AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85309

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85309.t1 MTR_2g045020 80.214 187 24 2 10 196 1 174 1.01e-96 279
MS.gene85309.t1 MTR_3g437790 64.848 165 54 4 35 197 12 174 1.58e-60 187
MS.gene85309.t1 MTR_8g022970 51.124 178 80 5 24 197 3 177 5.50e-47 152
MS.gene85309.t1 MTR_3g109930 52.448 143 64 3 56 197 21 160 2.35e-41 138
MS.gene85309.t1 MTR_2g105290 37.654 162 89 6 36 190 5 161 7.37e-18 77.4
MS.gene85309.t1 MTR_7g028448 33.824 136 76 3 56 190 31 153 1.70e-17 76.3
MS.gene85309.t1 MTR_4g036915 33.824 136 76 3 56 190 31 153 1.70e-17 76.3
MS.gene85309.t1 MTR_8g086290 36.076 158 92 6 36 190 10 161 6.90e-15 69.7
MS.gene85309.t1 MTR_8g043650 33.918 171 87 8 24 184 2 156 3.38e-14 68.9
MS.gene85309.t1 MTR_2g030740 33.728 169 91 7 29 187 2 159 1.01e-13 67.8
MS.gene85309.t1 MTR_5g053390 30.864 162 105 6 29 187 2 159 4.71e-13 65.9
MS.gene85309.t1 MTR_3g052920 35.366 164 82 8 37 187 7 159 5.72e-13 65.5
MS.gene85309.t1 MTR_1g106070 33.951 162 87 8 37 187 7 159 9.14e-13 64.3
MS.gene85309.t1 MTR_1g105910 32.530 166 91 7 29 184 2 156 1.08e-12 64.7
MS.gene85309.t1 MTR_3g080940 28.834 163 95 6 38 190 11 162 3.01e-12 63.2
MS.gene85309.t1 MTR_1g012570 30.120 166 101 7 29 187 2 159 4.43e-12 63.2
MS.gene85309.t1 MTR_3g030770 31.138 167 98 6 29 187 2 159 2.03e-11 61.2
MS.gene85309.t1 MTR_1g105920 31.361 169 95 7 29 187 2 159 4.54e-11 60.5
MS.gene85309.t1 MTR_1g108510 31.138 167 98 6 29 187 2 159 4.90e-11 60.1
MS.gene85309.t1 MTR_4g127140 35.714 140 71 7 56 186 31 160 5.59e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85309.t1 AT2G24840 29.605 152 103 4 38 187 65 214 9.75e-14 68.2
MS.gene85309.t1 AT5G60440 32.704 159 91 7 38 187 9 160 1.78e-13 67.8

Find 27 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAAGACTTTAAGAATTCTT+TGG 0.239126 2.4:-45431723 MS.gene85309:CDS
GTGCTTCATATTGAAGCCTT+AGG 0.338858 2.4:+45431873 None:intergenic
TAGAATTATTCCACCAATCA+TGG 0.397833 2.4:+45431771 None:intergenic
TGATGTTGAATGAAACAAAC+TGG 0.408161 2.4:-45432252 MS.gene85309:CDS
TGCTTCATATTGAAGCCTTA+GGG 0.444644 2.4:+45431874 None:intergenic
GCATAGAACTTGTTCTTGTC+CGG 0.453036 2.4:+45431998 None:intergenic
GTGATGTCAATTTCCATGAT+TGG 0.461626 2.4:-45431784 MS.gene85309:CDS
ACGATGAATGACAGCATCAC+AGG 0.499770 2.4:+45431964 None:intergenic
TGTTCCAGCATTCTTTCTCT+CGG 0.500346 2.4:+45432177 None:intergenic
ATCCTCGACCATCATATGTC+CGG 0.509285 2.4:+45431934 None:intergenic
ATGAAATTGCTGAAACCCTA+AGG 0.533334 2.4:-45431889 MS.gene85309:CDS
GGACATATGATGGTCGAGGA+TGG 0.543275 2.4:-45431932 MS.gene85309:CDS
TGCAATCATCGTCAAATCGC+CGG 0.556447 2.4:-45432017 MS.gene85309:CDS
GAGTTCTCAAGACGCAAACT+CGG 0.557665 2.4:-45432088 MS.gene85309:CDS
TGTCTGAAAAGAACACTGCT+AGG 0.558447 2.4:-45432204 MS.gene85309:CDS
GACATATGATGGTCGAGGAT+GGG 0.560153 2.4:-45431931 MS.gene85309:CDS
AATTTACGTGCAGCAAGCGA+AGG 0.589056 2.4:-45431686 MS.gene85309:CDS
CGATGAATGACAGCATCACA+GGG 0.591570 2.4:+45431965 None:intergenic
GACCGGACATATGATGGTCG+AGG 0.605126 2.4:-45431936 MS.gene85309:CDS
GCTTCCGAGAGAAAGAATGC+TGG 0.609518 2.4:-45432181 MS.gene85309:CDS
GTCTGAAAAGAACACTGCTA+GGG 0.626438 2.4:-45432203 MS.gene85309:CDS
ATGTCAATTTCCATGATTGG+TGG 0.630551 2.4:-45431781 MS.gene85309:CDS
AAGAACAAGTTCTATGCATG+TGG 0.639320 2.4:-45431992 MS.gene85309:CDS
GAACAAAACTGAACAACACA+CGG 0.651271 2.4:-45432159 MS.gene85309:CDS
GATGTTGAATGAAACAAACT+GGG 0.726719 2.4:-45432251 MS.gene85309:CDS
GAAAGCTGTCAAAGTCACCG+AGG 0.773790 2.4:-45431816 MS.gene85309:CDS
GATGAATGACAGCATCACAG+GGG 0.800398 2.4:+45431966 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAAAGAAGAAAAACTGAA+CGG - chr2.4:45431814-45431833 MS.gene85309:CDS 25.0%
!! TGAAGACTTTAAGAATTCTT+TGG - chr2.4:45432206-45432225 MS.gene85309:CDS 25.0%
!!! AATTCTTTGGAGAGTTTTAA+GGG - chr2.4:45432219-45432238 MS.gene85309:CDS 25.0%
TAGAATTATTCCACCAATCA+TGG + chr2.4:45432161-45432180 None:intergenic 30.0%
TCAAGAAAAACTTGAAGAAG+AGG - chr2.4:45432080-45432099 MS.gene85309:CDS 30.0%
!! GAATTCTTTGGAGAGTTTTA+AGG - chr2.4:45432218-45432237 MS.gene85309:CDS 30.0%
AAGAACAAGTTCTATGCATG+TGG - chr2.4:45431937-45431956 MS.gene85309:CDS 35.0%
ATGAAATTGCTGAAACCCTA+AGG - chr2.4:45432040-45432059 MS.gene85309:CDS 35.0%
ATGTCAATTTCCATGATTGG+TGG - chr2.4:45432148-45432167 MS.gene85309:CDS 35.0%
GAACAAAACTGAACAACACA+CGG - chr2.4:45431770-45431789 MS.gene85309:CDS 35.0%
GTGATGTCAATTTCCATGAT+TGG - chr2.4:45432145-45432164 MS.gene85309:CDS 35.0%
TGCTTCATATTGAAGCCTTA+GGG + chr2.4:45432058-45432077 None:intergenic 35.0%
! CGATGATTGCAGTTTTTGAT+TGG + chr2.4:45431903-45431922 None:intergenic 35.0%
GTCTGAAAAGAACACTGCTA+GGG - chr2.4:45431726-45431745 MS.gene85309:CDS 40.0%
GTGCTTCATATTGAAGCCTT+AGG + chr2.4:45432059-45432078 None:intergenic 40.0%
TGTCTGAAAAGAACACTGCT+AGG - chr2.4:45431725-45431744 MS.gene85309:CDS 40.0%
TGTTCCAGCATTCTTTCTCT+CGG + chr2.4:45431755-45431774 None:intergenic 40.0%
! GCATAGAACTTGTTCTTGTC+CGG + chr2.4:45431934-45431953 None:intergenic 40.0%
! GTCATTCATCGTTTTCTGAC+CGG - chr2.4:45431976-45431995 MS.gene85309:CDS 40.0%
! TTTTCTGACCGGACATATGA+TGG - chr2.4:45431987-45432006 MS.gene85309:CDS 40.0%
AATTTACGTGCAGCAAGCGA+AGG - chr2.4:45432243-45432262 MS.gene85309:CDS 45.0%
ACGATGAATGACAGCATCAC+AGG + chr2.4:45431968-45431987 None:intergenic 45.0%
ATCCTCGACCATCATATGTC+CGG + chr2.4:45431998-45432017 None:intergenic 45.0%
CGATGAATGACAGCATCACA+GGG + chr2.4:45431967-45431986 None:intergenic 45.0%
GACATATGATGGTCGAGGAT+GGG - chr2.4:45431998-45432017 MS.gene85309:CDS 45.0%
GAGTTCTCAAGACGCAAACT+CGG - chr2.4:45431841-45431860 MS.gene85309:CDS 45.0%
GATGAATGACAGCATCACAG+GGG + chr2.4:45431966-45431985 None:intergenic 45.0%
TGCAATCATCGTCAAATCGC+CGG - chr2.4:45431912-45431931 MS.gene85309:CDS 45.0%
! GACATCACTCTTTTGTGCCT+CGG + chr2.4:45432133-45432152 None:intergenic 45.0%
GAAAGCTGTCAAAGTCACCG+AGG - chr2.4:45432113-45432132 MS.gene85309:CDS 50.0%
GCTTCCGAGAGAAAGAATGC+TGG - chr2.4:45431748-45431767 MS.gene85309:CDS 50.0%
GGACATATGATGGTCGAGGA+TGG - chr2.4:45431997-45432016 MS.gene85309:CDS 50.0%
GACCGGACATATGATGGTCG+AGG - chr2.4:45431993-45432012 MS.gene85309:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 45431679 45432272 45431679 ID=MS.gene85309
chr2.4 mRNA 45431679 45432272 45431679 ID=MS.gene85309.t1;Parent=MS.gene85309
chr2.4 exon 45431679 45432272 45431679 ID=MS.gene85309.t1.exon1;Parent=MS.gene85309.t1
chr2.4 CDS 45431679 45432272 45431679 ID=cds.MS.gene85309.t1;Parent=MS.gene85309.t1
Gene Sequence

>MS.gene85309

ATGTTGAATGAAACAAACTGGGACAACATGAATAAGAATTGTGAACTGTCTGAAAAGAACACTGCTAGGGCTTCCGAGAGAAAGAATGCTGGAACAAAACTGAACAACACACGGAAGAGAAAGATGCATGAAATCAAGAAAGAAGAAAAACTGAACGGTTCTGAGTTCTCAAGACGCAAACTCGGAATATTCAACAAAGCAATAGAACTGTCTATTCTATGCCAATCAAAAACTGCAATCATCGTCAAATCGCCGGACAAGAACAAGTTCTATGCATGTGGCTACCCCTGTGATGCTGTCATTCATCGTTTTCTGACCGGACATATGATGGTCGAGGATGGGAAAAAGAAGAAACAAGATGATGAAATTGCTGAAACCCTAAGGCTTCAATATGAAGCACTTCAAGAAAAACTTGAAGAAGAGGATGATAATTTGAAAGCTGTCAAAGTCACCGAGGCACAAAAGAGTGATGTCAATTTCCATGATTGGTGGAATAATTCTATTGATGATATGAATTTAGCATCTCTTGAAGACTTTAAGAATTCTTTGGAGAGTTTTAAGGGTAATTTACGTGCAGCAAGCGAAGGAAAGTAG
Protein sequence

>MS.gene85309.t1

MLNETNWDNMNKNCELSEKNTARASERKNAGTKLNNTRKRKMHEIKKEEKLNGSEFSRRKLGIFNKAIELSILCQSKTAIIVKSPDKNKFYACGYPCDAVIHRFLTGHMMVEDGKKKKQDDEIAETLRLQYEALQEKLEEEDDNLKAVKVTEAQKSDVNFHDWWNNSIDDMNLASLEDFKNSLESFKGNLRAASEGK