCAAGCTATGAGGATCACTTCCTACCACCTAAGAAACGGCAAGTGCTAAGAAGAAGTTATATGAATAATGATGACGATGCTATTGCAGCTGAAACTCTGTTGGATATATCTCGTGGCGGTTTCGACGGATCAACTACCAATATCAATTTGAATCACCGTGGTGCTAAAAGGCAAAAACTCTTTTGCAATATGATGGATGCTAATATGATGGATGATATTGAGAAGACGAAGAAGGAGAAAGAACAAGGTGTGTTGCTAACAAGTGCTACAGACATGATTTTTCAAACATCACAAGATTGCAAGCAACCTGCTGCCTCTAATCAAAGTATTGAAGAGAAGAAGATTAATGAAGGTGAAACAGAATTAGGGTCAAAAGTTGTGAATTTTTTTGATTTGAACGAGCTTCCAAGTGATGATGTGATGAATTTTGAGCTTCCAAGTGATGATGTGAAGAATTTTGATTTGAATGAGCTTCCAAGTGATGATTTTGAAGATGAAATCAATTAG
Protein sequence

>MS.gene035030.t1

MSSFDHKPKTNHVDHSSLQKPKYPSFSFIDYSNPNHNKTKNFSSTTNDAGKQKIIWFFSYSVPNDAGKQKKHSCDVCNKVFTSNKALNGHMICHSPTVAPSSSASYEDHFLPPKKRQVLRRSYMNNDDDAIAAETLLDISRGGFDGSTTNINLNHRGAKRQKLFCNMMDANMMDDIEKTKKEKEQGVLLTSATDMIFQTSQDCKQPAASNQSIEEKKINEGETELGSKVVNFFDLNELPSDDVMNFELPSDDVKNFDLNELPSDDFEDEIN