AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene021963

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene021963.t1 MTR_7g015750 88.321 137 16 0 21 157 215 351 5.86e-87 258
MS.gene021963.t1 MTR_7g015760 78.676 136 29 0 27 162 207 342 1.28e-72 222
MS.gene021963.t1 MTR_7g015760 76.515 132 31 0 31 162 197 328 3.91e-68 210
MS.gene021963.t1 MTR_7g018130 72.656 128 35 0 28 155 211 338 1.72e-59 188
MS.gene021963.t1 MTR_7g015800 52.201 159 46 5 26 160 210 362 9.39e-39 135
MS.gene021963.t1 MTR_7g015800 55.882 136 34 5 26 160 210 320 4.81e-37 130
MS.gene021963.t1 MTR_7g015790 80.263 76 13 2 87 161 4 78 1.37e-35 119
MS.gene021963.t1 MTR_7g073660 38.400 125 66 3 27 149 708 823 7.64e-17 77.0
MS.gene021963.t1 MTR_8g037700 35.156 128 72 3 27 152 696 814 4.05e-14 69.3
MS.gene021963.t1 MTR_5g047120 33.083 133 79 3 27 156 680 805 1.81e-13 67.4
MS.gene021963.t1 MTR_5g047070 33.083 133 79 3 27 156 439 564 1.93e-13 67.4
MS.gene021963.t1 MTR_4g095012 36.290 124 68 3 27 148 640 754 2.56e-13 67.0
MS.gene021963.t1 MTR_4g095042 35.252 139 79 4 27 163 664 793 4.81e-13 66.2
MS.gene021963.t1 MTR_4g095045 34.532 139 80 3 27 163 473 602 7.60e-13 65.5
MS.gene021963.t1 MTR_4g109010 33.884 121 69 3 27 145 701 812 9.83e-13 65.5
MS.gene021963.t1 MTR_4g095032 33.813 139 81 3 27 163 605 734 1.56e-12 64.7
MS.gene021963.t1 MTR_7g115300 36.000 125 69 4 27 149 695 810 6.88e-12 62.8
MS.gene021963.t1 MTR_4g005130 33.582 134 72 4 25 151 657 780 1.17e-11 62.4
MS.gene021963.t1 MTR_1g080740 33.600 125 72 3 27 149 690 805 1.63e-11 62.0
MS.gene021963.t1 MTR_2g080220 32.258 124 77 1 27 150 668 784 1.77e-11 61.6
MS.gene021963.t1 MTR_6g015805 34.400 125 71 2 27 149 703 818 1.80e-11 61.6
MS.gene021963.t1 MTR_7g079320 29.825 114 73 1 26 139 520 626 1.92e-11 61.6
MS.gene021963.t1 MTR_4g061833 36.066 122 67 2 27 146 515 627 2.86e-11 61.2
MS.gene021963.t1 MTR_4g061833 36.066 122 67 2 27 146 666 778 3.15e-11 60.8
MS.gene021963.t1 MTR_4g061930 36.066 122 67 2 27 146 666 778 3.15e-11 60.8
MS.gene021963.t1 MTR_2g030310 34.266 143 76 5 27 162 687 818 5.99e-11 60.1
MS.gene021963.t1 MTR_2g030310 34.266 143 76 5 27 162 687 818 6.19e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene021963.t1 AT5G28680 39.062 128 67 3 27 152 687 805 7.65e-18 80.1
MS.gene021963.t1 AT5G28680 39.062 128 67 3 27 152 687 805 7.65e-18 80.1
MS.gene021963.t1 AT3G04690 40.000 125 64 3 27 149 683 798 3.89e-17 78.2
MS.gene021963.t1 AT4G39110 35.659 129 72 4 27 153 691 810 2.79e-13 67.0
MS.gene021963.t1 AT3G51550 35.200 125 70 3 27 149 703 818 5.12e-13 66.2
MS.gene021963.t1 AT2G23200 34.454 119 71 1 27 145 654 765 1.05e-12 65.5
MS.gene021963.t1 AT2G21480 34.091 132 76 4 27 156 690 812 1.18e-12 65.1
MS.gene021963.t1 AT5G24010 35.484 124 69 3 27 148 655 769 2.64e-12 64.3
MS.gene021963.t1 AT5G59700 35.246 122 68 3 27 146 648 760 4.79e-12 63.5
MS.gene021963.t1 AT3G46290 36.066 122 67 3 27 146 651 763 5.53e-12 63.2

Find 37 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTAATCCAGCTAACATTT+TGG 0.240668 7.1:+80624113 MS.gene021963:CDS
GATGAACTCCACAATATTAT+TGG 0.262371 7.1:+80623535 None:intergenic
TTAGAGGAAGCACTGAAATT+AGG 0.268944 7.1:+80623578 MS.gene021963:CDS
TTTGATAAGATGGTCAAGTT+AGG 0.329967 7.1:+80624063 MS.gene021963:CDS
TTACCATGGTGCTTGGAAAA+AGG 0.346723 7.1:-80624343 None:intergenic
CCTATCGTCGGCCTTTCATT+TGG 0.354301 7.1:-80624243 None:intergenic
ATTGATAGCGCCGCAATGTT+TGG 0.361539 7.1:+80624179 MS.gene021963:CDS
AAATGTGATGTCTATTCCTT+TGG 0.386619 7.1:+80623994 MS.gene021963:CDS
GCAATGTTTGGAAGTGTTCA+TGG 0.398019 7.1:+80624191 MS.gene021963:CDS
CGCTATCAATCTCATGAGAA+TGG 0.418530 7.1:-80624166 None:intergenic
TGAGCATGCTCTGGCACTGC+AGG 0.438038 7.1:+80624284 MS.gene021963:CDS
AAATACTATCTTTGATAAGA+TGG 0.443976 7.1:+80624053 MS.gene021963:CDS
TCAAGTTAGGGAACACAGAT+TGG 0.450398 7.1:+80624076 MS.gene021963:CDS
TTGACAGGTTCGACTGGCCA+TGG 0.471347 7.1:+80623928 MS.gene021963:intron
TTGATAAGATGGTCAAGTTA+GGG 0.477431 7.1:+80624064 MS.gene021963:CDS
AACCTCTCCAAAATGTTAGC+TGG 0.478553 7.1:-80624120 None:intergenic
TATTTGTGAAAGCATTGGTT+CGG 0.481438 7.1:-80623972 None:intergenic
ACATTTATTTGTGAAAGCAT+TGG 0.486826 7.1:-80623977 None:intergenic
GGTTGAACTTGAGCATGCTC+TGG 0.512369 7.1:+80624275 MS.gene021963:CDS
TGGCAGCTTACCATGGTGCT+TGG 0.513023 7.1:-80624350 None:intergenic
TGATGTCTATTCCTTTGGTA+CGG 0.514268 7.1:+80623999 MS.gene021963:CDS
GCTATCAATCTCATGAGAAT+GGG 0.528960 7.1:-80624165 None:intergenic
TTCGACTGGCCATGGATACA+TGG 0.535162 7.1:+80623936 MS.gene021963:CDS
GCCGACGATAGGTGAGGTTG+AGG 0.546327 7.1:+80624254 MS.gene021963:CDS
ATAAATTACCAATAATATTG+TGG 0.549794 7.1:-80623543 None:intergenic
CTGCAGGAGGAAGCAGATTG+TGG 0.554239 7.1:+80624300 MS.gene021963:CDS
GCATTGGTTCGGACACACTC+TGG 0.554480 7.1:-80623961 None:intergenic
ACTCTGGCGCCATGTATCCA+TGG 0.572611 7.1:-80623945 None:intergenic
TGAATATAGAACCAAATGAA+AGG 0.579421 7.1:+80624232 MS.gene021963:CDS
CCAAATGAAAGGCCGACGAT+AGG 0.582094 7.1:+80624243 MS.gene021963:CDS
GCATGCTCTGGCACTGCAGG+AGG 0.586226 7.1:+80624287 MS.gene021963:CDS
TTCAAGTAGAACCGTACCAA+AGG 0.586745 7.1:-80624010 None:intergenic
ACGGTTCTACTTGAAGTAGC+AGG 0.599069 7.1:+80624018 MS.gene021963:CDS
GCCAGAATGGCAGCTTACCA+TGG 0.613533 7.1:-80624357 None:intergenic
ACCTCAACCTCACCTATCGT+CGG 0.631236 7.1:-80624255 None:intergenic
ATGAACACTTCCAAACATTG+CGG 0.671973 7.1:-80624189 None:intergenic
TGAAAGGCCGACGATAGGTG+AGG 0.679048 7.1:+80624248 MS.gene021963:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATATTATTATTTTTTTA+AGG + chr7.1:80623659-80623678 MS.gene021963:intron 0.0%
!! AAATTATTGAATAACTAAAA+TGG + chr7.1:80623851-80623870 MS.gene021963:intron 10.0%
!!! TTATTTTCTTTTATTTTTAG+AGG + chr7.1:80623562-80623581 MS.gene021963:CDS 10.0%
!! ATAAATTACCAATAATATTG+TGG - chr7.1:80623546-80623565 None:intergenic 15.0%
!!! TTTTAAGAAGTAGAAAATAT+GGG - chr7.1:80623783-80623802 None:intergenic 15.0%
!! AAATACTATCTTTGATAAGA+TGG + chr7.1:80624053-80624072 MS.gene021963:CDS 20.0%
!! TCAAATTCTACATCAAAAAA+AGG - chr7.1:80623691-80623710 None:intergenic 20.0%
!!! CTTTTAAGAAGTAGAAAATA+TGG - chr7.1:80623784-80623803 None:intergenic 20.0%
! TGAATATAGAACCAAATGAA+AGG + chr7.1:80624232-80624251 MS.gene021963:CDS 25.0%
! TTTCTTAATATACCTTCTCT+TGG + chr7.1:80623714-80623733 MS.gene021963:intron 25.0%
!! ACATTTATTTGTGAAAGCAT+TGG - chr7.1:80623980-80623999 None:intergenic 25.0%
AAATGTGATGTCTATTCCTT+TGG + chr7.1:80623994-80624013 MS.gene021963:CDS 30.0%
AGTAGAAAATATGGGCATTT+AGG - chr7.1:80623775-80623794 None:intergenic 30.0%
GATCAAAAATTTCATCAGCT+GGG - chr7.1:80624146-80624165 None:intergenic 30.0%
GTAGAAAATATGGGCATTTA+GGG - chr7.1:80623774-80623793 None:intergenic 30.0%
TGAAATTAGGTAAGGAATTC+TGG + chr7.1:80623591-80623610 MS.gene021963:intron 30.0%
TTGATAAGATGGTCAAGTTA+GGG + chr7.1:80624064-80624083 MS.gene021963:CDS 30.0%
TTTGATAAGATGGTCAAGTT+AGG + chr7.1:80624063-80624082 MS.gene021963:CDS 30.0%
! ATCTAATCCAGCTAACATTT+TGG + chr7.1:80624113-80624132 MS.gene021963:CDS 30.0%
!! TATTTGTGAAAGCATTGGTT+CGG - chr7.1:80623975-80623994 None:intergenic 30.0%
ATGAACACTTCCAAACATTG+CGG - chr7.1:80624192-80624211 None:intergenic 35.0%
GCAGATTGTGGAAAAAGTAA+TGG + chr7.1:80624312-80624331 MS.gene021963:CDS 35.0%
GCTATCAATCTCATGAGAAT+GGG - chr7.1:80624168-80624187 None:intergenic 35.0%
GGATCAAAAATTTCATCAGC+TGG - chr7.1:80624147-80624166 None:intergenic 35.0%
TGATGTCTATTCCTTTGGTA+CGG + chr7.1:80623999-80624018 MS.gene021963:CDS 35.0%
! CACAAAATGCTTTTGTTGAC+AGG + chr7.1:80623913-80623932 MS.gene021963:intron 35.0%
!! TTAGAGGAAGCACTGAAATT+AGG + chr7.1:80623578-80623597 MS.gene021963:CDS 35.0%
AACCTCTCCAAAATGTTAGC+TGG - chr7.1:80624123-80624142 None:intergenic 40.0%
CGCTATCAATCTCATGAGAA+TGG - chr7.1:80624169-80624188 None:intergenic 40.0%
TCAAGTTAGGGAACACAGAT+TGG + chr7.1:80624076-80624095 MS.gene021963:CDS 40.0%
TTACCATGGTGCTTGGAAAA+AGG - chr7.1:80624346-80624365 None:intergenic 40.0%
TTCAAGTAGAACCGTACCAA+AGG - chr7.1:80624013-80624032 None:intergenic 40.0%
! GTTTTCATTGCACCAAGAGA+AGG - chr7.1:80623729-80623748 None:intergenic 40.0%
! TTACCTTTTTCCAAGCACCA+TGG + chr7.1:80624340-80624359 MS.gene021963:CDS 40.0%
!! ATCCAGCTAACATTTTGGAG+AGG + chr7.1:80624118-80624137 MS.gene021963:CDS 40.0%
!! GCAATGTTTGGAAGTGTTCA+TGG + chr7.1:80624191-80624210 MS.gene021963:CDS 40.0%
!! GGAAGCACTGAAATTAGGTA+AGG + chr7.1:80623583-80623602 MS.gene021963:intron 40.0%
ACGGTTCTACTTGAAGTAGC+AGG + chr7.1:80624018-80624037 MS.gene021963:CDS 45.0%
CTGTTGCGTGCATCATTAGT+AGG + chr7.1:80623620-80623639 MS.gene021963:intron 45.0%
! CTTTTGTTGACAGGTTCGAC+TGG + chr7.1:80623922-80623941 MS.gene021963:intron 45.0%
!! ATTGATAGCGCCGCAATGTT+TGG + chr7.1:80624179-80624198 MS.gene021963:CDS 45.0%
ACCTCAACCTCACCTATCGT+CGG - chr7.1:80624258-80624277 None:intergenic 50.0%
CCAAATGAAAGGCCGACGAT+AGG + chr7.1:80624243-80624262 MS.gene021963:CDS 50.0%
CCTATCGTCGGCCTTTCATT+TGG - chr7.1:80624246-80624265 None:intergenic 50.0%
GGTTGAACTTGAGCATGCTC+TGG + chr7.1:80624275-80624294 MS.gene021963:CDS 50.0%
! TTCGACTGGCCATGGATACA+TGG + chr7.1:80623936-80623955 MS.gene021963:CDS 50.0%
ACTCTGGCGCCATGTATCCA+TGG - chr7.1:80623948-80623967 None:intergenic 55.0%
CTGCAGGAGGAAGCAGATTG+TGG + chr7.1:80624300-80624319 MS.gene021963:CDS 55.0%
TGAAAGGCCGACGATAGGTG+AGG + chr7.1:80624248-80624267 MS.gene021963:CDS 55.0%
! TTGACAGGTTCGACTGGCCA+TGG + chr7.1:80623928-80623947 MS.gene021963:intron 55.0%
!! GCATTGGTTCGGACACACTC+TGG - chr7.1:80623964-80623983 None:intergenic 55.0%
GCCGACGATAGGTGAGGTTG+AGG + chr7.1:80624254-80624273 MS.gene021963:CDS 60.0%
TGAGCATGCTCTGGCACTGC+AGG + chr7.1:80624284-80624303 MS.gene021963:CDS 60.0%
GCATGCTCTGGCACTGCAGG+AGG + chr7.1:80624287-80624306 MS.gene021963:CDS 65.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 80623536 80624365 80623536 ID=MS.gene021963
chr7.1 mRNA 80623536 80624365 80623536 ID=MS.gene021963.t1;Parent=MS.gene021963
chr7.1 exon 80623536 80623599 80623536 ID=MS.gene021963.t1.exon1;Parent=MS.gene021963.t1
chr7.1 CDS 80623536 80623599 80623536 ID=cds.MS.gene021963.t1;Parent=MS.gene021963.t1
chr7.1 exon 80623935 80624365 80623935 ID=MS.gene021963.t1.exon2;Parent=MS.gene021963.t1
chr7.1 CDS 80623935 80624365 80623935 ID=cds.MS.gene021963.t1;Parent=MS.gene021963.t1
Gene Sequence

>MS.gene021963

ATGAACTCCACAATATTATTGGTAATTTATTTTCTTTTATTTTTAGAGGAAGCACTGAAATTAGGTAAGGAATTCTGGTTGAAACTGTTGCGTGCATCATTAGTAGGATGAATAACATCACATTTTATATTATTATTTTTTTAAGGTTTTTTCCTTTTTTTGATGTAGAATTTGAGTTTTTCTTAATATACCTTCTCTTGGTGCAATGAAAACGATAAAGCTTAGACATTTTAGTCCCTAAATGCCCATATTTTCTACTTCTTAAAAGAGCAATGTATTCTAATATTTTAATTCTCAAGCACTAATTATGAAAGAAAATTATTGAATAACTAAAATGGTATATGCAAGTTTTGTCGATAATTTCTGAAGTTAAGTTACACAAAATGCTTTTGTTGACAGGTTCGACTGGCCATGGATACATGGCGCCAGAGTGTGTCCGAACCAATGCTTTCACAAATAAATGTGATGTCTATTCCTTTGGTACGGTTCTACTTGAAGTAGCAGGAACAGATTACAAAAATACTATCTTTGATAAGATGGTCAAGTTAGGGAACACAGATTGGTTTTTAGAAAAGTCATCTAATCCAGCTAACATTTTGGAGAGGTTCCCAGCTGATGAAATTTTTGATCCCATTCTCATGAGATTGATAGCGCCGCAATGTTTGGAAGTGTTCATGGATATCATGAAAAGATGCTTGAATATAGAACCAAATGAAAGGCCGACGATAGGTGAGGTTGAGGTTGAACTTGAGCATGCTCTGGCACTGCAGGAGGAAGCAGATTGTGGAAAAAGTAATGGTGATTTTACCTTTTTCCAAGCACCATGGTAA
Protein sequence

>MS.gene021963.t1

MNSTILLVIYFLLFLEEALKLGSTGHGYMAPECVRTNAFTNKCDVYSFGTVLLEVAGTDYKNTIFDKMVKLGNTDWFLEKSSNPANILERFPADEIFDPILMRLIAPQCLEVFMDIMKRCLNIEPNERPTIGEVEVELEHALALQEEADCGKSNGDFTFFQAPW