AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53519

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53519.t1 MTR_1g044785 98.696 230 3 0 1 230 1 230 3.95e-171 470
MS.gene53519.t1 MTR_1g073350 74.153 236 51 4 4 230 180 414 5.04e-114 332
MS.gene53519.t1 MTR_2g068730 61.194 67 26 0 115 181 144 210 1.22e-22 93.2
MS.gene53519.t1 MTR_8g098725 67.797 59 19 0 120 178 215 273 6.28e-22 92.4
MS.gene53519.t1 MTR_8g098725 67.797 59 19 0 120 178 211 269 6.41e-22 92.4
MS.gene53519.t1 MTR_5g010120 51.064 94 38 2 107 192 142 235 5.65e-21 88.6
MS.gene53519.t1 MTR_4g061823 57.812 64 27 0 119 182 130 193 1.19e-19 84.7
MS.gene53519.t1 MTR_4g061910 57.812 64 27 0 119 182 130 193 1.19e-19 84.7
MS.gene53519.t1 MTR_2g096080 54.286 70 32 0 110 179 131 200 1.73e-18 81.6
MS.gene53519.t1 MTR_1g008220 32.704 159 89 4 22 179 136 277 3.01e-16 76.3
MS.gene53519.t1 MTR_3g091340 65.306 49 17 0 130 178 197 245 9.45e-16 74.3
MS.gene53519.t1 MTR_3g091340 65.306 49 17 0 130 178 190 238 1.05e-15 73.9
MS.gene53519.t1 MTR_3g091340 65.306 49 17 0 130 178 226 274 1.91e-15 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53519.t1 AT1G04500 57.377 244 80 11 7 230 138 377 2.11e-77 238
MS.gene53519.t1 AT1G04500 57.377 244 80 11 7 230 147 386 2.43e-77 238
MS.gene53519.t1 AT1G04500 57.377 244 80 11 7 230 147 386 2.43e-77 238
MS.gene53519.t1 AT2G33350 57.143 238 83 8 8 230 165 398 3.48e-76 235
MS.gene53519.t1 AT2G33350 57.143 238 83 8 8 230 176 409 4.72e-76 235
MS.gene53519.t1 AT2G33350 57.143 238 83 8 8 230 185 418 6.51e-76 235
MS.gene53519.t1 AT2G33350 56.904 239 83 9 8 230 176 410 3.11e-74 231
MS.gene53519.t1 AT2G33350 51.250 160 62 7 8 155 176 331 3.27e-38 135
MS.gene53519.t1 AT1G04500 50.898 167 60 10 7 155 147 309 6.62e-36 130
MS.gene53519.t1 AT1G63820 44.828 145 67 4 59 196 118 256 1.77e-28 109
MS.gene53519.t1 AT5G41380 62.667 75 23 1 120 194 201 270 1.30e-24 99.4
MS.gene53519.t1 AT3G12890 52.747 91 39 1 121 211 126 212 7.94e-24 96.3
MS.gene53519.t1 AT4G27900 39.806 103 36 2 82 179 178 259 2.61e-16 75.9
MS.gene53519.t1 AT4G27900 39.806 103 36 2 82 179 178 259 2.61e-16 75.9
MS.gene53519.t1 AT5G53420 65.957 47 16 0 132 178 137 183 1.35e-15 72.8
MS.gene53519.t1 AT5G53420 65.957 47 16 0 132 178 137 183 1.35e-15 72.8
MS.gene53519.t1 AT5G53420 65.957 47 16 0 132 178 137 183 1.35e-15 72.8
MS.gene53519.t1 AT5G59990 41.322 121 52 2 109 227 138 241 2.07e-15 73.2
MS.gene53519.t1 AT5G53420 65.957 47 16 0 132 178 216 262 2.66e-15 73.2
MS.gene53519.t1 AT2G24790 40.000 75 41 1 112 182 203 277 4.29e-11 61.6

Find 45 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGCAAAGAATGATGATTT+TGG 0.172826 1.2:+27765913 MS.gene53519:CDS
GCTGATAGTTCTAGCTTATT+TGG 0.217917 1.2:+27764696 MS.gene53519:CDS
TTGGATTATCAAGGTGAAAA+TGG 0.259352 1.2:+27764759 MS.gene53519:CDS
TCCTCCAAGTGTGAAATTTC+TGG 0.285986 1.2:-27765642 None:intergenic
TTACTTCATCATCATCTTCA+TGG 0.288489 1.2:-27765963 None:intergenic
TTTGGTGGAGGAATTCTATT+AGG 0.299732 1.2:+27764714 MS.gene53519:CDS
TGAAATGCAGACACAAGATT+TGG 0.326244 1.2:+27764740 MS.gene53519:CDS
GATAGCCGACCGCGAGTTAG+AGG 0.377396 1.2:+27765886 MS.gene53519:CDS
TTGTACAGATTCTGTTCAAC+AGG 0.388571 1.2:+27764791 MS.gene53519:CDS
GAGGACTCTTCTTTGAAAGT+TGG 0.400610 1.2:+27765660 MS.gene53519:CDS
GAGAATCACAAACTAGTATC+TGG 0.409472 1.2:+27765591 MS.gene53519:CDS
TCTTGTTCTTATCTTAGTAA+TGG 0.420390 1.2:+27764627 MS.gene53519:CDS
TGTTAAAGAAGAAGATGATA+TGG 0.428400 1.2:+27766207 MS.gene53519:CDS
TCTTATCTTAGTAATGGCTT+AGG 0.445374 1.2:+27764633 MS.gene53519:CDS
GATAGTTCTAGCTTATTTGG+TGG 0.459834 1.2:+27764699 MS.gene53519:CDS
TGGAAGTTGTTCTGCCACTT+TGG 0.463869 1.2:+27765617 MS.gene53519:CDS
GGCACCAGAAATTTCACACT+TGG 0.479570 1.2:+27765638 MS.gene53519:CDS
TCTTCATGGTTGCTACTACC+TGG 0.484305 1.2:-27765949 None:intergenic
ACCAGAAATTTCACACTTGG+AGG 0.486593 1.2:+27765641 MS.gene53519:CDS
ACACAAGATTTGGATTATCA+AGG 0.487381 1.2:+27764750 MS.gene53519:CDS
TATATGCCTCATGGAAATCT+TGG 0.500992 1.2:+27764660 MS.gene53519:CDS
ATCATACCTGAAAATCTTGA+GGG 0.501022 1.2:-27764821 None:intergenic
GATGGAATAGTTGCATTTGA+AGG 0.501927 1.2:-27766272 None:intergenic
GAACAAGAAGGAGAATAAGA+AGG 0.504833 1.2:-27764612 None:intergenic
CACAAACTAGTATCTGGTGC+TGG 0.507442 1.2:+27765597 MS.gene53519:CDS
AGTTCTAGCTTATTTGGTGG+AGG 0.508335 1.2:+27764702 MS.gene53519:CDS
GAAAACTTTCTGTTGAGCAA+AGG 0.518365 1.2:+27765682 MS.gene53519:CDS
TCTAACTCGCGGTCGGCTAT+CGG 0.529354 1.2:-27765884 None:intergenic
GATTATCAAGGTGAAAATGG+TGG 0.531561 1.2:+27764762 MS.gene53519:CDS
GATCATACCTGAAAATCTTG+AGG 0.542555 1.2:-27764822 None:intergenic
CAATCATCTTCAAATACAGA+AGG 0.562025 1.2:-27764576 None:intergenic
AATTCAAATCAATGAGTGGA+TGG 0.563218 1.2:-27766290 None:intergenic
TTTGGGGAGAATCATAGGCC+AGG 0.573107 1.2:+27765931 MS.gene53519:CDS
AAATTTCAGCAAGAAAATCA+AGG 0.584947 1.2:+27765746 MS.gene53519:CDS
GATATCTTTGCACATATCAG+TGG 0.587582 1.2:+27766241 MS.gene53519:CDS
GCCGACCGCGAGTTAGAGGA+AGG 0.600682 1.2:+27765890 MS.gene53519:CDS
AATTAATTCAAATCAATGAG+TGG 0.607127 1.2:-27766294 None:intergenic
TTACTAAGATAAGAACAAGA+AGG 0.626377 1.2:-27764624 None:intergenic
AATCATCTTCAAATACAGAA+GGG 0.628034 1.2:-27764575 None:intergenic
TGAAATTTCTGGTGCCAAAG+TGG 0.631400 1.2:-27765631 None:intergenic
GCAAACCTTCCTCTAACTCG+CGG 0.633175 1.2:-27765895 None:intergenic
TTAGGTGTGTATATGCCTCA+TGG 0.638818 1.2:+27764651 MS.gene53519:CDS
ACCTTCCTCTAACTCGCGGT+CGG 0.662592 1.2:-27765891 None:intergenic
GATATGTGCAAAGATATCTG+AGG 0.713563 1.2:-27766236 None:intergenic
GCAGTACCAAGATTTCCATG+AGG 0.759579 1.2:-27764666 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAATTGTATTTTCTTTTAT+AGG + chr1.2:27765557-27765576 MS.gene53519:intron 10.0%
!!! ATCGTTTTGTTAAATAAATT+TGG - chr1.2:27765999-27766018 None:intergenic 15.0%
!!! ATTAAGAAATACTTTTGATT+TGG + chr1.2:27765195-27765214 MS.gene53519:intron 15.0%
!!! TTTTTATTATCAACTTAAAG+TGG - chr1.2:27765239-27765258 None:intergenic 15.0%
!! ATACCATCAAATAATTGAAA+AGG - chr1.2:27766142-27766161 None:intergenic 20.0%
!! TTGTTAAATAAATTTGGCTA+GGG - chr1.2:27765993-27766012 None:intergenic 20.0%
!! TTTGTTAAATAAATTTGGCT+AGG - chr1.2:27765994-27766013 None:intergenic 20.0%
!!! ATCTATTTCTTGATGTATAT+TGG - chr1.2:27765139-27765158 None:intergenic 20.0%
!!! TTTCCTTTTCAATTATTTGA+TGG + chr1.2:27766136-27766155 MS.gene53519:intron 20.0%
! AAATTTCAGCAAGAAAATCA+AGG + chr1.2:27765746-27765765 MS.gene53519:CDS 25.0%
! AATCATCTTCAAATACAGAA+GGG - chr1.2:27764578-27764597 None:intergenic 25.0%
! TCTTGTTCTTATCTTAGTAA+TGG + chr1.2:27764627-27764646 MS.gene53519:CDS 25.0%
! TGTTAAAGAAGAAGATGATA+TGG + chr1.2:27766207-27766226 MS.gene53519:CDS 25.0%
! TTACTAAGATAAGAACAAGA+AGG - chr1.2:27764627-27764646 None:intergenic 25.0%
!! CTAAAGTAAGTTGAACATTT+CGG - chr1.2:27766077-27766096 None:intergenic 25.0%
!! TATTTTCTTTTATAGGCACT+TGG + chr1.2:27765564-27765583 MS.gene53519:intron 25.0%
!! TTGCAAAGAATGATGATTTT+GGG + chr1.2:27765914-27765933 MS.gene53519:CDS 25.0%
!! TTTGCAAAGAATGATGATTT+TGG + chr1.2:27765913-27765932 MS.gene53519:CDS 25.0%
AAAAAAGACTGAAAGTGATG+TGG - chr1.2:27766115-27766134 None:intergenic 30.0%
ACACAAGATTTGGATTATCA+AGG + chr1.2:27764750-27764769 MS.gene53519:CDS 30.0%
ATCATACCTGAAAATCTTGA+GGG - chr1.2:27764824-27764843 None:intergenic 30.0%
ATCTGCAAGTACAAAATGAA+AGG - chr1.2:27766184-27766203 None:intergenic 30.0%
ATCTTAAGCTGAAAACTCAT+AGG + chr1.2:27765111-27765130 MS.gene53519:intron 30.0%
ATGTCTAACATCAACATATG+TGG - chr1.2:27765468-27765487 None:intergenic 30.0%
CAATCAAGGAAAACTTAACA+AGG - chr1.2:27764869-27764888 None:intergenic 30.0%
CAATCATCTTCAAATACAGA+AGG - chr1.2:27764579-27764598 None:intergenic 30.0%
CATTGAACCAATCATAAAGA+TGG - chr1.2:27765301-27765320 None:intergenic 30.0%
GAAAAGACCATCTTTATGAT+TGG + chr1.2:27765291-27765310 MS.gene53519:intron 30.0%
GCTTCTATAATAAGCAATCA+AGG - chr1.2:27764883-27764902 None:intergenic 30.0%
TCTTATCTTAGTAATGGCTT+AGG + chr1.2:27764633-27764652 MS.gene53519:CDS 30.0%
TGTTAGACATTGATACATGT+TGG + chr1.2:27765478-27765497 MS.gene53519:intron 30.0%
TTACTTCATCATCATCTTCA+TGG - chr1.2:27765966-27765985 None:intergenic 30.0%
TTGGATTATCAAGGTGAAAA+TGG + chr1.2:27764759-27764778 MS.gene53519:CDS 30.0%
! AATGCAGCTGACTTTATAAA+AGG - chr1.2:27765178-27765197 None:intergenic 30.0%
! TCATTTTACAATTGTTCTCG+AGG + chr1.2:27766027-27766046 MS.gene53519:intron 30.0%
! TGCAAAGAATGATGATTTTG+GGG + chr1.2:27765915-27765934 MS.gene53519:CDS 30.0%
! TTTTAACCCTCAAGATTTTC+AGG + chr1.2:27764815-27764834 MS.gene53519:CDS 30.0%
!! ATGTCATCGATTTGAAGTAT+CGG + chr1.2:27765510-27765529 MS.gene53519:intron 30.0%
!! CTATATCAGAAGTGTACTTT+TGG + chr1.2:27765066-27765085 MS.gene53519:intron 30.0%
AGTGGTTATTCCTTTCTACT+AGG - chr1.2:27765221-27765240 None:intergenic 35.0%
GAAAACTTTCTGTTGAGCAA+AGG + chr1.2:27765682-27765701 MS.gene53519:CDS 35.0%
GAACAAGAAGGAGAATAAGA+AGG - chr1.2:27764615-27764634 None:intergenic 35.0%
GAGAATCACAAACTAGTATC+TGG + chr1.2:27765591-27765610 MS.gene53519:CDS 35.0%
GATATCTTTGCACATATCAG+TGG + chr1.2:27766241-27766260 MS.gene53519:CDS 35.0%
GATATGTGCAAAGATATCTG+AGG - chr1.2:27766239-27766258 None:intergenic 35.0%
GATCATACCTGAAAATCTTG+AGG - chr1.2:27764825-27764844 None:intergenic 35.0%
GATGGAATAGTTGCATTTGA+AGG - chr1.2:27766275-27766294 None:intergenic 35.0%
GATTATCAAGGTGAAAATGG+TGG + chr1.2:27764762-27764781 MS.gene53519:CDS 35.0%
TATATGCCTCATGGAAATCT+TGG + chr1.2:27764660-27764679 MS.gene53519:CDS 35.0%
TGAAATGCAGACACAAGATT+TGG + chr1.2:27764740-27764759 MS.gene53519:CDS 35.0%
TTGTACAGATTCTGTTCAAC+AGG + chr1.2:27764791-27764810 MS.gene53519:CDS 35.0%
TTTGGTGGAGGAATTCTATT+AGG + chr1.2:27764714-27764733 MS.gene53519:CDS 35.0%
!! ATGATTTTGGGGAGAATCAT+AGG + chr1.2:27765926-27765945 MS.gene53519:CDS 35.0%
!! GATAGTTCTAGCTTATTTGG+TGG + chr1.2:27764699-27764718 MS.gene53519:CDS 35.0%
!! GCTGATAGTTCTAGCTTATT+TGG + chr1.2:27764696-27764715 MS.gene53519:CDS 35.0%
!! GTACTTTTGGTTAAAGCTCA+TGG + chr1.2:27765079-27765098 MS.gene53519:intron 35.0%
!! TTTGATTTGGCCTAGTAGAA+AGG + chr1.2:27765208-27765227 MS.gene53519:intron 35.0%
ACCAGAAATTTCACACTTGG+AGG + chr1.2:27765641-27765660 MS.gene53519:CDS 40.0%
AGTTGAACATTTCGGAGTCT+AGG - chr1.2:27766069-27766088 None:intergenic 40.0%
GTTGAACATTTCGGAGTCTA+GGG - chr1.2:27766068-27766087 None:intergenic 40.0%
TCCTCCAAGTGTGAAATTTC+TGG - chr1.2:27765645-27765664 None:intergenic 40.0%
TTAGGTGTGTATATGCCTCA+TGG + chr1.2:27764651-27764670 MS.gene53519:CDS 40.0%
! GAGGACTCTTCTTTGAAAGT+TGG + chr1.2:27765660-27765679 MS.gene53519:CDS 40.0%
!! AGTTCTAGCTTATTTGGTGG+AGG + chr1.2:27764702-27764721 MS.gene53519:CDS 40.0%
!! TGAAATTTCTGGTGCCAAAG+TGG - chr1.2:27765634-27765653 None:intergenic 40.0%
CACAAACTAGTATCTGGTGC+TGG + chr1.2:27765597-27765616 MS.gene53519:CDS 45.0%
GCAGTACCAAGATTTCCATG+AGG - chr1.2:27764669-27764688 None:intergenic 45.0%
GGCACCAGAAATTTCACACT+TGG + chr1.2:27765638-27765657 MS.gene53519:CDS 45.0%
TCTTCATGGTTGCTACTACC+TGG - chr1.2:27765952-27765971 None:intergenic 45.0%
! TGGAAGTTGTTCTGCCACTT+TGG + chr1.2:27765617-27765636 MS.gene53519:CDS 45.0%
GCAAACCTTCCTCTAACTCG+CGG - chr1.2:27765898-27765917 None:intergenic 50.0%
TTTGGGGAGAATCATAGGCC+AGG + chr1.2:27765931-27765950 MS.gene53519:CDS 50.0%
ACCTTCCTCTAACTCGCGGT+CGG - chr1.2:27765894-27765913 None:intergenic 55.0%
TCTAACTCGCGGTCGGCTAT+CGG - chr1.2:27765887-27765906 None:intergenic 55.0%
GATAGCCGACCGCGAGTTAG+AGG + chr1.2:27765886-27765905 MS.gene53519:CDS 60.0%
GCCGACCGCGAGTTAGAGGA+AGG + chr1.2:27765890-27765909 MS.gene53519:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27764561 27766309 27764561 ID=MS.gene53519
chr1.2 mRNA 27764561 27766309 27764561 ID=MS.gene53519.t1;Parent=MS.gene53519
chr1.2 exon 27764561 27764836 27764561 ID=MS.gene53519.t1.exon1;Parent=MS.gene53519.t1
chr1.2 CDS 27764561 27764836 27764561 ID=cds.MS.gene53519.t1;Parent=MS.gene53519.t1
chr1.2 exon 27765579 27765767 27765579 ID=MS.gene53519.t1.exon2;Parent=MS.gene53519.t1
chr1.2 CDS 27765579 27765767 27765579 ID=cds.MS.gene53519.t1;Parent=MS.gene53519.t1
chr1.2 exon 27765862 27765981 27765862 ID=MS.gene53519.t1.exon3;Parent=MS.gene53519.t1
chr1.2 CDS 27765862 27765981 27765862 ID=cds.MS.gene53519.t1;Parent=MS.gene53519.t1
chr1.2 exon 27766202 27766309 27766202 ID=MS.gene53519.t1.exon4;Parent=MS.gene53519.t1
chr1.2 CDS 27766202 27766309 27766202 ID=cds.MS.gene53519.t1;Parent=MS.gene53519.t1
Gene Sequence

>MS.gene53519

ATGAGTGCTTCATTCCCTTCTGTATTTGAAGATGATTGCATATCTTCAATTCCTTCTTATTCTCCTTCTTGTTCTTATCTTAGTAATGGCTTAGGTGTGTATATGCCTCATGGAAATCTTGGTACTGCTTTATCTGCTGATAGTTCTAGCTTATTTGGTGGAGGAATTCTATTAGGTTCTGAAATGCAGACACAAGATTTGGATTATCAAGGTGAAAATGGTGGAATTTATTGTACAGATTCTGTTCAACAGGTTTTTAACCCTCAAGATTTTCAGGTATGATCAATAATACTCAAACTATACTACCTTGTTAAGTTTTCCTTGATTGCTTATTATAGAAGCTTTTGAAATTGCATTTTGAAAATTGATTGATTATTATGAGAATTCTGAAAAATATCAAATATTGTTTTTTAGCTTTCATCTTCTCTCTATCACAACATAAAGAGTAAAAATTGAAAATGTATTCATTGTAAGTGTGAAGTTAAAGTTATTAAAAAATTAGATGCTATATCAGAAGTGTACTTTTGGTTAAAGCTCATGGTACAAAAATATCTTAAGCTGAAAACTCATAGGTGCCAATATACATCAAGAAATAGATAACATATAATACAAGTCCTTTTATAAAGTCAGCTGCATTAAGAAATACTTTTGATTTGGCCTAGTAGAAAGGAATAACCACTTTAAGTTGATAATAAAAAAAGAAAAGATAATATAGACAAAAGCATCATTAGAAAAGACCATCTTTATGATTGGTTCAATGTGTATATCTCTTTCTACAGTCTATAATAAAAGTAGTATTTTATTACTATGAAGCACAAACACTTGCACGAACGCAAAACATAACACTGACGTTGAAACGCAAAAATCAGTAATAATTTAAGAAAATAAAAATGATTAAACGTAACCACATATGTTGATGTTAGACATTGATACATGTTGGACATCAGACATGTCATCGATTTGAAGTATCGGTGCGACATGTTATAATTGATCTTTATAATTGTATTTTCTTTTATAGGCACTTGGTACTGAGAATCACAAACTAGTATCTGGTGCTGGAAGTTGTTCTGCCACTTTGGCACCAGAAATTTCACACTTGGAGGACTCTTCTTTGAAAGTTGGAAAACTTTCTGTTGAGCAAAGGAAAGAGAAGATTCATAGATATATGAAGAAAAGAAATGAAAGAAATTTCAGCAAGAAAATCAAGGTACTATATGATACATAGATTTCAATACATTCATCTATCAAAATTCATTTATATTTCAAAATTCAGCTAATGATGCAAAAAAATACATATGCAGTATGCTTGTCGAAAAACTTTAGCCGATAGCCGACCGCGAGTTAGAGGAAGGTTTGCAAAGAATGATGATTTTGGGGAGAATCATAGGCCAGGTAGTAGCAACCATGAAGATGATGATGAAGTAAGATTCCCTAGCCAAATTTATTTAACAAAACGATATTAATAATCATTTTACAATTGTTCTCGAGGAGACTTAAACTTTAACCCTAGACTCCGAAATGTTCAACTTACTTTAGTCAATAAAAAAAATACCACATCACTTTCAGTCTTTTTTTTTTCCTTTTCAATTATTTGATGGTATAATTCTTTAATCTAAGATTCCTTTCATTTTGTACTTGCAGATAGCTGTTAAAGAAGAAGATGATATGGTTGATTCCTCAGATATCTTTGCACATATCAGTGGACTTAACTCCTTCAAATGCAACTATTCCATCCACTCATTGATTTGA
Protein sequence

>MS.gene53519.t1

MSASFPSVFEDDCISSIPSYSPSCSYLSNGLGVYMPHGNLGTALSADSSSLFGGGILLGSEMQTQDLDYQGENGGIYCTDSVQQVFNPQDFQALGTENHKLVSGAGSCSATLAPEISHLEDSSLKVGKLSVEQRKEKIHRYMKKRNERNFSKKIKYACRKTLADSRPRVRGRFAKNDDFGENHRPGSSNHEDDDEIAVKEEDDMVDSSDIFAHISGLNSFKCNYSIHSLI