AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29300

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29300.t1 MTR_7g114060 100.000 139 0 0 1 139 1 139 3.00e-97 276
MS.gene29300.t1 MTR_7g114040 100.000 139 0 0 1 139 1 139 3.00e-97 276
MS.gene29300.t1 MTR_7g108320 95.775 142 3 1 1 139 1 142 4.40e-93 265
MS.gene29300.t1 MTR_7g093910 87.313 134 17 0 6 139 9 142 6.22e-82 237
MS.gene29300.t1 MTR_7g114050 87.023 131 6 2 9 139 11 130 3.86e-72 212
MS.gene29300.t1 MTR_2g082510 86.777 121 12 1 10 126 3 123 3.42e-69 204
MS.gene29300.t1 MTR_2g082220 84.921 126 11 2 10 129 3 126 4.30e-69 204
MS.gene29300.t1 MTR_2g096610 75.000 120 30 0 18 137 21 140 1.15e-59 181
MS.gene29300.t1 MTR_7g113160 76.068 117 28 0 9 125 16 132 3.78e-59 179
MS.gene29300.t1 MTR_4g063280 79.091 110 23 0 18 127 17 126 2.93e-58 177
MS.gene29300.t1 MTR_2g096570 81.132 106 20 0 19 124 23 128 5.36e-58 177
MS.gene29300.t1 MTR_4g063410 79.439 107 22 0 19 125 24 130 5.44e-58 177
MS.gene29300.t1 MTR_4g071150 80.374 107 21 0 19 125 24 130 6.46e-58 177
MS.gene29300.t1 MTR_4g064005 81.132 106 20 0 19 124 24 129 6.49e-58 177
MS.gene29300.t1 MTR_8g086640 81.132 106 20 0 19 124 24 129 7.30e-58 177
MS.gene29300.t1 MTR_4g064967 81.132 106 20 0 19 124 24 129 8.16e-58 176
MS.gene29300.t1 MTR_6g005150 61.345 119 37 2 19 136 26 136 5.87e-42 136
MS.gene29300.t1 MTR_1g011750 58.197 122 49 2 3 123 10 130 1.06e-39 130
MS.gene29300.t1 MTR_1g011850 58.197 122 49 2 3 123 10 130 1.06e-39 130
MS.gene29300.t1 MTR_1g114050 62.857 105 37 2 20 123 24 127 5.35e-38 125
MS.gene29300.t1 MTR_1g071040 63.462 104 36 2 21 123 28 130 1.15e-37 125
MS.gene29300.t1 MTR_4g063300 67.708 96 23 1 40 127 10 105 7.05e-36 120
MS.gene29300.t1 MTR_4g005910 88.889 45 5 0 82 126 4 48 6.44e-23 85.5
MS.gene29300.t1 MTR_7g010440 54.444 90 41 0 47 136 96 185 2.92e-22 89.7
MS.gene29300.t1 MTR_4g048490 44.860 107 30 2 19 125 26 103 2.83e-20 80.1
MS.gene29300.t1 MTR_1g069770 55.224 67 30 0 62 128 32 98 1.19e-18 75.9
MS.gene29300.t1 MTR_7g027610 41.818 110 32 3 18 123 13 94 8.02e-16 68.9
MS.gene29300.t1 MTR_0653s0030 52.830 53 25 0 50 102 43 95 4.63e-12 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.gene29300.t1 AT1G54690 92.958 142 7 1 1 139 1 142 2.22e-90 258
MS.gene29300.t1 AT1G08880 94.118 136 8 0 4 139 7 142 5.41e-90 258
MS.gene29300.t1 AT4G27230 86.290 124 13 1 10 129 3 126 4.66e-70 207
MS.gene29300.t1 AT4G27230 86.290 124 13 1 10 129 3 126 4.66e-70 207
MS.gene29300.t1 AT5G54640 82.946 129 19 1 1 129 1 126 1.59e-69 205
MS.gene29300.t1 AT1G51060 83.871 124 16 1 10 129 3 126 1.51e-68 203
MS.gene29300.t1 AT3G20670 84.677 124 15 1 10 129 3 126 4.76e-68 202
MS.gene29300.t1 AT5G59870 73.643 129 29 2 1 124 1 129 1.24e-60 184
MS.gene29300.t1 AT5G27670 73.438 128 29 1 2 124 3 130 4.78e-58 177
MS.gene29300.t1 AT5G02560 79.439 107 22 0 18 124 23 129 5.23e-57 174
MS.gene29300.t1 AT5G02560 64.885 131 22 1 18 124 23 153 1.37e-51 162
MS.gene29300.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29300.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29300.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29300.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29300.t1 AT1G52740 61.905 105 38 2 20 123 27 130 2.42e-38 127
MS.gene29300.t1 AT3G54560 60.952 105 39 2 20 123 29 132 4.94e-37 123
MS.gene29300.t1 AT3G54560 60.952 105 39 2 20 123 29 132 4.94e-37 123
MS.gene29300.t1 AT4G13570 43.220 118 65 2 1 117 2 118 3.98e-23 87.8
MS.gene29300.t1 AT4G13570 49.451 91 44 2 28 117 35 124 9.39e-22 84.3

Find 52 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCCCTTTCCAACCTTCTT+AGG 0.222545 7.2:+3363635 None:intergenic
ATCTGCTTCTCAAGAATTCT+AGG 0.264115 7.2:-3363600 None:intergenic
TGAAGAACTCAGCAAGCTTT+TGG 0.286717 7.2:-3363714 MS.gene29300:CDS
GAAACTGATTTGGCAGCCTT+TGG 0.309618 7.2:+3364059 None:intergenic
AACACGTTCGGCGTATTTAC+CGG 0.321195 7.2:+3363977 None:intergenic
TGAAGATCTGGAAACTGATT+TGG 0.321558 7.2:+3364049 None:intergenic
GGAAAGGGCAAAGGAGAAAT+TGG 0.326882 7.2:-3363623 MS.gene29300:CDS
AGCAAAGTCTGATGAATATT+AGG 0.347792 7.2:+3363659 None:intergenic
TTTACCGGCCTTGAGGAATC+TGG 0.369624 7.2:+3363992 None:intergenic
AAGTCCTGCCTTTGAAGATC+TGG 0.372304 7.2:+3364037 None:intergenic
TCAGACTTTGCTACCTAAGA+AGG 0.421667 7.2:-3363648 MS.gene29300:CDS
GGCACATTCAGCTTGCTGTT+AGG 0.440630 7.2:-3363742 MS.gene29300:CDS
GAGTTCCACTGGCACAACTA+AGG 0.456467 7.2:-3364096 MS.gene29300:CDS
AGGACGGCGGAGAGGTAGAC+AGG 0.463287 7.2:+3363942 None:intergenic
GGGACTGTGACCATTGCTAA+TGG 0.468303 7.2:-3363692 MS.gene29300:CDS
AGCACCGGCACCAACACGTT+CGG 0.480590 7.2:+3363965 None:intergenic
CTGGCACAACTAAGGGCGGA+AGG 0.502885 7.2:-3364088 MS.gene29300:CDS
GTTTCCAGATCTTCAAAGGC+AGG 0.505528 7.2:-3364041 MS.gene29300:CDS
CTACCTAAGAAGGTTGGAAA+GGG 0.510822 7.2:-3363638 MS.gene29300:CDS
TCTGCTTCTCAAGAATTCTA+GGG 0.519604 7.2:-3363599 None:intergenic
GGCACAACTAAGGGCGGAAG+GGG 0.525782 7.2:-3364086 MS.gene29300:CDS
ATCAGTTTCCAGATCTTCAA+AGG 0.525986 7.2:-3364045 MS.gene29300:CDS
AATTGGCTGGGAACGCTGCA+AGG 0.533557 7.2:-3363793 MS.gene29300:CDS
ACTTTGCTACCTAAGAAGGT+TGG 0.535784 7.2:-3363644 MS.gene29300:CDS
TGGCACAACTAAGGGCGGAA+GGG 0.543224 7.2:-3364087 MS.gene29300:CDS
AGTTCCACTGGCACAACTAA+GGG 0.549244 7.2:-3364095 MS.gene29300:CDS
TACGCCGAACGTGTTGGTGC+CGG 0.556200 7.2:-3363969 MS.gene29300:CDS
GCTACCTAAGAAGGTTGGAA+AGG 0.557785 7.2:-3363639 MS.gene29300:CDS
ATTGGCTGGGAACGCTGCAA+GGG 0.562499 7.2:-3363792 MS.gene29300:CDS
ATCGCCAGATTCCTCAAGGC+CGG 0.565542 7.2:-3363996 MS.gene29300:CDS
ACAGCAAGCTGAATGTGCCT+TGG 0.570928 7.2:+3363746 None:intergenic
GAATGTGCCTTGGTACAATA+CGG 0.571461 7.2:+3363756 None:intergenic
GGGCGGAAGGGGTAAGCCAA+AGG 0.573881 7.2:-3364075 MS.gene29300:CDS
CGGCGTATTTACCGGCCTTG+AGG 0.577173 7.2:+3363985 None:intergenic
TCCGCCCTTAGTTGTGCCAG+TGG 0.580065 7.2:+3364091 None:intergenic
GAATCTGGCGATTCTTCCGA+CGG 0.590644 7.2:+3364007 None:intergenic
GGTAAATACGCCGAACGTGT+TGG 0.593895 7.2:-3363975 MS.gene29300:CDS
AATCTGGCGATTCTTCCGAC+GGG 0.598431 7.2:+3364008 None:intergenic
CCTTGAGTATCTCGCTGCTG+AGG 0.612329 7.2:-3363922 MS.gene29300:intron
AAGAAGGTTGGAAAGGGCAA+AGG 0.621113 7.2:-3363632 MS.gene29300:CDS
TAAAACACCACCATTAGCAA+TGG 0.630364 7.2:+3363682 None:intergenic
AAGAATCGCCAGATTCCTCA+AGG 0.631643 7.2:-3364000 MS.gene29300:CDS
CCTCAGCAGCGAGATACTCA+AGG 0.638807 7.2:+3363922 None:intergenic
GGAGAGGTAGACAGGAGCAC+CGG 0.644805 7.2:+3363950 None:intergenic
TCCACTGGCACAACTAAGGG+CGG 0.647888 7.2:-3364092 MS.gene29300:CDS
ACTGTGACCATTGCTAATGG+TGG 0.653058 7.2:-3363689 MS.gene29300:CDS
GATACTCAAGGACGGCGGAG+AGG 0.669935 7.2:+3363934 None:intergenic
GCAGGACTTCAATTCCCCGT+CGG 0.683210 7.2:-3364023 MS.gene29300:CDS
AGCAGCGAGATACTCAAGGA+CGG 0.684917 7.2:+3363926 None:intergenic
AGAAGAACCGTATTGTACCA+AGG 0.686303 7.2:-3363763 MS.gene29300:CDS
ATCTGGCGATTCTTCCGACG+GGG 0.702228 7.2:+3364009 None:intergenic
AGCGAGATACTCAAGGACGG+CGG 0.736224 7.2:+3363929 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATACAGTTTAATCAAAT+TGG + chr7.2:3363864-3363883 None:intergenic 15.0%
!!! ATTAAACTGTATTTTCATTT+TGG - chr7.2:3363869-3363888 MS.gene29300:intron 15.0%
!!! GTATTTTCATTTTGGTATTT+AGG - chr7.2:3363877-3363896 MS.gene29300:intron 20.0%
!!! TCTCTTTTTTGTATAATGTA+GGG - chr7.2:3363830-3363849 MS.gene29300:intron 20.0%
! ATACAAAAAAGAGAGTGAAA+GGG + chr7.2:3363824-3363843 None:intergenic 25.0%
! TATACAAAAAAGAGAGTGAA+AGG + chr7.2:3363825-3363844 None:intergenic 25.0%
!!! CTCTCTTTTTTGTATAATGT+AGG - chr7.2:3363829-3363848 MS.gene29300:intron 25.0%
!!! TCATTTTGGTATTTAGGTTT+TGG - chr7.2:3363883-3363902 MS.gene29300:intron 25.0%
AGCAAAGTCTGATGAATATT+AGG + chr7.2:3364043-3364062 None:intergenic 30.0%
!!! TGGTATTTAGGTTTTGGAAT+TGG - chr7.2:3363889-3363908 MS.gene29300:intron 30.0%
ATCAGTTTCCAGATCTTCAA+AGG - chr7.2:3363654-3363673 MS.gene29300:CDS 35.0%
TAAAACACCACCATTAGCAA+TGG + chr7.2:3364020-3364039 None:intergenic 35.0%
TGAAGATCTGGAAACTGATT+TGG + chr7.2:3363653-3363672 None:intergenic 35.0%
!!! ATTTAGGTTTTGGAATTGGC+TGG - chr7.2:3363893-3363912 MS.gene29300:intron 35.0%
!!! TTTAGGTTTTGGAATTGGCT+GGG - chr7.2:3363894-3363913 MS.gene29300:intron 35.0%
ACTTTGCTACCTAAGAAGGT+TGG - chr7.2:3364055-3364074 MS.gene29300:CDS 40.0%
AGAAGAACCGTATTGTACCA+AGG - chr7.2:3363936-3363955 MS.gene29300:CDS 40.0%
CTACCTAAGAAGGTTGGAAA+GGG - chr7.2:3364061-3364080 MS.gene29300:CDS 40.0%
GAATGTGCCTTGGTACAATA+CGG + chr7.2:3363946-3363965 None:intergenic 40.0%
GTGAAAGGGAACTTGAAGAA+AGG + chr7.2:3363810-3363829 None:intergenic 40.0%
TCAGACTTTGCTACCTAAGA+AGG - chr7.2:3364051-3364070 MS.gene29300:CDS 40.0%
! AAGAACTCAGCAAGCTTTTG+GGG - chr7.2:3363987-3364006 MS.gene29300:CDS 40.0%
! GAAGAACTCAGCAAGCTTTT+GGG - chr7.2:3363986-3364005 MS.gene29300:CDS 40.0%
! TGAAGAACTCAGCAAGCTTT+TGG - chr7.2:3363985-3364004 MS.gene29300:CDS 40.0%
AACACGTTCGGCGTATTTAC+CGG + chr7.2:3363725-3363744 None:intergenic 45.0%
AAGAAGGTTGGAAAGGGCAA+AGG - chr7.2:3364067-3364086 MS.gene29300:CDS 45.0%
AAGAATCGCCAGATTCCTCA+AGG - chr7.2:3363699-3363718 MS.gene29300:CDS 45.0%
ACTGTGACCATTGCTAATGG+TGG - chr7.2:3364010-3364029 MS.gene29300:CDS 45.0%
AGTTCCACTGGCACAACTAA+GGG - chr7.2:3363604-3363623 MS.gene29300:CDS 45.0%
GCTACCTAAGAAGGTTGGAA+AGG - chr7.2:3364060-3364079 MS.gene29300:CDS 45.0%
GGAAAGGGCAAAGGAGAAAT+TGG - chr7.2:3364076-3364095 MS.gene29300:CDS 45.0%
GTTTCCAGATCTTCAAAGGC+AGG - chr7.2:3363658-3363677 MS.gene29300:CDS 45.0%
TTGCCCTTTCCAACCTTCTT+AGG + chr7.2:3364067-3364086 None:intergenic 45.0%
! AAGTCCTGCCTTTGAAGATC+TGG + chr7.2:3363665-3363684 None:intergenic 45.0%
!! GAAACTGATTTGGCAGCCTT+TGG + chr7.2:3363643-3363662 None:intergenic 45.0%
AATCTGGCGATTCTTCCGAC+GGG + chr7.2:3363694-3363713 None:intergenic 50.0%
ACAGCAAGCTGAATGTGCCT+TGG + chr7.2:3363956-3363975 None:intergenic 50.0%
AGCAGCGAGATACTCAAGGA+CGG + chr7.2:3363776-3363795 None:intergenic 50.0%
GAATCTGGCGATTCTTCCGA+CGG + chr7.2:3363695-3363714 None:intergenic 50.0%
GAGTTCCACTGGCACAACTA+AGG - chr7.2:3363603-3363622 MS.gene29300:CDS 50.0%
GGGACTGTGACCATTGCTAA+TGG - chr7.2:3364007-3364026 MS.gene29300:CDS 50.0%
GGTAAATACGCCGAACGTGT+TGG - chr7.2:3363724-3363743 MS.gene29300:CDS 50.0%
TTTACCGGCCTTGAGGAATC+TGG + chr7.2:3363710-3363729 None:intergenic 50.0%
!! GGCACATTCAGCTTGCTGTT+AGG - chr7.2:3363957-3363976 MS.gene29300:CDS 50.0%
AATTGGCTGGGAACGCTGCA+AGG - chr7.2:3363906-3363925 MS.gene29300:intron 55.0%
AGCGAGATACTCAAGGACGG+CGG + chr7.2:3363773-3363792 None:intergenic 55.0%
ATCGCCAGATTCCTCAAGGC+CGG - chr7.2:3363703-3363722 MS.gene29300:CDS 55.0%
ATCTGGCGATTCTTCCGACG+GGG + chr7.2:3363693-3363712 None:intergenic 55.0%
ATTGGCTGGGAACGCTGCAA+GGG - chr7.2:3363907-3363926 MS.gene29300:intron 55.0%
CCTCAGCAGCGAGATACTCA+AGG + chr7.2:3363780-3363799 None:intergenic 55.0%
CCTTGAGTATCTCGCTGCTG+AGG - chr7.2:3363777-3363796 MS.gene29300:CDS 55.0%
GCAGGACTTCAATTCCCCGT+CGG - chr7.2:3363676-3363695 MS.gene29300:CDS 55.0%
TCCACTGGCACAACTAAGGG+CGG - chr7.2:3363607-3363626 MS.gene29300:CDS 55.0%
TGGCACAACTAAGGGCGGAA+GGG - chr7.2:3363612-3363631 MS.gene29300:CDS 55.0%
CGGCGTATTTACCGGCCTTG+AGG + chr7.2:3363717-3363736 None:intergenic 60.0%
CTGGCACAACTAAGGGCGGA+AGG - chr7.2:3363611-3363630 MS.gene29300:CDS 60.0%
GATACTCAAGGACGGCGGAG+AGG + chr7.2:3363768-3363787 None:intergenic 60.0%
GGCACAACTAAGGGCGGAAG+GGG - chr7.2:3363613-3363632 MS.gene29300:CDS 60.0%
TCCGCCCTTAGTTGTGCCAG+TGG + chr7.2:3363611-3363630 None:intergenic 60.0%
! GGAGAGGTAGACAGGAGCAC+CGG + chr7.2:3363752-3363771 None:intergenic 60.0%
! TACGCCGAACGTGTTGGTGC+CGG - chr7.2:3363730-3363749 MS.gene29300:CDS 60.0%
!! AGCACCGGCACCAACACGTT+CGG + chr7.2:3363737-3363756 None:intergenic 60.0%
AGGACGGCGGAGAGGTAGAC+AGG + chr7.2:3363760-3363779 None:intergenic 65.0%
GGGCGGAAGGGGTAAGCCAA+AGG - chr7.2:3363624-3363643 MS.gene29300:CDS 65.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 3363601 3364120 3363601 ID=MS.gene29300
chr7.2 mRNA 3363601 3364120 3363601 ID=MS.gene29300.t1;Parent=MS.gene29300
chr7.2 exon 3363923 3364120 3363923 ID=MS.gene29300.t1.exon1;Parent=MS.gene29300.t1
chr7.2 CDS 3363923 3364120 3363923 ID=cds.MS.gene29300.t1;Parent=MS.gene29300.t1
chr7.2 exon 3363601 3363822 3363601 ID=MS.gene29300.t1.exon2;Parent=MS.gene29300.t1
chr7.2 CDS 3363601 3363822 3363601 ID=cds.MS.gene29300.t1;Parent=MS.gene29300.t1
Gene Sequence

>MS.gene29300

ATGAGTTCCACTGGCACAACTAAGGGCGGAAGGGGTAAGCCAAAGGCTGCCAAATCAGTTTCCAGATCTTCAAAGGCAGGACTTCAATTCCCCGTCGGAAGAATCGCCAGATTCCTCAAGGCCGGTAAATACGCCGAACGTGTTGGTGCCGGTGCTCCTGTCTACCTCTCCGCCGTCCTTGAGTATCTCGCTGCTGAGGTTTGTTTCCTTTCTTCAAGTTCCCTTTCACTCTCTTTTTTGTATAATGTAGGGTTCTAGATCCAATTTGATTAAACTGTATTTTCATTTTGGTATTTAGGTTTTGGAATTGGCTGGGAACGCTGCAAGGGACAACAAGAAGAACCGTATTGTACCAAGGCACATTCAGCTTGCTGTTAGGAACGATGAAGAACTCAGCAAGCTTTTGGGGACTGTGACCATTGCTAATGGTGGTGTTTTACCTAATATTCATCAGACTTTGCTACCTAAGAAGGTTGGAAAGGGCAAAGGAGAAATTGGATCTGCTTCTCAAGAATTCTAG
Protein sequence

>MS.gene29300.t1

MSSTGTTKGGRGKPKAAKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQTLLPKKVGKGKGEIGSASQEF