AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene27310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene27310.t1 MTR_1g022290 100.000 93 0 0 1 93 1 93 1.72e-66 194
MS.gene27310.t1 MTR_3g111880 73.404 94 21 2 1 93 1 91 1.04e-44 139
MS.gene27310.t1 MTR_3g116720 73.134 67 18 0 5 71 14 80 2.79e-34 112
MS.gene27310.t1 MTR_3g013440 57.447 94 33 3 1 93 4 91 3.18e-32 108
MS.gene27310.t1 MTR_5g020170 65.217 69 24 0 2 70 14 82 2.31e-28 98.6
MS.gene27310.t1 MTR_7g089210 60.256 78 25 1 9 86 14 85 2.83e-28 98.2
MS.gene27310.t1 MTR_6g004250 58.571 70 29 0 2 71 5 74 3.99e-28 97.4
MS.gene27310.t1 MTR_3g111920 49.398 83 39 1 6 85 2 84 3.78e-26 92.4
MS.gene27310.t1 MTR_8g077380 55.224 67 29 1 4 70 2 67 7.89e-26 91.3
MS.gene27310.t1 MTR_8g077390 55.224 67 29 1 4 70 2 67 7.89e-26 91.3
MS.gene27310.t1 MTR_8g077360 55.224 67 29 1 4 70 2 67 7.93e-26 91.3
MS.gene27310.t1 MTR_1g033600 50.602 83 41 0 1 83 6 88 4.88e-25 91.3
MS.gene27310.t1 MTR_8g077420 56.338 71 30 1 4 74 2 71 5.12e-24 86.7
MS.gene27310.t1 MTR_5g020540 61.905 63 23 1 5 67 2 63 7.42e-24 86.3
MS.gene27310.t1 MTR_8g063870 44.660 103 44 3 4 93 5 107 5.40e-22 86.7
MS.gene27310.t1 MTR_5g081860 55.882 68 30 0 2 69 22 89 2.21e-21 85.1
MS.gene27310.t1 MTR_8g063600 53.623 69 32 0 1 69 4 72 1.77e-20 82.8
MS.gene27310.t1 MTR_3g462790 52.113 71 34 0 4 74 40 110 3.61e-20 82.4
MS.gene27310.t1 MTR_5g069710 51.389 72 34 1 4 75 26 96 4.00e-20 82.4
MS.gene27310.t1 MTR_7g067080 50.000 72 36 0 2 73 30 101 1.72e-19 80.5
MS.gene27310.t1 MTR_4g111975 48.000 75 35 2 1 71 1 75 1.42e-17 75.5
MS.gene27310.t1 MTR_1g111830 42.254 71 41 0 7 77 24 94 2.33e-16 71.2
MS.gene27310.t1 MTR_1g086180 49.153 59 29 1 5 62 9 67 2.71e-14 62.8
MS.gene27310.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.gene27310.t1 AT4G39250 58.621 87 36 0 7 93 14 100 5.85e-36 117
MS.gene27310.t1 AT1G75250 72.464 69 19 0 2 70 7 75 2.03e-33 112
MS.gene27310.t1 AT1G75250 72.464 69 19 0 2 70 7 75 2.42e-33 111
MS.gene27310.t1 AT2G21650 55.682 88 38 1 7 93 14 101 1.23e-31 107
MS.gene27310.t1 AT1G19510 69.841 63 19 0 10 72 15 77 1.54e-28 99.0
MS.gene27310.t1 AT2G18328 65.079 63 22 0 10 72 14 76 5.19e-27 94.7
MS.gene27310.t1 AT5G05790 52.632 76 35 1 4 79 28 102 2.40e-21 85.1
MS.gene27310.t1 AT5G05790 52.632 76 35 1 4 79 28 102 2.40e-21 85.1
MS.gene27310.t1 AT5G58900 53.030 66 31 0 4 69 31 96 2.56e-20 82.4
MS.gene27310.t1 AT2G38090 55.556 63 28 0 7 69 29 91 3.17e-20 82.4
MS.gene27310.t1 AT3G11280 49.315 73 37 0 7 79 33 105 3.28e-19 79.3
MS.gene27310.t1 AT3G11280 49.315 73 37 0 7 79 33 105 3.28e-19 79.3
MS.gene27310.t1 AT4G36570 72.727 44 12 0 7 50 12 55 4.90e-19 73.9
MS.gene27310.t1 AT5G08520 43.590 78 44 0 1 78 6 83 1.11e-16 72.8
MS.gene27310.t1 AT1G49010 43.836 73 38 1 2 71 3 75 7.95e-16 70.9
MS.gene27310.t1 AT5G23650 46.377 69 37 0 1 69 7 75 4.82e-14 65.9
MS.gene27310.t1 AT5G01200 43.662 71 39 1 5 74 28 98 1.55e-13 63.9
MS.gene27310.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 1.2:+2336159 None:intergenic
GCTAGCTTCTGCCACCTATC+TGG 0.154946 1.2:+2336280 None:intergenic
AGAAATGCTGCAACAATTAA+AGG 0.224298 1.2:-2336151 MS.gene27310:CDS
CTAGCTTCTGCCACCTATCT+GGG 0.322954 1.2:+2336281 None:intergenic
GTTGCAGCATTTCTGTATTT+GGG 0.335288 1.2:+2336160 None:intergenic
CAAAAGATTTGAGAATGCTT+TGG 0.369296 1.2:-2336323 MS.gene27310:CDS
TGGGGTGTCCTTATCATAGA+TGG 0.425086 1.2:+2336300 None:intergenic
TGAAGATTTGAAGCAAATTG+AGG 0.447717 1.2:-2336200 MS.gene27310:CDS
TGCTTTGGCCATCTATGATA+AGG 0.453055 1.2:-2336308 MS.gene27310:CDS
ATAGGTGGCAGAAGCTAGCA+AGG 0.504876 1.2:-2336276 MS.gene27310:CDS
CAGAAGCTAGCAAGGGCTGT+TGG 0.521879 1.2:-2336268 MS.gene27310:CDS
GCATTTCTGTATTTGGGCAA+AGG 0.525051 1.2:+2336166 None:intergenic
ATGATAAGGACACCCCAGAT+AGG 0.538561 1.2:-2336294 MS.gene27310:CDS
TTCTGTCAATACTTCACTGA+AGG 0.539972 1.2:+2335503 None:intergenic
AAGCTAGCAAGGGCTGTTGG+AGG 0.552500 1.2:-2336265 MS.gene27310:CDS
GAATGTCCTCAAGTTCAGCT+TGG 0.559569 1.2:-2336360 MS.gene27310:CDS
AGCTAGCAAGGGCTGTTGGA+GGG 0.566835 1.2:-2336264 MS.gene27310:CDS
AGACAGTTGAGGAAGTGAAA+AGG 0.586038 1.2:-2336240 MS.gene27310:CDS
TGTTGTCCAAGCTGAACTTG+AGG 0.595382 1.2:+2336354 None:intergenic
GATTTGAAGCAAATTGAGGA+AGG 0.610917 1.2:-2336196 MS.gene27310:CDS
TAGCTTCTGCCACCTATCTG+GGG 0.629096 1.2:+2336282 None:intergenic
TAGGTGGCAGAAGCTAGCAA+GGG 0.655725 1.2:-2336275 MS.gene27310:CDS
ATAAGGACACCCCAGATAGG+TGG 0.660087 1.2:-2336291 MS.gene27310:CDS
ATTACAGTGACGAAGAACAA+AGG 0.662329 1.2:-2336123 MS.gene27310:intron
TGTTGGAGGGAAGACAGTTG+AGG 0.663833 1.2:-2336251 MS.gene27310:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATATTTTGTATATCTAATT+TGG - chr1.2:2336086-2336105 MS.gene27310:intron 10.0%
!!! TATCTACAATTTTTTTTTTA+AGG + chr1.2:2335795-2335814 None:intergenic 10.0%
!!! TAATGTAGATTTTTATTACT+AGG + chr1.2:2336129-2336148 None:intergenic 15.0%
!!! TTTTTTCACTAAATTTAATG+AGG - chr1.2:2336046-2336065 MS.gene27310:intron 15.0%
!!! CTTCTTCTTGTTTATAAATA+TGG - chr1.2:2336278-2336297 MS.gene27310:CDS 20.0%
! CGTATAAAACAGTAAGTTTA+TGG + chr1.2:2336235-2336254 None:intergenic 25.0%
!! ATGGAGAAGATTTTTATTGT+GGG - chr1.2:2336297-2336316 MS.gene27310:CDS 25.0%
!! GTTCGTCTTACTAATATTTT+TGG - chr1.2:2335885-2335904 MS.gene27310:intron 25.0%
!! TATGGAGAAGATTTTTATTG+TGG - chr1.2:2336296-2336315 MS.gene27310:CDS 25.0%
AGAAATGCTGCAACAATTAA+AGG - chr1.2:2335723-2335742 MS.gene27310:intron 30.0%
AGCAACACAAATTTAAAGAG+AGG - chr1.2:2336002-2336021 MS.gene27310:intron 30.0%
AGTCATTAGAAACTCATACA+CGG - chr1.2:2335828-2335847 MS.gene27310:intron 30.0%
CAAAAGATTTGAGAATGCTT+TGG - chr1.2:2335551-2335570 MS.gene27310:intron 30.0%
GTCTATTGTATTTGTAATGC+AGG - chr1.2:2336334-2336353 MS.gene27310:CDS 30.0%
! TGAAGATTTGAAGCAAATTG+AGG - chr1.2:2335674-2335693 MS.gene27310:intron 30.0%
ATTACAGTGACGAAGAACAA+AGG - chr1.2:2335751-2335770 MS.gene27310:intron 35.0%
GTTGCAGCATTTCTGTATTT+GGG + chr1.2:2335717-2335736 None:intergenic 35.0%
TGTTGCAGCATTTCTGTATT+TGG + chr1.2:2335718-2335737 None:intergenic 35.0%
TTCATTTACACACACCACAA+AGG - chr1.2:2336194-2336213 MS.gene27310:CDS 35.0%
! GATTTGAAGCAAATTGAGGA+AGG - chr1.2:2335678-2335697 MS.gene27310:intron 35.0%
AGACAGTTGAGGAAGTGAAA+AGG - chr1.2:2335634-2335653 MS.gene27310:intron 40.0%
AGTAAGTTTATGGTCCCTCA+TGG + chr1.2:2336225-2336244 None:intergenic 40.0%
GCATTTCTGTATTTGGGCAA+AGG + chr1.2:2335711-2335730 None:intergenic 40.0%
TGCTTTGGCCATCTATGATA+AGG - chr1.2:2335566-2335585 MS.gene27310:intron 40.0%
ATACACGGATAGACGAGTCA+GGG - chr1.2:2335843-2335862 MS.gene27310:intron 45.0%
ATGATAAGGACACCCCAGAT+AGG - chr1.2:2335580-2335599 MS.gene27310:intron 45.0%
TGTTGTCCAAGCTGAACTTG+AGG + chr1.2:2335523-2335542 None:intergenic 45.0%
! ACCACAAAGGTACAACCATG+AGG - chr1.2:2336207-2336226 MS.gene27310:CDS 45.0%
! CCACAAAGGTACAACCATGA+GGG - chr1.2:2336208-2336227 MS.gene27310:CDS 45.0%
! TGGGGTGTCCTTATCATAGA+TGG + chr1.2:2335577-2335596 None:intergenic 45.0%
ATAAGGACACCCCAGATAGG+TGG - chr1.2:2335583-2335602 MS.gene27310:intron 50.0%
ATAGGTGGCAGAAGCTAGCA+AGG - chr1.2:2335598-2335617 MS.gene27310:intron 50.0%
CATACACGGATAGACGAGTC+AGG - chr1.2:2335842-2335861 MS.gene27310:intron 50.0%
CCCTCATGGTTGTACCTTTG+TGG + chr1.2:2336211-2336230 None:intergenic 50.0%
CTAGCTTCTGCCACCTATCT+GGG + chr1.2:2335596-2335615 None:intergenic 50.0%
GTAAGACGAACGAAGTGACC+TGG + chr1.2:2335876-2335895 None:intergenic 50.0%
TAGCTTCTGCCACCTATCTG+GGG + chr1.2:2335595-2335614 None:intergenic 50.0%
TAGGTGGCAGAAGCTAGCAA+GGG - chr1.2:2335599-2335618 MS.gene27310:intron 50.0%
TGTTGGAGGGAAGACAGTTG+AGG - chr1.2:2335623-2335642 MS.gene27310:intron 50.0%
! ACGAGTCAGGGTTTGAAACC+AGG - chr1.2:2335855-2335874 MS.gene27310:intron 50.0%
AAGCTAGCAAGGGCTGTTGG+AGG - chr1.2:2335609-2335628 MS.gene27310:intron 55.0%
AGCTAGCAAGGGCTGTTGGA+GGG - chr1.2:2335610-2335629 MS.gene27310:intron 55.0%
CAGAAGCTAGCAAGGGCTGT+TGG - chr1.2:2335606-2335625 MS.gene27310:intron 55.0%
! GCTAGCTTCTGCCACCTATC+TGG + chr1.2:2335597-2335616 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 2335516 2336380 2335516 ID=MS.gene27310
chr1.2 mRNA 2335516 2336380 2335516 ID=MS.gene27310.t1;Parent=MS.gene27310
chr1.2 exon 2336124 2336380 2336124 ID=MS.gene27310.t1.exon1;Parent=MS.gene27310.t1
chr1.2 CDS 2336124 2336380 2336124 ID=cds.MS.gene27310.t1;Parent=MS.gene27310.t1
chr1.2 exon 2335516 2335540 2335516 ID=MS.gene27310.t1.exon2;Parent=MS.gene27310.t1
chr1.2 CDS 2335516 2335540 2335516 ID=cds.MS.gene27310.t1;Parent=MS.gene27310.t1
Gene Sequence

>MS.gene27310

ATGTCCTCAAGTTCAGCTTGGACAACAAAGCAAAACAAAAGATTTGAGAATGCTTTGGCCATCTATGATAAGGACACCCCAGATAGGTGGCAGAAGCTAGCAAGGGCTGTTGGAGGGAAGACAGTTGAGGAAGTGAAAAGGCATTATGAGATGTTAGTTGAAGATTTGAAGCAAATTGAGGAAGGTCATGTTCCTTTGCCCAAATACAGAAATGCTGCAACAATTAAAGGTTACAATTACAGTGACGAAGAACAAAGGTAATTTTTACTACTTAATCCTTAAAAAAAAAATTGTAGATAGACAAAATATAATAGTCATTAGAAACTCATACACGGATAGACGAGTCAGGGTTTGAAACCAGGTCACTTCGTTCGTCTTACTAATATTTTTGGTACTTTTGACACTTGAGCACTACTTAATCGTTATTTTGTCATTAGCAATCGCTTGCATATGATTCAATTTGACACTGTTAGATAAAATTAATTTAGCAACACAAATTTAAAGAGAGGTTATATGAAATATGTATCTAATTTTTTCACTAAATTTAATGAGGAAAATTAAACAAGAATTTATATTTTGTATATCTAATTTGGTCTCTAATTTTATTTTTCCTAGTAATAAAAATCTACATTATAATCTAAACTATAGTTTTATATCATTTATGTTCATTTTCTCTGTTTCATTTACACACACCACAAAGGTACAACCATGAGGGACCATAAACTTACTGTTTTATACGTTTTTTTTCTTCTTCTTCTTCTTCTTCTTCTTGTTTATAAATATGGAGAAGATTTTTATTGTGGGTGTGAGCTGAGTGAGTCTATTGTATTTGTAATGCAGGTTGAAGTATCTAAGCCTTCAGTGA
Protein sequence

>MS.gene27310.t1

MSSSSAWTTKQNKRFENALAIYDKDTPDRWQKLARAVGGKTVEEVKRHYEMLVEDLKQIEEGHVPLPKYRNAATIKGYNYSDEEQRLKYLSLQ