AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24276

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24276.t1 MTR_1g022290 100.000 93 0 0 1 93 1 93 1.72e-66 194
MS.gene24276.t1 MTR_3g111880 73.404 94 21 2 1 93 1 91 1.04e-44 139
MS.gene24276.t1 MTR_3g116720 73.134 67 18 0 5 71 14 80 2.79e-34 112
MS.gene24276.t1 MTR_3g013440 57.447 94 33 3 1 93 4 91 3.18e-32 108
MS.gene24276.t1 MTR_5g020170 65.217 69 24 0 2 70 14 82 2.31e-28 98.6
MS.gene24276.t1 MTR_7g089210 60.256 78 25 1 9 86 14 85 2.83e-28 98.2
MS.gene24276.t1 MTR_6g004250 58.571 70 29 0 2 71 5 74 3.99e-28 97.4
MS.gene24276.t1 MTR_3g111920 49.398 83 39 1 6 85 2 84 3.78e-26 92.4
MS.gene24276.t1 MTR_8g077380 55.224 67 29 1 4 70 2 67 7.89e-26 91.3
MS.gene24276.t1 MTR_8g077390 55.224 67 29 1 4 70 2 67 7.89e-26 91.3
MS.gene24276.t1 MTR_8g077360 55.224 67 29 1 4 70 2 67 7.93e-26 91.3
MS.gene24276.t1 MTR_1g033600 50.602 83 41 0 1 83 6 88 4.88e-25 91.3
MS.gene24276.t1 MTR_8g077420 56.338 71 30 1 4 74 2 71 5.12e-24 86.7
MS.gene24276.t1 MTR_5g020540 61.905 63 23 1 5 67 2 63 7.42e-24 86.3
MS.gene24276.t1 MTR_8g063870 44.660 103 44 3 4 93 5 107 5.40e-22 86.7
MS.gene24276.t1 MTR_5g081860 55.882 68 30 0 2 69 22 89 2.21e-21 85.1
MS.gene24276.t1 MTR_8g063600 53.623 69 32 0 1 69 4 72 1.77e-20 82.8
MS.gene24276.t1 MTR_3g462790 52.113 71 34 0 4 74 40 110 3.61e-20 82.4
MS.gene24276.t1 MTR_5g069710 51.389 72 34 1 4 75 26 96 4.00e-20 82.4
MS.gene24276.t1 MTR_7g067080 50.000 72 36 0 2 73 30 101 1.72e-19 80.5
MS.gene24276.t1 MTR_4g111975 48.000 75 35 2 1 71 1 75 1.42e-17 75.5
MS.gene24276.t1 MTR_1g111830 42.254 71 41 0 7 77 24 94 2.33e-16 71.2
MS.gene24276.t1 MTR_1g086180 49.153 59 29 1 5 62 9 67 2.71e-14 62.8
MS.gene24276.t1 MTR_7g110580 47.619 63 32 1 3 64 4 66 2.08e-13 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24276.t1 AT4G39250 58.621 87 36 0 7 93 14 100 5.85e-36 117
MS.gene24276.t1 AT1G75250 72.464 69 19 0 2 70 7 75 2.03e-33 112
MS.gene24276.t1 AT1G75250 72.464 69 19 0 2 70 7 75 2.42e-33 111
MS.gene24276.t1 AT2G21650 55.682 88 38 1 7 93 14 101 1.23e-31 107
MS.gene24276.t1 AT1G19510 69.841 63 19 0 10 72 15 77 1.54e-28 99.0
MS.gene24276.t1 AT2G18328 65.079 63 22 0 10 72 14 76 5.19e-27 94.7
MS.gene24276.t1 AT5G05790 52.632 76 35 1 4 79 28 102 2.40e-21 85.1
MS.gene24276.t1 AT5G05790 52.632 76 35 1 4 79 28 102 2.40e-21 85.1
MS.gene24276.t1 AT5G58900 53.030 66 31 0 4 69 31 96 2.56e-20 82.4
MS.gene24276.t1 AT2G38090 55.556 63 28 0 7 69 29 91 3.17e-20 82.4
MS.gene24276.t1 AT3G11280 49.315 73 37 0 7 79 33 105 3.28e-19 79.3
MS.gene24276.t1 AT3G11280 49.315 73 37 0 7 79 33 105 3.28e-19 79.3
MS.gene24276.t1 AT4G36570 72.727 44 12 0 7 50 12 55 4.90e-19 73.9
MS.gene24276.t1 AT5G08520 43.590 78 44 0 1 78 6 83 1.11e-16 72.8
MS.gene24276.t1 AT1G49010 43.836 73 38 1 2 71 3 75 7.95e-16 70.9
MS.gene24276.t1 AT5G23650 46.377 69 37 0 1 69 7 75 4.82e-14 65.9
MS.gene24276.t1 AT5G01200 43.662 71 39 1 5 74 28 98 1.55e-13 63.9
MS.gene24276.t1 AT5G04760 40.299 67 39 1 3 69 2 67 6.35e-13 62.0

Find 25 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGCAGCATTTCTGTATT+TGG 0.079428 1.1:+2004864 None:intergenic
GCTAGCTTCTGCCACCTATC+TGG 0.154946 1.1:+2004985 None:intergenic
AGAAATGCTGCAACAATTAA+AGG 0.224298 1.1:-2004856 MS.gene24276:CDS
CTAGCTTCTGCCACCTATCT+GGG 0.322954 1.1:+2004986 None:intergenic
GTTGCAGCATTTCTGTATTT+GGG 0.335288 1.1:+2004865 None:intergenic
CAAAAGATTTGAGAATGCTT+TGG 0.369296 1.1:-2005028 MS.gene24276:CDS
TGGGGTGTCCTTATCATAGA+TGG 0.425086 1.1:+2005005 None:intergenic
TGAAGATTTGAAGCAAATTG+AGG 0.447717 1.1:-2004905 MS.gene24276:CDS
TGCTTTGGCCATCTATGATA+AGG 0.453055 1.1:-2005013 MS.gene24276:CDS
ATAGGTGGCAGAAGCTAGCA+AGG 0.504876 1.1:-2004981 MS.gene24276:CDS
CAGAAGCTAGCAAGGGCTGT+TGG 0.521879 1.1:-2004973 MS.gene24276:CDS
GCATTTCTGTATTTGGGCAA+AGG 0.525051 1.1:+2004871 None:intergenic
ATGATAAGGACACCCCAGAT+AGG 0.538561 1.1:-2004999 MS.gene24276:CDS
TTCTGTCAATACTTCACTGA+AGG 0.539972 1.1:+2004205 None:intergenic
AAGCTAGCAAGGGCTGTTGG+AGG 0.552500 1.1:-2004970 MS.gene24276:CDS
GAATGTCCTCAAGTTCAGCT+TGG 0.559569 1.1:-2005065 MS.gene24276:CDS
AGCTAGCAAGGGCTGTTGGA+GGG 0.566835 1.1:-2004969 MS.gene24276:CDS
AGACAGTTGAGGAAGTGAAA+AGG 0.586038 1.1:-2004945 MS.gene24276:CDS
TGTTGTCCAAGCTGAACTTG+AGG 0.595382 1.1:+2005059 None:intergenic
GATTTGAAGCAAATTGAGGA+AGG 0.610917 1.1:-2004901 MS.gene24276:CDS
TAGCTTCTGCCACCTATCTG+GGG 0.629096 1.1:+2004987 None:intergenic
TAGGTGGCAGAAGCTAGCAA+GGG 0.655725 1.1:-2004980 MS.gene24276:CDS
ATAAGGACACCCCAGATAGG+TGG 0.660087 1.1:-2004996 MS.gene24276:CDS
ATTACAGTGACGAAGAACAA+AGG 0.662329 1.1:-2004828 MS.gene24276:intron
TGTTGGAGGGAAGACAGTTG+AGG 0.663833 1.1:-2004956 MS.gene24276:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATATTTTGTATATCTAATT+TGG - chr1.1:2004788-2004807 MS.gene24276:intron 10.0%
!!! TATCTACAATTTTTTTTTTA+AGG + chr1.1:2004497-2004516 None:intergenic 10.0%
!!! TAATGTAGATTTTTATTACT+AGG + chr1.1:2004831-2004850 None:intergenic 15.0%
!!! TTTTTTCACTAAATTTAATG+AGG - chr1.1:2004748-2004767 MS.gene24276:intron 15.0%
!!! CTTCTTCTTGTTTATAAATA+TGG - chr1.1:2004983-2005002 MS.gene24276:CDS 20.0%
! CGTATAAAACAGTAAGTTTA+TGG + chr1.1:2004937-2004956 None:intergenic 25.0%
!! ATGGAGAAGATTTTTATTGT+GGG - chr1.1:2005002-2005021 MS.gene24276:CDS 25.0%
!! GTTCGTCTTACTAATATTTT+TGG - chr1.1:2004587-2004606 MS.gene24276:intron 25.0%
!! TATGGAGAAGATTTTTATTG+TGG - chr1.1:2005001-2005020 MS.gene24276:CDS 25.0%
AGAAATGCTGCAACAATTAA+AGG - chr1.1:2004425-2004444 MS.gene24276:intron 30.0%
AGCAACACAAATTTAAAGAG+AGG - chr1.1:2004704-2004723 MS.gene24276:intron 30.0%
AGTCATTAGAAACTCATACA+CGG - chr1.1:2004530-2004549 MS.gene24276:intron 30.0%
CAAAAGATTTGAGAATGCTT+TGG - chr1.1:2004253-2004272 MS.gene24276:intron 30.0%
GTCTATTGTATTTGTAATGC+AGG - chr1.1:2005039-2005058 MS.gene24276:CDS 30.0%
! TGAAGATTTGAAGCAAATTG+AGG - chr1.1:2004376-2004395 MS.gene24276:intron 30.0%
ATTACAGTGACGAAGAACAA+AGG - chr1.1:2004453-2004472 MS.gene24276:intron 35.0%
GTTGCAGCATTTCTGTATTT+GGG + chr1.1:2004419-2004438 None:intergenic 35.0%
TGTTGCAGCATTTCTGTATT+TGG + chr1.1:2004420-2004439 None:intergenic 35.0%
TTCATTTACACACACCACAA+AGG - chr1.1:2004896-2004915 MS.gene24276:CDS 35.0%
! GATTTGAAGCAAATTGAGGA+AGG - chr1.1:2004380-2004399 MS.gene24276:intron 35.0%
AGACAGTTGAGGAAGTGAAA+AGG - chr1.1:2004336-2004355 MS.gene24276:intron 40.0%
AGTAAGTTTATGGTCCCTCA+TGG + chr1.1:2004927-2004946 None:intergenic 40.0%
GCATTTCTGTATTTGGGCAA+AGG + chr1.1:2004413-2004432 None:intergenic 40.0%
TGCTTTGGCCATCTATGATA+AGG - chr1.1:2004268-2004287 MS.gene24276:intron 40.0%
ATACACGGATAGACGAGTCA+GGG - chr1.1:2004545-2004564 MS.gene24276:intron 45.0%
ATGATAAGGACACCCCAGAT+AGG - chr1.1:2004282-2004301 MS.gene24276:intron 45.0%
TGTTGTCCAAGCTGAACTTG+AGG + chr1.1:2004225-2004244 None:intergenic 45.0%
! ACCACAAAGGTACAACCATG+AGG - chr1.1:2004909-2004928 MS.gene24276:CDS 45.0%
! CCACAAAGGTACAACCATGA+GGG - chr1.1:2004910-2004929 MS.gene24276:CDS 45.0%
! TGGGGTGTCCTTATCATAGA+TGG + chr1.1:2004279-2004298 None:intergenic 45.0%
ATAAGGACACCCCAGATAGG+TGG - chr1.1:2004285-2004304 MS.gene24276:intron 50.0%
ATAGGTGGCAGAAGCTAGCA+AGG - chr1.1:2004300-2004319 MS.gene24276:intron 50.0%
CATACACGGATAGACGAGTC+AGG - chr1.1:2004544-2004563 MS.gene24276:intron 50.0%
CCCTCATGGTTGTACCTTTG+TGG + chr1.1:2004913-2004932 None:intergenic 50.0%
CTAGCTTCTGCCACCTATCT+GGG + chr1.1:2004298-2004317 None:intergenic 50.0%
GTAAGACGAACGAAGTGACC+TGG + chr1.1:2004578-2004597 None:intergenic 50.0%
TAGCTTCTGCCACCTATCTG+GGG + chr1.1:2004297-2004316 None:intergenic 50.0%
TAGGTGGCAGAAGCTAGCAA+GGG - chr1.1:2004301-2004320 MS.gene24276:intron 50.0%
TGTTGGAGGGAAGACAGTTG+AGG - chr1.1:2004325-2004344 MS.gene24276:intron 50.0%
! ACGAGTCAGGGTTTGAAACC+AGG - chr1.1:2004557-2004576 MS.gene24276:intron 50.0%
AAGCTAGCAAGGGCTGTTGG+AGG - chr1.1:2004311-2004330 MS.gene24276:intron 55.0%
AGCTAGCAAGGGCTGTTGGA+GGG - chr1.1:2004312-2004331 MS.gene24276:intron 55.0%
CAGAAGCTAGCAAGGGCTGT+TGG - chr1.1:2004308-2004327 MS.gene24276:intron 55.0%
! GCTAGCTTCTGCCACCTATC+TGG + chr1.1:2004299-2004318 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 2004218 2005085 2004218 ID=MS.gene24276
chr1.1 mRNA 2004218 2005085 2004218 ID=MS.gene24276.t1;Parent=MS.gene24276
chr1.1 exon 2004829 2005085 2004829 ID=MS.gene24276.t1.exon1;Parent=MS.gene24276.t1
chr1.1 CDS 2004829 2005085 2004829 ID=cds.MS.gene24276.t1;Parent=MS.gene24276.t1
chr1.1 exon 2004218 2004242 2004218 ID=MS.gene24276.t1.exon2;Parent=MS.gene24276.t1
chr1.1 CDS 2004218 2004242 2004218 ID=cds.MS.gene24276.t1;Parent=MS.gene24276.t1
Gene Sequence

>MS.gene24276

ATGTCCTCAAGTTCAGCTTGGACAACAAAGCAAAACAAAAGATTTGAGAATGCTTTGGCCATCTATGATAAGGACACCCCAGATAGGTGGCAGAAGCTAGCAAGGGCTGTTGGAGGGAAGACAGTTGAGGAAGTGAAAAGGCATTATGAGATGTTAGTTGAAGATTTGAAGCAAATTGAGGAAGGTCATGTTCCTTTGCCCAAATACAGAAATGCTGCAACAATTAAAGGTTACAATTACAGTGACGAAGAACAAAGGTAATTTTTACTACTTAATCCTTAAAAAAAAAATTGTAGATAGACAAAATATAATAGTCATTAGAAACTCATACACGGATAGACGAGTCAGGGTTTGAAACCAGGTCACTTCGTTCGTCTTACTAATATTTTTGGTACTTTTGACACTTGAGCACTACTTAATCGTTATTTTGTCATTAGCAATCGCTTGCATATGATTCAATTTGACACTGTTAGATAAAATTAATTTAGCAACACAAATTTAAAGAGAGGTTATATGAAATATGTATCTAATTTTTTCACTAAATTTAATGAGGAAAATTAAACAAGAATTTATATTTTGTATATCTAATTTGGTCTCTAATTTTATTTTTCCTAGTAATAAAAATCTACATTATAATCTAAACTATAGTTTTATATCATTTATGTTCATTTTCTCTGTTTCATTTACACACACCACAAAGGTACAACCATGAGGGACCATAAACTTACTGTTTTATACGTTTTTTTTCTTCTTCTTCTTCTTCTTCTTCTTCTTGTTTATAAATATGGAGAAGATTTTTATTGTGGGTGTGAGCTGAGTGAGTCTATTGTATTTGTAATGCAGGTTGAAGTATCTAAGCCTTCAGTGA
Protein sequence

>MS.gene24276.t1

MSSSSAWTTKQNKRFENALAIYDKDTPDRWQKLARAVGGKTVEEVKRHYEMLVEDLKQIEEGHVPLPKYRNAATIKGYNYSDEEQRLKYLSLQ