AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31470

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31470.t1 MTR_2g090365 92.500 200 15 0 1 200 254 453 1.52e-140 400
MS.gene31470.t1 MTR_2g078310 63.874 191 64 3 10 197 1 189 1.03e-74 224
MS.gene31470.t1 MTR_3g117270 51.562 192 85 5 10 195 1 190 1.09e-62 193
MS.gene31470.t1 MTR_3g117270 51.562 192 85 5 10 195 1 190 1.87e-62 193
MS.gene31470.t1 MTR_3g117270 54.601 163 68 4 10 166 1 163 8.08e-56 174
MS.gene31470.t1 MTR_3g117270 54.601 163 68 4 10 166 1 163 8.80e-56 174
MS.gene31470.t1 MTR_3g117280 50.568 176 81 3 25 199 2 172 1.45e-55 175
MS.gene31470.t1 MTR_5g097190 40.476 126 65 4 82 198 20 144 2.61e-20 87.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31470.t1 AT4G22140 59.296 199 68 3 10 197 1 197 1.38e-75 227
MS.gene31470.t1 AT4G22140 59.296 199 68 3 10 197 1 197 1.71e-75 227
MS.gene31470.t1 AT4G22140 59.296 199 68 3 10 197 1 197 1.71e-75 227
MS.gene31470.t1 AT4G39100 51.099 182 85 3 21 200 14 193 2.78e-61 191
MS.gene31470.t1 AT4G04260 56.970 165 67 3 34 197 10 171 1.18e-54 173
MS.gene31470.t1 AT4G04260 57.895 152 61 2 46 197 10 158 4.32e-52 166
MS.gene31470.t1 AT4G39100 54.362 149 66 2 21 167 14 162 7.71e-52 164
MS.gene31470.t1 AT4G04260 54.286 140 60 3 10 145 1 140 6.13e-41 136

Find 45 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAATGTTCACCTGATTTAA+AGG 0.193987 2.4:-10339874 MS.gene31470:CDS
AAAGGCATGCCCACGCATTT+AGG 0.253844 2.4:+10339939 None:intergenic
TTCACCTGATTTAAAGGATT+AGG 0.322143 2.4:-10339868 None:intergenic
TCACCTGATTTAAAGGATTA+GGG 0.322613 2.4:-10339867 None:intergenic
ACGATTACTTTAGCAGGTTC+TGG 0.332292 2.4:-10340383 MS.gene31470:CDS
ATTAACCTATCCGGGTTATA+AGG 0.334701 2.4:+10340185 None:intergenic
TTATAACCCGGATAGGTTAA+TGG 0.355817 2.4:-10340183 MS.gene31470:CDS
GATTTCATTGCTTCATCAAA+AGG 0.383487 2.4:+10339921 None:intergenic
ACTTACACTTCAACGCGTTC+AGG 0.403385 2.4:+10340333 None:intergenic
CACAGCACCATTAACCTATC+CGG 0.404617 2.4:+10340176 None:intergenic
AGTCCCTAATCCTTTAAATC+AGG 0.432271 2.4:+10339864 None:intergenic
TTGGTTTGTTCCTGCCAGTA+TGG 0.439578 2.4:+10340634 None:intergenic
CGACAACAAGGCAAGGGAAA+AGG 0.450024 2.4:-10341132 MS.gene31470:CDS
AAAACATACGCGTCCTTCAA+TGG 0.453876 2.4:+10340527 None:intergenic
GGCACCAACACGGTCGTTAG+AGG 0.459119 2.4:-10341091 MS.gene31470:intron
GTGCTAACGATTACTTTAGC+AGG 0.480077 2.4:-10340389 MS.gene31470:CDS
CAGCAACCTACAGAACATAA+TGG 0.494473 2.4:-10341155 MS.gene31470:CDS
AGGATAATATGAACAGAATG+AGG 0.500778 2.4:-10340584 MS.gene31470:CDS
CGTCCTTCAATGGTTTCCTC+AGG 0.503827 2.4:+10340537 None:intergenic
AAAAGGAACAAATACACAAT+CGG 0.520774 2.4:-10341115 MS.gene31470:CDS
CATAGTGCTGACACAATTGA+AGG 0.525786 2.4:-10340462 MS.gene31470:CDS
TACATGAAGCTTGAAGTTGT+AGG 0.537934 2.4:-10340411 MS.gene31470:CDS
TTGTCGCCATTATGTTCTGT+AGG 0.543808 2.4:+10341149 None:intergenic
CGACCTGAGGAAACCATTGA+AGG 0.551081 2.4:-10340540 MS.gene31470:CDS
AAATGCCTTATAACCCGGAT+AGG 0.557757 2.4:-10340190 MS.gene31470:CDS
GAATGAGGGTCTATGTAAGA+AGG 0.562196 2.4:-10340569 MS.gene31470:CDS
CCGTGTGGAAAAGATTGAGC+AGG 0.565789 2.4:-10340604 MS.gene31470:CDS
TTATGTTCTGTAGGTTGCTG+CGG 0.575653 2.4:+10341158 None:intergenic
CAGGTACCATCCTAAATGCG+TGG 0.581382 2.4:-10339949 MS.gene31470:CDS
ACAGCACCATTAACCTATCC+GGG 0.588194 2.4:+10340177 None:intergenic
ATGTGAAATGCCTTATAACC+CGG 0.595533 2.4:-10340195 MS.gene31470:CDS
GCATGCCCACGCATTTAGGA+TGG 0.615056 2.4:+10339943 None:intergenic
ATAATGGCGACAACAAGGCA+AGG 0.623162 2.4:-10341139 MS.gene31470:CDS
AGGTACCATCCTAAATGCGT+GGG 0.636148 2.4:-10339948 MS.gene31470:CDS
AGAACATAATGGCGACAACA+AGG 0.636635 2.4:-10341144 MS.gene31470:CDS
TGTGTGGAAGTTGCAATCAA+AGG 0.645860 2.4:-10340157 MS.gene31470:intron
GGATAATATGAACAGAATGA+GGG 0.654950 2.4:-10340583 MS.gene31470:CDS
ATAGTGCTGACACAATTGAA+GGG 0.668881 2.4:-10340461 MS.gene31470:CDS
ATTACCTCTAACGACCGTGT+TGG 0.672565 2.4:+10341087 None:intergenic
CACAATCGGAGGCACCAACA+CGG 0.673961 2.4:-10341101 MS.gene31470:CDS
TAATGGCGACAACAAGGCAA+GGG 0.678546 2.4:-10341138 MS.gene31470:CDS
AGGAACAAATACACAATCGG+AGG 0.686184 2.4:-10341112 MS.gene31470:CDS
CAAACCAATCATAGCCCGTG+TGG 0.703357 2.4:-10340619 MS.gene31470:CDS
AAGAAGGTATTATCGACCTG+AGG 0.704026 2.4:-10340553 MS.gene31470:CDS
GATAGGTTAATGGTGCTGTG+TGG 0.736018 2.4:-10340173 MS.gene31470:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTATAATGAATTATTATGC+AGG - chr2.4:10340922-10340941 MS.gene31470:intron 20.0%
!!! AAACACTGATATTTTTTTCT+AGG - chr2.4:10340724-10340743 MS.gene31470:intron 20.0%
!!! AACACTGATATTTTTTTCTA+GGG - chr2.4:10340725-10340744 MS.gene31470:intron 20.0%
!!! ATTTTACTTTTATGTTTCGA+AGG - chr2.4:10340806-10340825 MS.gene31470:intron 20.0%
!!! TTGTTTTAATGAATGTATGA+TGG + chr2.4:10340958-10340977 None:intergenic 20.0%
! AAAAGGAACAAATACACAAT+CGG - chr2.4:10339917-10339936 MS.gene31470:CDS 25.0%
! AAAATGTTCACCTGATTTAA+AGG - chr2.4:10341158-10341177 MS.gene31470:CDS 25.0%
! AAGTAGATAGTTCAAAAACA+TGG - chr2.4:10340044-10340063 MS.gene31470:intron 25.0%
! GAAATATTTCAATTTCTTGC+AGG - chr2.4:10341064-10341083 MS.gene31470:intron 25.0%
!! ATCAAAGGTAAATTGGATTT+TGG - chr2.4:10340890-10340909 MS.gene31470:intron 25.0%
!! TCAAAGGTAAATTGGATTTT+GGG - chr2.4:10340891-10340910 MS.gene31470:intron 25.0%
!!! ACACTGATATTTTTTTCTAG+GGG - chr2.4:10340726-10340745 MS.gene31470:intron 25.0%
!!! GTTTTAAATTGCACTTATTG+TGG + chr2.4:10340290-10340309 None:intergenic 25.0%
AGATCTGTAAGGAAATAAAC+TGG + chr2.4:10341037-10341056 None:intergenic 30.0%
AGGATAATATGAACAGAATG+AGG - chr2.4:10340448-10340467 MS.gene31470:CDS 30.0%
AGTTGCAATCAAAGGTAAAT+TGG - chr2.4:10340883-10340902 MS.gene31470:intron 30.0%
GATTTCATTGCTTCATCAAA+AGG + chr2.4:10341114-10341133 None:intergenic 30.0%
GGATAATATGAACAGAATGA+GGG - chr2.4:10340449-10340468 MS.gene31470:CDS 30.0%
TGAATGTATGATGGCAAATA+AGG + chr2.4:10340949-10340968 None:intergenic 30.0%
TTTCTGTCATAAGATCTGTA+AGG + chr2.4:10341048-10341067 None:intergenic 30.0%
! TTTGAAGCAATTTGCTTAAC+AGG + chr2.4:10340000-10340019 None:intergenic 30.0%
ATGTGAAATGCCTTATAACC+CGG - chr2.4:10340837-10340856 MS.gene31470:intron 35.0%
ATTAACCTATCCGGGTTATA+AGG + chr2.4:10340850-10340869 None:intergenic 35.0%
TACATGAAGCTTGAAGTTGT+AGG - chr2.4:10340621-10340640 MS.gene31470:CDS 35.0%
TCTAAGAAGTAATGCTGTGT+TGG - chr2.4:10341002-10341021 MS.gene31470:intron 35.0%
TTATAACCCGGATAGGTTAA+TGG - chr2.4:10340849-10340868 MS.gene31470:intron 35.0%
! AAGCAATTTGCTTAACAGGA+AGG + chr2.4:10339996-10340015 None:intergenic 35.0%
! CGTATGTTTTCATGGAGATA+AGG - chr2.4:10340518-10340537 MS.gene31470:CDS 35.0%
! TCTGGTACAATGCTTTTACT+GGG - chr2.4:10340667-10340686 MS.gene31470:intron 35.0%
! TTCTGGTACAATGCTTTTAC+TGG - chr2.4:10340666-10340685 MS.gene31470:intron 35.0%
!! ATAGTGCTGACACAATTGAA+GGG - chr2.4:10340571-10340590 MS.gene31470:CDS 35.0%
AAAACATACGCGTCCTTCAA+TGG + chr2.4:10340508-10340527 None:intergenic 40.0%
AAATGCCTTATAACCCGGAT+AGG - chr2.4:10340842-10340861 MS.gene31470:intron 40.0%
ACGATTACTTTAGCAGGTTC+TGG - chr2.4:10340649-10340668 MS.gene31470:CDS 40.0%
AGAACATAATGGCGACAACA+AGG - chr2.4:10339888-10339907 MS.gene31470:CDS 40.0%
AGGAACAAATACACAATCGG+AGG - chr2.4:10339920-10339939 MS.gene31470:CDS 40.0%
ATTGCAGTGCAATGTTGAAG+AGG + chr2.4:10340124-10340143 None:intergenic 40.0%
CAGCAACCTACAGAACATAA+TGG - chr2.4:10339877-10339896 MS.gene31470:CDS 40.0%
CTATGTAAACGACGCTGATA+TGG + chr2.4:10340324-10340343 None:intergenic 40.0%
GAATGAGGGTCTATGTAAGA+AGG - chr2.4:10340463-10340482 MS.gene31470:CDS 40.0%
GTGCTAACGATTACTTTAGC+AGG - chr2.4:10340643-10340662 MS.gene31470:CDS 40.0%
TGGTGTGGTTACGAATAATG+TGG + chr2.4:10340177-10340196 None:intergenic 40.0%
TGTGTGGAAGTTGCAATCAA+AGG - chr2.4:10340875-10340894 MS.gene31470:intron 40.0%
TTATGTTCTGTAGGTTGCTG+CGG + chr2.4:10339877-10339896 None:intergenic 40.0%
TTGTCGCCATTATGTTCTGT+AGG + chr2.4:10339886-10339905 None:intergenic 40.0%
! AGTTTGCTCCACAGTTGTTA+GGG + chr2.4:10340212-10340231 None:intergenic 40.0%
! CTGGTACAATGCTTTTACTG+GGG - chr2.4:10340668-10340687 MS.gene31470:intron 40.0%
! GCTTCAAATCGTTCCTTTTG+CGG - chr2.4:10340012-10340031 MS.gene31470:intron 40.0%
! TCCACAGTTGTTAGGGTTTT+GGG + chr2.4:10340205-10340224 None:intergenic 40.0%
! TTGCTTAACAGGAAGGTGTA+AGG + chr2.4:10339989-10340008 None:intergenic 40.0%
!! AAGAAGGTATTATCGACCTG+AGG - chr2.4:10340479-10340498 MS.gene31470:CDS 40.0%
!! CATAGTGCTGACACAATTGA+AGG - chr2.4:10340570-10340589 MS.gene31470:CDS 40.0%
!! TAAGGAGAGAAGGGTTTTGA+GGG + chr2.4:10339971-10339990 None:intergenic 40.0%
ACAGCACCATTAACCTATCC+GGG + chr2.4:10340858-10340877 None:intergenic 45.0%
ACTTACACTTCAACGCGTTC+AGG + chr2.4:10340702-10340721 None:intergenic 45.0%
ACTTCACTCGATTCCGCAAA+AGG + chr2.4:10340028-10340047 None:intergenic 45.0%
AGGTACCATCCTAAATGCGT+GGG - chr2.4:10341084-10341103 MS.gene31470:intron 45.0%
ATAATGGCGACAACAAGGCA+AGG - chr2.4:10339893-10339912 MS.gene31470:CDS 45.0%
ATTACCTCTAACGACCGTGT+TGG + chr2.4:10339948-10339967 None:intergenic 45.0%
CACAGCACCATTAACCTATC+CGG + chr2.4:10340859-10340878 None:intergenic 45.0%
CTGCCATAACAGCGATATTG+CGG + chr2.4:10340101-10340120 None:intergenic 45.0%
TAATGGCGACAACAAGGCAA+GGG - chr2.4:10339894-10339913 MS.gene31470:CDS 45.0%
! AGGAAGGTGTAAGGAGAGAA+GGG + chr2.4:10339980-10339999 None:intergenic 45.0%
! CAGTTTGCTCCACAGTTGTT+AGG + chr2.4:10340213-10340232 None:intergenic 45.0%
! CCACAGTTGTTAGGGTTTTG+GGG + chr2.4:10340204-10340223 None:intergenic 45.0%
! CCTGCTCAATCTTTTCCACA+CGG + chr2.4:10340431-10340450 None:intergenic 45.0%
! CTCCACAGTTGTTAGGGTTT+TGG + chr2.4:10340206-10340225 None:intergenic 45.0%
! CTGCTCAATCTTTTCCACAC+GGG + chr2.4:10340430-10340449 None:intergenic 45.0%
! GAAGGACGCGTATGTTTTCA+TGG - chr2.4:10340510-10340529 MS.gene31470:CDS 45.0%
! GTAAGGAGAGAAGGGTTTTG+AGG + chr2.4:10339972-10339991 None:intergenic 45.0%
! TGTGTTTTGCTACGCCATAC+TGG - chr2.4:10340384-10340403 MS.gene31470:CDS 45.0%
!! GATAGGTTAATGGTGCTGTG+TGG - chr2.4:10340859-10340878 MS.gene31470:intron 45.0%
!! TTGGTTTGTTCCTGCCAGTA+TGG + chr2.4:10340401-10340420 None:intergenic 45.0%
!! TTTTCCACACGGGCTATGAT+TGG + chr2.4:10340420-10340439 None:intergenic 45.0%
!!! TGTTAGGGTTTTGGGGTAGT+TGG + chr2.4:10340197-10340216 None:intergenic 45.0%
CAAACCAATCATAGCCCGTG+TGG - chr2.4:10340413-10340432 MS.gene31470:CDS 50.0%
CAGCCGCAATATCGCTGTTA+TGG - chr2.4:10340095-10340114 MS.gene31470:intron 50.0%
CAGGTACCATCCTAAATGCG+TGG - chr2.4:10341083-10341102 MS.gene31470:intron 50.0%
CCCCAAAACCCTAACAACTG+TGG - chr2.4:10340201-10340220 MS.gene31470:CDS 50.0%
CCGTGTGGAAAAGATTGAGC+AGG - chr2.4:10340428-10340447 MS.gene31470:CDS 50.0%
CGACAACAAGGCAAGGGAAA+AGG - chr2.4:10339900-10339919 MS.gene31470:CDS 50.0%
CGACCTGAGGAAACCATTGA+AGG - chr2.4:10340492-10340511 MS.gene31470:CDS 50.0%
CGATATTGCGGCTGCAATTG+CGG + chr2.4:10340089-10340108 None:intergenic 50.0%
CGTCCTTCAATGGTTTCCTC+AGG + chr2.4:10340498-10340517 None:intergenic 50.0%
GACACACATTGCGGTCATTG+TGG + chr2.4:10340260-10340279 None:intergenic 50.0%
! AAAGGCATGCCCACGCATTT+AGG + chr2.4:10341096-10341115 None:intergenic 50.0%
! CAGGAAGGTGTAAGGAGAGA+AGG + chr2.4:10339981-10340000 None:intergenic 50.0%
! TTTTGCTACGCCATACTGGC+AGG - chr2.4:10340388-10340407 MS.gene31470:CDS 50.0%
GCATGCCCACGCATTTAGGA+TGG + chr2.4:10341092-10341111 None:intergenic 55.0%
GGATGCTGCGACACACATTG+CGG + chr2.4:10340269-10340288 None:intergenic 55.0%
!! CACAATCGGAGGCACCAACA+CGG - chr2.4:10339931-10339950 MS.gene31470:CDS 55.0%
!!! GGGTTTTGGGGTAGTTGGTG+TGG + chr2.4:10340192-10340211 None:intergenic 55.0%
GGCACCAACACGGTCGTTAG+AGG - chr2.4:10339941-10339960 MS.gene31470:CDS 60.0%
TGCGGCTGCAATTGCGGTTG+CGG + chr2.4:10340083-10340102 None:intergenic 60.0%
GCGGCTGCAATTGCGGTTGC+GGG + chr2.4:10340082-10340101 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 10339869 10341185 10339869 ID=MS.gene31470
chr2.4 mRNA 10339869 10341185 10339869 ID=MS.gene31470.t1;Parent=MS.gene31470
chr2.4 exon 10341092 10341185 10341092 ID=MS.gene31470.t1.exon1;Parent=MS.gene31470.t1
chr2.4 CDS 10341092 10341185 10341092 ID=cds.MS.gene31470.t1;Parent=MS.gene31470.t1
chr2.4 exon 10340339 10340678 10340339 ID=MS.gene31470.t1.exon2;Parent=MS.gene31470.t1
chr2.4 CDS 10340339 10340678 10340339 ID=cds.MS.gene31470.t1;Parent=MS.gene31470.t1
chr2.4 exon 10340158 10340226 10340158 ID=MS.gene31470.t1.exon3;Parent=MS.gene31470.t1
chr2.4 CDS 10340158 10340226 10340158 ID=cds.MS.gene31470.t1;Parent=MS.gene31470.t1
chr2.4 exon 10339869 10339968 10339869 ID=MS.gene31470.t1.exon4;Parent=MS.gene31470.t1
chr2.4 CDS 10339869 10339968 10339869 ID=cds.MS.gene31470.t1;Parent=MS.gene31470.t1
Gene Sequence

>MS.gene31470

ATGCGCCGCAGCAACCTACAGAACATAATGGCGACAACAAGGCAAGGGAAAAGGAACAAATACACAATCGGAGGCACCAACACGGTCGTTAGAGGTAATCCCTCAAAACCCTTCTCTCCTTACACCTTCCTGTTAAGCAAATTGCTTCAAATCGTTCCTTTTGCGGAATCGAGTGAAGTAGATAGTTCAAAAACATGGTTTCAAATTGCACCCGCAACCGCAATTGCAGCCGCAATATCGCTGTTATGGCAGCCTCTTCAACATTGCACTGCAATTGCGATGTGATCTTCAATCACGTGTGTGTACCACATTATTCGTAACCACACCAACTACCCCAAAACCCTAACAACTGTGGAGCAAACTGAAACTTCTAAAAATTTATTTCACGCCACAATGACCGCAATGTGTGTCGCAGCATCCACAATAAGTGCAATTTAAAACAATATTCAAAACCATATCAGCGTCGTTTACATAGATTATGATTTTGCTTTTTTGTTTTTGTTGCAGCTAAAGACTGTGTTTTGCTACGCCATACTGGCAGGAACAAACCAATCATAGCCCGTGTGGAAAAGATTGAGCAGGATAATATGAACAGAATGAGGGTCTATGTAAGAAGGTATTATCGACCTGAGGAAACCATTGAAGGACGCGTATGTTTTCATGGAGATAAGGAGCTGTTTTTGTCTAATCATTATGATGTTCATAGTGCTGACACAATTGAAGGGAAGTGTTTTGTGCACACTTTGAAGAACTACATGAAGCTTGAAGTTGTAGGTGCTAACGATTACTTTAGCAGGTTCTGGTACAATGCTTTTACTGGGGCTATGACACCTGAACGCGTTGAAGTGTAAGTCTAAACACTGATATTTTTTTCTAGGGGAATTTTGAATATTTGATAAGTTTTTTTTTTTTTTTTTTTTTTAAATAAATTTTGTTGATTTTACTTTTATGTTTCGAAGGTTGTGCAAATGTGAAATGCCTTATAACCCGGATAGGTTAATGGTGCTGTGTGGAAGTTGCAATCAAAGGTAAATTGGATTTTGGGTTTATGTATGTATAATGAATTATTATGCAGGACCTTATTTGCCATCATACATTCATTAAAACAAAAAATTTGTTGTATTTACAGAGAATCTAAGAAGTAATGCTGTGTTGGTTTTATGAACCAGTTTATTTCCTTACAGATCTTATGACAGAAATATTTCAATTTCTTGCAGGTACCATCCTAAATGCGTGGGCATGCCTTTTGATGAAGCAATGAAATCAGAAGATTTTAGATTTGTTTGTTCAAAATGTTCACCTGATTTAAAGGATTAG
Protein sequence

>MS.gene31470.t1

MRRSNLQNIMATTRQGKRNKYTIGGTNTVVRAKDCVLLRHTGRNKPIIARVEKIEQDNMNRMRVYVRRYYRPEETIEGRVCFHGDKELFLSNHYDVHSADTIEGKCFVHTLKNYMKLEVVGANDYFSRFWYNAFTGAMTPERVEVLCKCEMPYNPDRLMVLCGSCNQRYHPKCVGMPFDEAMKSEDFRFVCSKCSPDLKD