AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048529


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048529.t1 MTR_3g465280 68.116 69 19 2 1 69 15 80 1.11e-25 100
MS.gene048529.t1 MTR_3g465280 47.253 91 41 3 1 91 110 193 2.05e-16 75.9
MS.gene048529.t1 MTR_2g090900 44.211 95 53 0 82 176 191 285 2.22e-18 81.6
MS.gene048529.t1 MTR_2g090900 44.211 95 53 0 82 176 191 285 3.30e-18 80.9
MS.gene048529.t1 MTR_4g079500 43.158 95 54 0 82 176 194 288 5.95e-18 80.5
MS.gene048529.t1 MTR_6g034945 38.053 113 70 0 81 193 150 262 5.20e-14 69.3
MS.gene048529.t1 MTR_5g075390 31.875 160 95 3 23 174 98 251 4.36e-13 67.0
MS.gene048529.t1 MTR_3g094020 32.639 144 87 3 41 174 57 200 9.26e-13 65.9
MS.gene048529.t1 MTR_3g467120 39.362 94 57 0 81 174 176 269 1.48e-12 65.5
MS.gene048529.t1 MTR_4g072090 36.893 103 65 0 82 184 360 462 2.50e-12 65.1
MS.gene048529.t1 MTR_2g099050 38.542 96 59 0 81 176 220 315 2.51e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048529.t1 AT3G58120 41.593 113 65 1 64 176 185 296 7.05e-20 85.9
MS.gene048529.t1 AT2G42380 40.179 112 67 0 65 176 169 280 2.06e-19 84.3
MS.gene048529.t1 AT3G58120 43.299 97 54 1 64 160 185 280 1.35e-17 79.0
MS.gene048529.t1 AT2G42380 41.667 96 56 0 65 160 169 264 3.47e-17 77.4
MS.gene048529.t1 AT2G42380 35.714 112 61 1 65 176 169 269 7.63e-14 68.9
MS.gene048529.t1 AT1G43700 41.489 94 55 0 81 174 193 286 5.10e-13 66.6
MS.gene048529.t1 AT1G06070 26.866 201 126 4 5 189 122 317 1.50e-12 65.5
MS.gene048529.t1 AT2G40620 39.362 94 57 0 81 174 147 240 1.54e-12 65.5
MS.gene048529.t1 AT2G31370 37.736 106 66 0 81 186 200 305 1.56e-12 65.5
MS.gene048529.t1 AT2G31370 37.736 106 66 0 81 186 200 305 2.49e-12 65.1
MS.gene048529.t1 AT2G31370 37.736 106 66 0 81 186 200 305 2.49e-12 65.1
MS.gene048529.t1 AT2G31370 37.736 106 66 0 81 186 200 305 2.49e-12 65.1
MS.gene048529.t1 AT2G31370 37.736 106 66 0 81 186 200 305 2.49e-12 65.1
MS.gene048529.t1 AT2G31370 37.736 106 66 0 81 186 200 305 2.49e-12 65.1
MS.gene048529.t1 AT2G31370 37.736 106 66 0 81 186 200 305 2.49e-12 65.1
MS.gene048529.t1 AT1G06850 40.426 94 56 0 81 174 147 240 2.54e-12 64.7
MS.gene048529.t1 AT5G07160 40.860 93 55 0 82 174 48 140 3.75e-12 61.6
MS.gene048529.t1 AT4G38900 37.634 93 58 0 82 174 394 486 4.94e-12 64.3
MS.gene048529.t1 AT4G38900 37.634 93 58 0 82 174 394 486 4.94e-12 64.3
MS.gene048529.t1 AT2G21230 37.383 107 62 1 82 188 370 471 1.72e-11 62.8
MS.gene048529.t1 AT2G21230 37.383 107 62 1 82 188 370 471 1.72e-11 62.8

Find 34 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGCGATTTCAAGTCTTAAT+TGG 0.217186 3.3:+52715679 None:intergenic
GCTCGATTATATTGCTGATT+TGG 0.235809 3.3:-52716333 MS.gene048529:CDS
GCATGACCAAGATTTGATTT+TGG 0.261059 3.3:+52716984 None:intergenic
ATAAGAGAGCTGAGCTGAAT+AGG 0.366186 3.3:-52715526 MS.gene048529:CDS
TCAGCAGTGGTTGTTGACTA+TGG 0.374097 3.3:-52715709 MS.gene048529:CDS
TTCGACCATGGCAACCCTCT+TGG 0.426532 3.3:-52717094 MS.gene048529:CDS
GTATACCGTTTGAGCCTCTT+CGG 0.444805 3.3:+52716885 None:intergenic
TTCTTAGGATCCTAGCAAAT+CGG 0.449690 3.3:-52716385 MS.gene048529:intron
AGTGTACCAAAATCAAATCT+TGG 0.459311 3.3:-52716990 MS.gene048529:CDS
TGGATCCGAAGAGGCTCAAA+CGG 0.511736 3.3:-52716890 MS.gene048529:intron
AAACAAGAGGCGAGTAGCAG+TGG 0.519033 3.3:-52717053 MS.gene048529:CDS
CGATTTCAAGTCTTAATTGG+TGG 0.523508 3.3:+52715682 None:intergenic
GTGCAGAAGTCCGATTTGCT+AGG 0.528204 3.3:+52716375 None:intergenic
TATTGCTGATTTGGAGCGGA+AGG 0.534850 3.3:-52716324 MS.gene048529:CDS
AGACTTCAACTTGTGGGCGA+AGG 0.537269 3.3:+52715739 None:intergenic
GAGCTGAGCTGAATAGGCTG+AGG 0.543232 3.3:-52715520 MS.gene048529:CDS
CTCTTCCAAGAGGGTTGCCA+TGG 0.560623 3.3:+52717089 None:intergenic
GCATCTGCATGTGTTGGTGT+TGG 0.564639 3.3:-52716933 MS.gene048529:CDS
GGTAGTGCATCTGCATGTGT+TGG 0.568494 3.3:-52716939 MS.gene048529:CDS
TACTCGCCTCTTGTTTATCG+AGG 0.587188 3.3:+52717060 None:intergenic
ATGGTTAGACCCTTCTCACA+TGG 0.603263 3.3:-52717131 MS.gene048529:CDS
AGCTGAGCTGAATAGGCTGA+GGG 0.608093 3.3:-52715519 MS.gene048529:CDS
CATCATCAACATTTCGACCA+TGG 0.616367 3.3:-52717106 MS.gene048529:CDS
AAAGAAAGGATACTTCAAGA+AGG 0.624481 3.3:-52715648 MS.gene048529:intron
GATGATGATCCATGTGAGAA+GGG 0.625849 3.3:+52717122 None:intergenic
CATTGACCTCGATAAACAAG+AGG 0.636248 3.3:-52717066 MS.gene048529:CDS
ATGCACTACCACCACTGATG+TGG 0.638397 3.3:+52716952 None:intergenic
AGGTCAATGCTCTTCCAAGA+GGG 0.642523 3.3:+52717080 None:intergenic
TGATGATGATCCATGTGAGA+AGG 0.644091 3.3:+52717121 None:intergenic
GCTGAGAAGAACCACATCAG+TGG 0.651233 3.3:-52716963 MS.gene048529:CDS
GGACTTCTGCACAGAAATCG+AGG 0.651506 3.3:-52716364 MS.gene048529:CDS
ATTATATTGCTGATTTGGAG+CGG 0.651960 3.3:-52716328 MS.gene048529:CDS
GAGGTCAATGCTCTTCCAAG+AGG 0.655392 3.3:+52717079 None:intergenic
GAGAAGAACCACATCAGTGG+TGG 0.658310 3.3:-52716960 MS.gene048529:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTATTTCAATTTCAATT+TGG + chr3.3:52716464-52716483 None:intergenic 10.0%
!! AGAAAAAAAAATCTAATAAT+AGG - chr3.3:52715873-52715892 MS.gene048529:intron 10.0%
!! ATTAAAATAAATCTATATGT+TGG - chr3.3:52715989-52716008 MS.gene048529:intron 10.0%
!!! TATTAGATTTTTTTTTCTTC+AGG + chr3.3:52715871-52715890 None:intergenic 15.0%
!! ACAATTGAATTCCAAATTAT+AGG + chr3.3:52716659-52716678 None:intergenic 20.0%
!! CAAATTAAAATTCATTGAAG+TGG + chr3.3:52716545-52716564 None:intergenic 20.0%
!! GTCGATTATTTGTATTAATT+TGG - chr3.3:52716564-52716583 MS.gene048529:intron 20.0%
!!! ATATTTTATCGATTATGTGT+AGG + chr3.3:52716155-52716174 None:intergenic 20.0%
! AAATTCATTGAAGTGGTAAT+CGG + chr3.3:52716538-52716557 None:intergenic 25.0%
! ACATACTCATGTGAAATAAA+TGG + chr3.3:52717022-52717041 None:intergenic 25.0%
! AGTTGGCAAGTTAAAAAATA+TGG - chr3.3:52715766-52715785 MS.gene048529:intron 25.0%
! ATAGATCGATTATGATTGAA+TGG + chr3.3:52716625-52716644 None:intergenic 25.0%
! CAAATCAACTATATTAGTCA+GGG + chr3.3:52716064-52716083 None:intergenic 25.0%
! CATAACACTAAAAGTTTGAT+GGG - chr3.3:52715808-52715827 MS.gene048529:intron 25.0%
! TAATAGGAGTTGTTCTATTT+AGG - chr3.3:52715889-52715908 MS.gene048529:intron 25.0%
! TCAAATCAACTATATTAGTC+AGG + chr3.3:52716065-52716084 None:intergenic 25.0%
! TCATAACACTAAAAGTTTGA+TGG - chr3.3:52715807-52715826 MS.gene048529:intron 25.0%
!! TTTTATAGACTTCAACTTGT+GGG + chr3.3:52716860-52716879 None:intergenic 25.0%
!! TTTTTATAGACTTCAACTTG+TGG + chr3.3:52716861-52716880 None:intergenic 25.0%
!!! ATGAGTATGTTTATTTTCAG+TGG - chr3.3:52717032-52717051 MS.gene048529:CDS 25.0%
AAAGAAAGGATACTTCAAGA+AGG - chr3.3:52716942-52716961 MS.gene048529:CDS 30.0%
AAGTCTATAAAAATCAGCAG+TGG - chr3.3:52716868-52716887 MS.gene048529:intron 30.0%
AGTGTACCAAAATCAAATCT+TGG - chr3.3:52715600-52715619 MS.gene048529:intron 30.0%
GATTCTCATCTAAAGATCAT+AGG + chr3.3:52716418-52716437 None:intergenic 30.0%
TCACGTATCAACCTATAATT+TGG - chr3.3:52716645-52716664 MS.gene048529:intron 30.0%
TGTTTGATCCTAAACAACAA+GGG - chr3.3:52716741-52716760 MS.gene048529:intron 30.0%
TTGCTGAAGCAAAAAATAAG+AGG - chr3.3:52717112-52717131 MS.gene048529:CDS 30.0%
TTGTTTGATCCTAAACAACA+AGG - chr3.3:52716740-52716759 MS.gene048529:intron 30.0%
! TCTCTTCACAAGTTTTTGTT+TGG + chr3.3:52716790-52716809 None:intergenic 30.0%
!! AGTTTTTGTTTGGGTAGATA+TGG + chr3.3:52716780-52716799 None:intergenic 30.0%
!! ATTATATTGCTGATTTGGAG+CGG - chr3.3:52716262-52716281 MS.gene048529:intron 30.0%
!! CTCTTCACAAGTTTTTGTTT+GGG + chr3.3:52716789-52716808 None:intergenic 30.0%
!!! TTTTTAGTTTTGTTGTCGTG+TGG + chr3.3:52715576-52715595 None:intergenic 30.0%
GTGTAGGAAATAAACAAGCA+AGG + chr3.3:52716139-52716158 None:intergenic 35.0%
TCGCTGTAAGAGAAAAAGAA+AGG - chr3.3:52716928-52716947 MS.gene048529:CDS 35.0%
TGAGCAACACAAAAATCAGT+TGG - chr3.3:52715749-52715768 MS.gene048529:CDS 35.0%
TGATCAAGCAACACAAAAAC+TGG - chr3.3:52715680-52715699 MS.gene048529:CDS 35.0%
TGTTCTATTTAGGCTTGTCA+TGG - chr3.3:52715899-52715918 MS.gene048529:intron 35.0%
TTCTTAGGATCCTAGCAAAT+CGG - chr3.3:52716205-52716224 MS.gene048529:intron 35.0%
TTTGTTTGGGTAGATATGGT+GGG + chr3.3:52716776-52716795 None:intergenic 35.0%
! ATATTGCTCTAGATGTAGAG+CGG - chr3.3:52716512-52716531 MS.gene048529:intron 35.0%
! CAGCGATTTCAAGTCTTAAT+TGG + chr3.3:52716914-52716933 None:intergenic 35.0%
! CGATTTCAAGTCTTAATTGG+TGG + chr3.3:52716911-52716930 None:intergenic 35.0%
! GCTCGATTATATTGCTGATT+TGG - chr3.3:52716257-52716276 MS.gene048529:intron 35.0%
! TTTTGTCTTCCGTTGTTCTT+AGG - chr3.3:52716190-52716209 MS.gene048529:intron 35.0%
!! ATATGGATCCCTTGTTGTTT+AGG + chr3.3:52716752-52716771 None:intergenic 35.0%
!! GCATGACCAAGATTTGATTT+TGG + chr3.3:52715609-52715628 None:intergenic 35.0%
!! TTTTGTTTGGGTAGATATGG+TGG + chr3.3:52716777-52716796 None:intergenic 35.0%
AGATCATAGGCTTTCACGAT+CGG + chr3.3:52716405-52716424 None:intergenic 40.0%
ATAAGAGAGCTGAGCTGAAT+AGG - chr3.3:52717064-52717083 MS.gene048529:CDS 40.0%
CATCATCAACATTTCGACCA+TGG - chr3.3:52715484-52715503 MS.gene048529:CDS 40.0%
CATTGACCTCGATAAACAAG+AGG - chr3.3:52715524-52715543 MS.gene048529:CDS 40.0%
GATGATGATCCATGTGAGAA+GGG + chr3.3:52715471-52715490 None:intergenic 40.0%
GCGGAAGGAAAAATATTTGC+AGG - chr3.3:52716281-52716300 MS.gene048529:intron 40.0%
TGCTAGGATCCTAAGAACAA+CGG + chr3.3:52716202-52716221 None:intergenic 40.0%
! TGATGATGATCCATGTGAGA+AGG + chr3.3:52715472-52715491 None:intergenic 40.0%
AGGTCAATGCTCTTCCAAGA+GGG + chr3.3:52715513-52715532 None:intergenic 45.0%
ATCATAGGCTTTCACGATCG+GGG + chr3.3:52716403-52716422 None:intergenic 45.0%
ATGGTTAGACCCTTCTCACA+TGG - chr3.3:52715459-52715478 MS.gene048529:CDS 45.0%
CACAAAAACTGGATCCGAAG+AGG - chr3.3:52715691-52715710 MS.gene048529:CDS 45.0%
GATCATAGGCTTTCACGATC+GGG + chr3.3:52716404-52716423 None:intergenic 45.0%
GTATACCGTTTGAGCCTCTT+CGG + chr3.3:52715708-52715727 None:intergenic 45.0%
! GGGTAGATATGGTGGGAATA+TGG + chr3.3:52716769-52716788 None:intergenic 45.0%
! TACTCGCCTCTTGTTTATCG+AGG + chr3.3:52715533-52715552 None:intergenic 45.0%
! TCAGCAGTGGTTGTTGACTA+TGG - chr3.3:52716881-52716900 MS.gene048529:intron 45.0%
!! TATTGCTGATTTGGAGCGGA+AGG - chr3.3:52716266-52716285 MS.gene048529:intron 45.0%
AAACAAGAGGCGAGTAGCAG+TGG - chr3.3:52715537-52715556 MS.gene048529:CDS 50.0%
AGACTTCAACTTGTGGGCGA+AGG + chr3.3:52716854-52716873 None:intergenic 50.0%
AGCTGAGCTGAATAGGCTGA+GGG - chr3.3:52717071-52717090 MS.gene048529:CDS 50.0%
ATGCACTACCACCACTGATG+TGG + chr3.3:52715641-52715660 None:intergenic 50.0%
GAGAAGAACCACATCAGTGG+TGG - chr3.3:52715630-52715649 MS.gene048529:intron 50.0%
GAGGTCAATGCTCTTCCAAG+AGG + chr3.3:52715514-52715533 None:intergenic 50.0%
GCTGAGAAGAACCACATCAG+TGG - chr3.3:52715627-52715646 MS.gene048529:intron 50.0%
GGACTTCTGCACAGAAATCG+AGG - chr3.3:52716226-52716245 MS.gene048529:intron 50.0%
GGTAGTGCATCTGCATGTGT+TGG - chr3.3:52715651-52715670 MS.gene048529:CDS 50.0%
TGGATCCGAAGAGGCTCAAA+CGG - chr3.3:52715700-52715719 MS.gene048529:CDS 50.0%
! GCATCTGCATGTGTTGGTGT+TGG - chr3.3:52715657-52715676 MS.gene048529:CDS 50.0%
! GTGCAGAAGTCCGATTTGCT+AGG + chr3.3:52716218-52716237 None:intergenic 50.0%
CTCTTCCAAGAGGGTTGCCA+TGG + chr3.3:52715504-52715523 None:intergenic 55.0%
GAGCTGAGCTGAATAGGCTG+AGG - chr3.3:52717070-52717089 MS.gene048529:CDS 55.0%
TTCGACCATGGCAACCCTCT+TGG - chr3.3:52715496-52715515 MS.gene048529:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 52715459 52717153 52715459 ID=MS.gene048529
chr3.3 mRNA 52715459 52717153 52715459 ID=MS.gene048529.t1;Parent=MS.gene048529
chr3.3 exon 52716891 52717153 52716891 ID=MS.gene048529.t1.exon1;Parent=MS.gene048529.t1
chr3.3 CDS 52716891 52717153 52716891 ID=cds.MS.gene048529.t1;Parent=MS.gene048529.t1
chr3.3 exon 52716310 52716400 52716310 ID=MS.gene048529.t1.exon2;Parent=MS.gene048529.t1
chr3.3 CDS 52716310 52716400 52716310 ID=cds.MS.gene048529.t1;Parent=MS.gene048529.t1
chr3.3 exon 52715649 52715775 52715649 ID=MS.gene048529.t1.exon3;Parent=MS.gene048529.t1
chr3.3 CDS 52715649 52715775 52715649 ID=cds.MS.gene048529.t1;Parent=MS.gene048529.t1
chr3.3 exon 52715459 52715560 52715459 ID=MS.gene048529.t1.exon4;Parent=MS.gene048529.t1
chr3.3 CDS 52715459 52715560 52715459 ID=cds.MS.gene048529.t1;Parent=MS.gene048529.t1
Gene Sequence

>MS.gene048529

ATGGTTAGACCCTTCTCACATGGATCATCATCAACATTTCGACCATGGCAACCCTCTTGGAAGAGCATTGACCTCGATAAACAAGAGGCGAGTAGCAGTGGAGTCAAAGCAACTCCACACGACAACAAAACTAAAAACATTAGTGTACCAAAATCAAATCTTGGTCATGCTGAGAAGAACCACATCAGTGGTGGTAGTGCATCTGCATGTGTTGGTGTTGGTGATCAAGCAACACAAAAACTGGATCCGAAGAGGCTCAAACGGTATACTTGTGTTACTTATTGTTGTTGTGAGCAACACAAAAATCAGTTGGCAAGTTAAAAAATATGGAAGATCGAAATTTTTGATTCATAACACTAAAAGTTTGATGGGAATAATATTTGTCTTTTATTACATTTTTTTTGTAAAACCTGAAGAAAAAAAAATCTAATAATAGGAGTTGTTCTATTTAGGCTTGTCATGGTCAACTGTGATTTTAATAATAAATTTAATAAATTTTGTAATTGTTTTCAGCTTATTTTTAATAAAAAATTAAAATAAATCTATATGTTGGTTTAATTTTCATTTTATTTAGAGTAGATTTATCATCTATGAATGTGATACCCTGACTAATATAGTTGATTTGATTGATTTTATTCTAATCAAATCTAAATCATTGAAAAAATTGAAACAAAATACCTTGCTTGTTTATTTCCTACACATAATCGATAAAATATATTTTTATTTTCATCTTTTGTCTTCCGTTGTTCTTAGGATCCTAGCAAATCGGACTTCTGCACAGAAATCGAGGTTGAAAAAGCTCGATTATATTGCTGATTTGGAGCGGAAGGAAAAATATTTGCAGGTTAACATCATTATCTATTGTATCTCAAAGATCGTAATTTATGAATTTTTTTGTCTTTTTAAAATATGTTAACGTGTCTCGAAGAGAACTAGATTATCCCCGATCGTGAAAGCCTATGATCTTTAGATGAGAATCAAACAACACAAATTCTAATTTCACCAAATTGAAATTGAAATAAATTCATATAACTTGTGTTGTTTGATCTTCATATATTGCTCTAGATGTAGAGCGGCCGATTACCACTTCAATGAATTTTAATTTGTCGATTATTTGTATTAATTTGGTGTAGACAAATACACAACAATCTTGCTGATTTGAACCATTCAATCATAATCGATCTATTCACGTATCAACCTATAATTTGGAATTCAATTGTAAAATTGACATGCGACTCATTCAATCTTGATCTGATTATTTGAATGACATAACTCAACAAATTGTTTGATCCTAAACAACAAGGGATCCATATTCCCACCATATCTACCCAAACAAAAACTTGTGAAGAGATGATTTTGAGATTTTTTGTATATGCAGACTGAGTTATCTTTCCTTCGCCCACAAGTTGAAGTCTATAAAAATCAGCAGTGGTTGTTGACTATGGAACACCACCAATTAAGACTTGAAATCGCTGTAAGAGAAAAAGAAAGGATACTTCAAGAAGGTGATAATACTCATTGTCTTTATTTATATCTCTAGCATTTATTATCGTTTCTCTACCATTTATTTCACATGAGTATGTTTATTTTCAGTGGAGATTGAGAATAAGAGAGCTGAGCTGAATAGGCTGAGGGAGCTTCAGAAGAAACTAGTTGCTGAAGCAAAAAATAAGAGGTATATTGAAATGCTTATTA

Protein sequence

>MS.gene048529.t1

MVRPFSHGSSSTFRPWQPSWKSIDLDKQEASSSGVKATPHDNKTKNISVPKSNLGHAEKNHISGGSASACVGVGDQATQKLDPKRLKRILANRTSAQKSRLKKLDYIADLERKEKYLQTELSFLRPQVEVYKNQQWLLTMEHHQLRLEIAVREKERILQEVEIENKRAELNRLRELQKKLVAEAKNKRYIEMLI