AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene28215

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28215.t1 MTR_3g025380 80.147 136 27 0 3 138 2 137 6.74e-68 202
MS.gene28215.t1 MTR_3g025510 50.667 150 58 4 1 137 1 147 5.02e-39 129
MS.gene28215.t1 MTR_3g025550 88.136 59 6 1 84 141 6 64 3.62e-33 111
MS.gene28215.t1 MTR_3g025620 64.000 50 18 0 89 138 2 51 2.94e-18 73.6
MS.gene28215.t1 MTR_2g058360 47.297 74 34 3 67 137 67 138 2.05e-15 68.6
MS.gene28215.t1 MTR_7g074170 45.000 60 32 1 78 136 327 386 4.67e-14 68.2
MS.gene28215.t1 MTR_3g088080 38.272 81 43 2 56 136 6 79 1.20e-13 62.8
MS.gene28215.t1 MTR_5g041310 30.000 120 70 4 31 139 44 160 3.00e-13 64.7
MS.gene28215.t1 MTR_4g110100 45.902 61 32 1 77 136 341 401 1.15e-12 64.3
MS.gene28215.t1 MTR_5g041330 29.661 118 68 3 31 136 32 146 2.54e-12 62.0
MS.gene28215.t1 MTR_6g079660 36.111 72 45 1 66 136 205 276 6.67e-12 62.0
MS.gene28215.t1 MTR_1g114620 38.028 71 42 1 66 136 237 305 7.57e-12 61.6
MS.gene28215.t1 MTR_3g072630 37.288 59 37 0 79 137 205 263 1.87e-11 60.5
MS.gene28215.t1 MTR_3g072630 37.288 59 37 0 79 137 205 263 2.25e-11 60.5
MS.gene28215.t1 MTR_2g097620 33.333 60 40 0 77 136 171 230 2.40e-11 60.5
MS.gene28215.t1 MTR_1g114320 34.286 70 45 1 68 136 166 235 2.99e-11 59.7
MS.gene28215.t1 MTR_5g058530 43.103 58 29 1 79 136 212 265 3.09e-11 60.1
MS.gene28215.t1 MTR_3g083480 44.898 49 27 0 88 136 230 278 3.13e-11 60.1
MS.gene28215.t1 MTR_2g007340 43.103 58 33 0 79 136 185 242 4.65e-11 59.3
MS.gene28215.t1 MTR_1g051105 48.837 43 22 0 95 137 159 201 7.94e-11 58.2
MS.gene28215.t1 MTR_8g056930 38.356 73 41 2 68 137 90 161 8.39e-11 57.0
MS.gene28215.t1 MTR_0186s0090 51.064 47 20 1 94 137 115 161 8.93e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28215.t1 AT1G14200 44.068 59 33 0 78 136 92 150 3.94e-14 66.2
MS.gene28215.t1 AT3G02340 27.143 140 82 3 1 136 253 376 4.59e-14 68.2
MS.gene28215.t1 AT3G02340 27.143 140 82 3 1 136 253 376 4.59e-14 68.2
MS.gene28215.t1 AT1G60360 51.163 43 21 0 95 137 224 266 4.92e-13 65.1
MS.gene28215.t1 AT5G60820 45.283 53 28 1 89 140 366 418 6.27e-13 65.1
MS.gene28215.t1 AT4G12190 46.032 63 29 2 79 136 4 66 7.23e-13 60.1
MS.gene28215.t1 AT4G05350 44.444 63 30 2 79 136 139 201 8.52e-13 63.2
MS.gene28215.t1 AT3G60080 37.500 72 42 1 65 136 142 210 1.06e-12 63.9
MS.gene28215.t1 AT5G15820 36.842 76 47 1 62 136 257 332 3.01e-12 62.8
MS.gene28215.t1 AT3G10815 38.333 60 37 0 78 137 104 163 3.54e-12 61.2
MS.gene28215.t1 AT2G44330 54.762 42 19 0 95 136 96 137 4.34e-12 60.8
MS.gene28215.t1 AT5G08139 41.818 55 31 1 86 139 300 354 4.39e-12 62.4
MS.gene28215.t1 AT5G01980 40.000 60 36 0 77 136 332 391 5.20e-12 62.4
MS.gene28215.t1 AT4G12140 50.000 50 23 1 91 138 149 198 8.62e-12 60.5
MS.gene28215.t1 AT4G12210 44.444 63 30 2 79 136 135 197 1.17e-11 60.1
MS.gene28215.t1 AT4G12150 49.091 55 26 1 82 134 140 194 1.39e-11 60.8
MS.gene28215.t1 AT2G40830 36.842 76 47 1 63 137 157 232 1.55e-11 60.8
MS.gene28215.t1 AT2G40830 36.842 76 47 1 63 137 157 232 1.55e-11 60.8
MS.gene28215.t1 AT2G40830 36.842 76 47 1 63 137 157 232 1.55e-11 60.8
MS.gene28215.t1 AT2G40830 36.842 76 47 1 63 137 157 232 1.55e-11 60.8
MS.gene28215.t1 AT5G64920 37.931 58 36 0 79 136 241 298 1.99e-11 60.5
MS.gene28215.t1 AT5G54990 51.111 45 22 0 92 136 171 215 2.74e-11 59.3
MS.gene28215.t1 AT3G30460 39.683 63 35 1 81 140 83 145 4.77e-11 57.4
MS.gene28215.t1 AT5G52140 27.922 154 83 5 11 136 122 275 5.31e-11 58.9
MS.gene28215.t1 AT3G30460 39.683 63 35 1 81 140 119 181 6.25e-11 57.8
MS.gene28215.t1 AT3G19950 37.288 59 36 1 79 136 199 257 8.17e-11 58.9
MS.gene28215.t1 AT1G21960 35.714 84 49 2 58 136 116 199 8.26e-11 57.8

Find 26 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATCACTTTCTACATTTAT+AGG 0.123833 3.3:-17495696 None:intergenic
TATCTGTTTGGCGGAGCTTT+TGG 0.296874 3.3:+17495953 MS.gene28215:CDS
CATATACAAACTCAGATATT+AGG 0.342493 3.3:-17496080 None:intergenic
GATTCCGATTAGAATGCCTT+TGG 0.406287 3.3:-17495878 None:intergenic
ACGAAGGATGTATTATGAAA+TGG 0.423422 3.3:+17496018 MS.gene28215:CDS
CTATCCAAAGGCATTCTAAT+CGG 0.424659 3.3:+17495874 MS.gene28215:CDS
TACATCCTTCGTGATACAAA+TGG 0.431096 3.3:-17496007 None:intergenic
GAACCTCGTTGATGAGGTTA+TGG 0.465779 3.3:-17495827 None:intergenic
AATGATGTGTTCTATCTGTT+TGG 0.466778 3.3:+17495941 MS.gene28215:CDS
AATTAGAGTTAAAGAAGGAA+AGG 0.503387 3.3:+17495908 MS.gene28215:CDS
ACATCCTTCGTGATACAAAT+GGG 0.519665 3.3:-17496006 None:intergenic
GATGTGTTCTATCTGTTTGG+CGG 0.555139 3.3:+17495944 MS.gene28215:CDS
GGATGTATTATGAAATGGCT+AGG 0.587358 3.3:+17496023 MS.gene28215:CDS
TTAGGAATCTGACGACACAT+AGG 0.588272 3.3:-17496062 None:intergenic
TAGGAATCTGACGACACATA+GGG 0.591647 3.3:-17496061 None:intergenic
GATTTAGATCAACAGCATCA+AGG 0.596305 3.3:-17495728 None:intergenic
TGGTTGGATCGCAAGCAACT+CGG 0.597083 3.3:+17495973 MS.gene28215:CDS
TAGTCTGAACCTCGTTGATG+AGG 0.610575 3.3:-17495833 None:intergenic
TTATGGTGGCGAAAAGCAGA+AGG 0.619203 3.3:-17495810 None:intergenic
CCTCGTTGATGAGGTTATGG+TGG 0.639922 3.3:-17495824 None:intergenic
TCGTGATACAAATGGGAACA+CGG 0.640220 3.3:-17495999 None:intergenic
GAAATACTGAAACTATCCAA+AGG 0.644867 3.3:+17495862 MS.gene28215:CDS
TGTTCCCATTTGTATCACGA+AGG 0.672601 3.3:+17496002 MS.gene28215:CDS
GCTCATCGTCGTCATACACA+TGG 0.711088 3.3:+17495753 MS.gene28215:CDS
ATGGTACAAATCGATCAACA+AGG 0.728585 3.3:+17495772 MS.gene28215:CDS
CCACCATAACCTCATCAACG+AGG 0.765219 3.3:+17495824 MS.gene28215:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATCACTTTCTACATTTAT+AGG - chr3.3:17495699-17495718 None:intergenic 20.0%
!! TCAAAAATTAGAGTTAAAGA+AGG + chr3.3:17495903-17495922 MS.gene28215:CDS 20.0%
! AATTAGAGTTAAAGAAGGAA+AGG + chr3.3:17495908-17495927 MS.gene28215:CDS 25.0%
AATGATGTGTTCTATCTGTT+TGG + chr3.3:17495941-17495960 MS.gene28215:CDS 30.0%
ACGAAGGATGTATTATGAAA+TGG + chr3.3:17496018-17496037 MS.gene28215:CDS 30.0%
GAAATACTGAAACTATCCAA+AGG + chr3.3:17495862-17495881 MS.gene28215:CDS 30.0%
ACATCCTTCGTGATACAAAT+GGG - chr3.3:17496009-17496028 None:intergenic 35.0%
ATGGTACAAATCGATCAACA+AGG + chr3.3:17495772-17495791 MS.gene28215:CDS 35.0%
GATTTAGATCAACAGCATCA+AGG - chr3.3:17495731-17495750 None:intergenic 35.0%
GGATGTATTATGAAATGGCT+AGG + chr3.3:17496023-17496042 MS.gene28215:CDS 35.0%
TACATCCTTCGTGATACAAA+TGG - chr3.3:17496010-17496029 None:intergenic 35.0%
!! CTATCCAAAGGCATTCTAAT+CGG + chr3.3:17495874-17495893 MS.gene28215:CDS 35.0%
GATGTGTTCTATCTGTTTGG+CGG + chr3.3:17495944-17495963 MS.gene28215:CDS 40.0%
GATTCCGATTAGAATGCCTT+TGG - chr3.3:17495881-17495900 None:intergenic 40.0%
TAGGAATCTGACGACACATA+GGG - chr3.3:17496064-17496083 None:intergenic 40.0%
TCGTGATACAAATGGGAACA+CGG - chr3.3:17496002-17496021 None:intergenic 40.0%
TGTTCCCATTTGTATCACGA+AGG + chr3.3:17496002-17496021 MS.gene28215:CDS 40.0%
TTAGGAATCTGACGACACAT+AGG - chr3.3:17496065-17496084 None:intergenic 40.0%
TAGTCTGAACCTCGTTGATG+AGG - chr3.3:17495836-17495855 None:intergenic 45.0%
! GAACCTCGTTGATGAGGTTA+TGG - chr3.3:17495830-17495849 None:intergenic 45.0%
! TATCTGTTTGGCGGAGCTTT+TGG + chr3.3:17495953-17495972 MS.gene28215:CDS 45.0%
! TTATGGTGGCGAAAAGCAGA+AGG - chr3.3:17495813-17495832 None:intergenic 45.0%
CCACCATAACCTCATCAACG+AGG + chr3.3:17495824-17495843 MS.gene28215:CDS 50.0%
GCTCATCGTCGTCATACACA+TGG + chr3.3:17495753-17495772 MS.gene28215:CDS 50.0%
TGGTTGGATCGCAAGCAACT+CGG + chr3.3:17495973-17495992 MS.gene28215:CDS 50.0%
! CCTCGTTGATGAGGTTATGG+TGG - chr3.3:17495827-17495846 None:intergenic 50.0%
! TGTTTGGCGGAGCTTTTGGT+TGG + chr3.3:17495957-17495976 MS.gene28215:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 17495666 17496091 17495666 ID=MS.gene28215
chr3.3 mRNA 17495666 17496091 17495666 ID=MS.gene28215.t1;Parent=MS.gene28215
chr3.3 exon 17495666 17496091 17495666 ID=MS.gene28215.t1.exon1;Parent=MS.gene28215.t1
chr3.3 CDS 17495666 17496091 17495666 ID=cds.MS.gene28215.t1;Parent=MS.gene28215.t1
Gene Sequence

>MS.gene28215

ATGGAGCAACAACAACGTAATATAAGAAGTCCTATAAATGTAGAAAGTGATTATGTAATGATCCTTGATGCTGTTGATCTAAATCTCGCTCATCGTCGTCATACACATGGTACAAATCGATCAACAAGGTTCACTCTCTTGCATCCTTCTGCTTTTCGCCACCATAACCTCATCAACGAGGTTCAGACTACTATAAGAAATACTGAAACTATCCAAAGGCATTCTAATCGGAATCTTTCAAAAATTAGAGTTAAAGAAGGAAAGGAGTCTGAAGCAATGATGTGTTCTATCTGTTTGGCGGAGCTTTTGGTTGGATCGCAAGCAACTCGGTTGCCGTGTTCCCATTTGTATCACGAAGGATGTATTATGAAATGGCTAGGTAGATCAAACACTTGCCCTATGTGTCGTCAGATTCCTAATATCTGA
Protein sequence

>MS.gene28215.t1

MEQQQRNIRSPINVESDYVMILDAVDLNLAHRRHTHGTNRSTRFTLLHPSAFRHHNLINEVQTTIRNTETIQRHSNRNLSKIRVKEGKESEAMMCSICLAELLVGSQATRLPCSHLYHEGCIMKWLGRSNTCPMCRQIPNI