AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene44073


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44073.t1 MTR_1g082480 94.690 339 14 3 1 337 1 337 0.0 629
MS.gene44073.t1 MTR_1g082480 94.822 309 12 3 1 307 1 307 0.0 568
MS.gene44073.t1 MTR_7g113830 56.571 350 102 10 1 337 1 313 1.40e-124 360
MS.gene44073.t1 MTR_3g099620 50.606 330 138 7 14 333 1 315 8.74e-102 302
MS.gene44073.t1 MTR_5g064950 43.077 325 152 8 14 334 1 296 7.66e-79 243
MS.gene44073.t1 MTR_8g066770 52.778 216 87 2 126 336 104 309 2.76e-73 229
MS.gene44073.t1 MTR_5g064950 42.617 298 138 8 14 307 1 269 6.01e-69 218
MS.gene44073.t1 MTR_0194s0050 47.005 217 110 2 118 330 166 381 8.11e-57 189
MS.gene44073.t1 MTR_8g024210 49.758 207 86 3 126 330 171 361 1.59e-56 187
MS.gene44073.t1 MTR_1g028470 33.220 295 140 9 54 325 30 290 1.15e-35 131
MS.gene44073.t1 MTR_2g022280 39.583 192 105 4 136 325 1 183 2.14e-34 125
MS.gene44073.t1 MTR_3g090850 34.524 252 121 7 117 325 76 326 5.83e-34 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44073.t1 AT1G72210 45.954 346 133 10 14 334 1 317 6.21e-81 249
MS.gene44073.t1 AT1G22490 44.023 343 131 11 14 334 1 304 1.18e-78 243
MS.gene44073.t1 AT1G72210 46.395 319 117 11 14 307 1 290 2.72e-71 224
MS.gene44073.t1 AT1G22490 43.671 316 117 11 14 307 1 277 5.70e-67 213
MS.gene44073.t1 AT3G24140 43.304 224 118 3 115 331 176 397 3.10e-54 183
MS.gene44073.t1 AT3G24140 43.304 224 118 3 115 331 176 397 3.61e-54 183
MS.gene44073.t1 AT4G01460 44.076 211 110 3 126 335 105 308 1.07e-52 176
MS.gene44073.t1 AT4G01460 44.076 211 110 3 126 335 105 308 1.07e-52 176
MS.gene44073.t1 AT5G65320 45.024 211 110 3 124 333 90 295 3.20e-51 172
MS.gene44073.t1 AT5G46690 45.532 235 91 6 126 333 78 302 2.50e-50 171
MS.gene44073.t1 AT2G46810 45.771 201 92 4 127 326 112 296 5.44e-48 164
MS.gene44073.t1 AT2G46810 45.320 203 94 4 127 328 172 358 2.13e-47 164
MS.gene44073.t1 AT2G46810 45.320 203 94 4 127 328 184 370 2.75e-47 164
MS.gene44073.t1 AT3G61950 46.040 202 91 4 126 326 117 301 1.01e-46 160
MS.gene44073.t1 AT3G61950 45.098 204 94 4 126 328 168 354 5.32e-46 160
MS.gene44073.t1 AT5G65320 46.196 184 94 2 124 307 90 268 3.75e-44 153
MS.gene44073.t1 AT2G46810 40.260 231 93 5 127 328 112 326 2.61e-42 149
MS.gene44073.t1 AT3G61950 47.337 169 72 3 126 294 117 268 1.73e-40 144
MS.gene44073.t1 AT3G61950 46.746 169 73 3 126 294 168 319 8.74e-40 143
MS.gene44073.t1 AT5G46690 44.498 209 79 5 126 307 78 276 4.36e-39 140
MS.gene44073.t1 AT3G06120 35.897 195 92 3 136 313 1 179 1.04e-31 118
MS.gene44073.t1 AT5G53210 56.923 65 28 0 134 198 100 164 6.31e-20 89.7
MS.gene44073.t1 AT5G53210 56.923 65 28 0 134 198 100 164 7.06e-20 89.7
MS.gene44073.t1 AT3G61950 71.429 42 12 0 126 167 168 209 4.57e-13 67.8
MS.gene44073.t1 AT3G61950 71.429 42 12 0 126 167 168 209 4.57e-13 67.8
MS.gene44073.t1 AT1G32640 26.500 200 109 7 116 307 435 604 6.55e-11 63.9

Find 44 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTTGATTCCATAACTAAA+AGG 0.292800 1.3:+58063999 None:intergenic
GGTGATCAAGCTTCTATAAT+TGG 0.293785 1.3:-58063291 MS.gene44073:CDS
ACTCTATCTCTTTCCTCTTC+AGG 0.299868 1.3:+58064068 None:intergenic
CAGCTCTTGAAAATGGTATC+TGG 0.309667 1.3:-58062979 MS.gene44073:CDS
AATGAAAAGAATTCAGAAAA+TGG 0.318161 1.3:+58063162 None:intergenic
GCCAAAACAGCTCTTGAAAA+TGG 0.324313 1.3:-58062986 MS.gene44073:CDS
TCTAATTCTGCAGCTACTAT+TGG 0.326308 1.3:-58063102 MS.gene44073:CDS
GTTGAAGATGATTGCAAGTT+GGG 0.350399 1.3:-58062762 MS.gene44073:CDS
CATTTAAATGTTACTACTAC+TGG 0.355694 1.3:-58062928 MS.gene44073:CDS
ATTGTCCTCCTTATGTAGAT+TGG 0.357399 1.3:-58063887 MS.gene44073:CDS
TTTCTTGAACTTCATTCAAA+TGG 0.360903 1.3:+58063835 None:intergenic
CTAAAAGGATCTTGTGTTTG+TGG 0.365756 1.3:+58064014 None:intergenic
TTCTTGAACTTCATTCAAAT+GGG 0.379399 1.3:+58063836 None:intergenic
TCTTTACTCTCTCAGTGTTA+AGG 0.389543 1.3:-58062896 MS.gene44073:intron
GTTGAATCCTATTGACCATC+TGG 0.393376 1.3:+58062709 None:intergenic
CTGTATACCAGATGGTCAAT+AGG 0.406963 1.3:-58062716 MS.gene44073:CDS
ACCCTTTGGATGTAAGAATC+TGG 0.440881 1.3:+58063597 None:intergenic
GGTTGAAGATGATTGCAAGT+TGG 0.450829 1.3:-58062763 MS.gene44073:CDS
TTGTTATTCCAATCTACATA+AGG 0.465642 1.3:+58063879 None:intergenic
TTAAAATAAGATCAAGAAAG+AGG 0.490885 1.3:-58063008 MS.gene44073:CDS
TGCCAGATTCTTACATCCAA+AGG 0.505226 1.3:-58063599 MS.gene44073:CDS
GCCAGATTCTTACATCCAAA+GGG 0.516817 1.3:-58063598 MS.gene44073:intron
TTAGTAATAGTATTACTACT+TGG 0.517777 1.3:+58063801 None:intergenic
TGTTATGTGTTTACCTGAAG+AGG 0.521964 1.3:-58064081 None:intergenic
ACACAGTTATTCGTCCGAAA+AGG 0.534814 1.3:-58063743 MS.gene44073:CDS
GATCAAGCTTCTATAATTGG+AGG 0.557225 1.3:-58063288 MS.gene44073:CDS
TGAACTTCATTCAAATGGGG+TGG 0.566537 1.3:+58063840 None:intergenic
ATTACTACTTGGATCAGTAG+TGG 0.576946 1.3:+58063812 None:intergenic
TGATTGCAAGTTGGGATCAG+TGG 0.579380 1.3:-58062754 MS.gene44073:CDS
TTTCCACAGTATTCAACAAG+TGG 0.589381 1.3:-58063141 MS.gene44073:CDS
GGTCAATAGGATTCAACAAG+AGG 0.595940 1.3:-58062703 MS.gene44073:CDS
AGCTTCAGCTGTATACCAGA+TGG 0.597796 1.3:-58062724 MS.gene44073:CDS
TATGTAGATTGGAATAACAA+TGG 0.602597 1.3:-58063876 MS.gene44073:CDS
TTATTCCAATCTACATAAGG+AGG 0.614549 1.3:+58063882 None:intergenic
TCTTGAACTTCATTCAAATG+GGG 0.614700 1.3:+58063837 None:intergenic
ACGAATAACTGTGTTCACAG+AGG 0.614740 1.3:+58063752 None:intergenic
CGAATAACTGTGTTCACAGA+GGG 0.620805 1.3:+58063753 None:intergenic
CTACCACTTGTTGAATACTG+TGG 0.624417 1.3:+58063138 None:intergenic
AGACATGGCACTAGAAGCAG+TGG 0.632855 1.3:-58064042 MS.gene44073:CDS
AAGAGATAGAGTGAAAGACA+TGG 0.656321 1.3:-58064057 MS.gene44073:CDS
GTGAAATCTGATGAAGCTGG+TGG 0.684533 1.3:-58063198 MS.gene44073:CDS
TGCTGACATAGAAGTGACAA+TGG 0.687267 1.3:-58063049 MS.gene44073:CDS
GAAGTGAAATCTGATGAAGC+TGG 0.693568 1.3:-58063201 MS.gene44073:CDS
TGACATAGAAGTGACAATGG+TGG 0.780182 1.3:-58063046 MS.gene44073:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGAAAAGAATTCAGAAAA+TGG + chr1.3:58063607-58063626 None:intergenic 20.0%
!! TTAAAATAAGATCAAGAAAG+AGG - chr1.3:58063758-58063777 MS.gene44073:CDS 20.0%
!! TTAGTAATAGTATTACTACT+TGG + chr1.3:58062968-58062987 None:intergenic 20.0%
!!! AGATTTCTTTGAACAATTTT+TGG - chr1.3:58063933-58063952 MS.gene44073:CDS 20.0%
!!! ATCTTATTTTAAGATTTGCA+TGG + chr1.3:58063750-58063769 None:intergenic 20.0%
! CATTTAAATGTTACTACTAC+TGG - chr1.3:58063838-58063857 MS.gene44073:CDS 25.0%
! TATGTAGATTGGAATAACAA+TGG - chr1.3:58062890-58062909 MS.gene44073:intron 25.0%
! TCTTTGATTCCATAACTAAA+AGG + chr1.3:58062770-58062789 None:intergenic 25.0%
! TTCTTGAACTTCATTCAAAT+GGG + chr1.3:58062933-58062952 None:intergenic 25.0%
! TTTCTTGAACTTCATTCAAA+TGG + chr1.3:58062934-58062953 None:intergenic 25.0%
!! TTGTTATTCCAATCTACATA+AGG + chr1.3:58062890-58062909 None:intergenic 25.0%
!!! TGTGTTTGTTTTTTTGTTGT+TGG - chr1.3:58063443-58063462 MS.gene44073:intron 25.0%
TCTTGAACTTCATTCAAATG+GGG + chr1.3:58062932-58062951 None:intergenic 30.0%
TTATTCCAATCTACATAAGG+AGG + chr1.3:58062887-58062906 None:intergenic 30.0%
! GAGGACAATTATTTTCTGTT+TGG + chr1.3:58062868-58062887 None:intergenic 30.0%
!! ACACAAGATCCTTTTAGTTA+TGG - chr1.3:58062758-58062777 MS.gene44073:CDS 30.0%
AACATGCAGTTACATGTTCT+TGG - chr1.3:58063342-58063361 MS.gene44073:intron 35.0%
AAGAGATAGAGTGAAAGACA+TGG - chr1.3:58062709-58062728 MS.gene44073:CDS 35.0%
ATTACTACTTGGATCAGTAG+TGG + chr1.3:58062957-58062976 None:intergenic 35.0%
ATTGTCCTCCTTATGTAGAT+TGG - chr1.3:58062879-58062898 MS.gene44073:intron 35.0%
CAGTGAGTTTAGTAGAATCA+CGG - chr1.3:58063237-58063256 MS.gene44073:CDS 35.0%
CTAAAAGGATCTTGTGTTTG+TGG + chr1.3:58062755-58062774 None:intergenic 35.0%
GATCAAGCTTCTATAATTGG+AGG - chr1.3:58063478-58063497 MS.gene44073:intron 35.0%
GCTACTATTGGTGAAAAAGT+TGG - chr1.3:58063676-58063695 MS.gene44073:CDS 35.0%
GGTGATCAAGCTTCTATAAT+TGG - chr1.3:58063475-58063494 MS.gene44073:intron 35.0%
GTTGAAGATGATTGCAAGTT+GGG - chr1.3:58064004-58064023 MS.gene44073:CDS 35.0%
TCTAATTCTGCAGCTACTAT+TGG - chr1.3:58063664-58063683 MS.gene44073:CDS 35.0%
TCTTTACTCTCTCAGTGTTA+AGG - chr1.3:58063870-58063889 MS.gene44073:CDS 35.0%
TGTAAGTAGTAAGTACCCTT+TGG + chr1.3:58063186-58063205 None:intergenic 35.0%
TTTCCACAGTATTCAACAAG+TGG - chr1.3:58063625-58063644 MS.gene44073:CDS 35.0%
! AGCTCTGGTAATCTAAAGTT+CGG + chr1.3:58063378-58063397 None:intergenic 35.0%
! GAGCACAAGTTTCATTTTCT+TGG - chr1.3:58063526-58063545 MS.gene44073:intron 35.0%
!! ACCATTTTCAAGAGCTGTTT+TGG + chr1.3:58063784-58063803 None:intergenic 35.0%
!!! TTTTGTTGTTGGTGAATGCA+GGG - chr1.3:58063454-58063473 MS.gene44073:intron 35.0%
!!! TTTTTGTTGTTGGTGAATGC+AGG - chr1.3:58063453-58063472 MS.gene44073:intron 35.0%
ACACAGTTATTCGTCCGAAA+AGG - chr1.3:58063023-58063042 MS.gene44073:CDS 40.0%
ACCCTTTGGATGTAAGAATC+TGG + chr1.3:58063172-58063191 None:intergenic 40.0%
ACGAATAACTGTGTTCACAG+AGG + chr1.3:58063017-58063036 None:intergenic 40.0%
ACTCTATCTCTTTCCTCTTC+AGG + chr1.3:58062701-58062720 None:intergenic 40.0%
CAGCTCTTGAAAATGGTATC+TGG - chr1.3:58063787-58063806 MS.gene44073:CDS 40.0%
CGAATAACTGTGTTCACAGA+GGG + chr1.3:58063016-58063035 None:intergenic 40.0%
CTGTATACCAGATGGTCAAT+AGG - chr1.3:58064050-58064069 MS.gene44073:CDS 40.0%
GAAGTGAAATCTGATGAAGC+TGG - chr1.3:58063565-58063584 MS.gene44073:intron 40.0%
GCCAAAACAGCTCTTGAAAA+TGG - chr1.3:58063780-58063799 MS.gene44073:CDS 40.0%
GCCAGATTCTTACATCCAAA+GGG - chr1.3:58063168-58063187 MS.gene44073:CDS 40.0%
GGTCAATAGGATTCAACAAG+AGG - chr1.3:58064063-58064082 MS.gene44073:CDS 40.0%
GGTTGAAGATGATTGCAAGT+TGG - chr1.3:58064003-58064022 MS.gene44073:CDS 40.0%
GTTGAATCCTATTGACCATC+TGG + chr1.3:58064060-58064079 None:intergenic 40.0%
TGAACTTCATTCAAATGGGG+TGG + chr1.3:58062929-58062948 None:intergenic 40.0%
TGACATAGAAGTGACAATGG+TGG - chr1.3:58063720-58063739 MS.gene44073:CDS 40.0%
TGCCAGATTCTTACATCCAA+AGG - chr1.3:58063167-58063186 MS.gene44073:CDS 40.0%
TGCTGACATAGAAGTGACAA+TGG - chr1.3:58063717-58063736 MS.gene44073:CDS 40.0%
! CCCTCTAGTTTCTAGAAGAA+GGG + chr1.3:58063401-58063420 None:intergenic 40.0%
! CCCTTCTTCTAGAAACTAGA+GGG - chr1.3:58063398-58063417 MS.gene44073:intron 40.0%
! CTACCACTTGTTGAATACTG+TGG + chr1.3:58063631-58063650 None:intergenic 40.0%
! TCCCTTCTTCTAGAAACTAG+AGG - chr1.3:58063397-58063416 MS.gene44073:intron 40.0%
AGCTTCAGCTGTATACCAGA+TGG - chr1.3:58064042-58064061 MS.gene44073:CDS 45.0%
CAAATGGGGTGGTGAAAAAG+TGG + chr1.3:58062918-58062937 None:intergenic 45.0%
GTGAAATCTGATGAAGCTGG+TGG - chr1.3:58063568-58063587 MS.gene44073:intron 45.0%
! GCCCTCTAGTTTCTAGAAGA+AGG + chr1.3:58063402-58063421 None:intergenic 45.0%
! TGATTGCAAGTTGGGATCAG+TGG - chr1.3:58064012-58064031 MS.gene44073:CDS 45.0%
! TTTCTAGAAGAAGGGAGCTC+TGG + chr1.3:58063393-58063412 None:intergenic 45.0%
!!! TTGAATTTTTTTTTTTATTT+AGG - chr1.3:58063982-58064001 MS.gene44073:CDS 5.0%
AGACATGGCACTAGAAGCAG+TGG - chr1.3:58062724-58062743 MS.gene44073:CDS 50.0%
!!! CTTCTAGCTCTGCGCCTTTT+CGG + chr1.3:58063040-58063059 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 58062689 58064099 58062689 ID=MS.gene44073
chr1.3 mRNA 58062689 58064099 58062689 ID=MS.gene44073.t1;Parent=MS.gene44073
chr1.3 exon 58063599 58064099 58063599 ID=MS.gene44073.t1.exon1;Parent=MS.gene44073.t1
chr1.3 CDS 58063599 58064099 58063599 ID=cds.MS.gene44073.t1;Parent=MS.gene44073.t1
chr1.3 exon 58062897 58063313 58062897 ID=MS.gene44073.t1.exon2;Parent=MS.gene44073.t1
chr1.3 CDS 58062897 58063313 58062897 ID=cds.MS.gene44073.t1;Parent=MS.gene44073.t1
chr1.3 exon 58062689 58062784 58062689 ID=MS.gene44073.t1.exon3;Parent=MS.gene44073.t1
chr1.3 CDS 58062689 58062784 58062689 ID=cds.MS.gene44073.t1;Parent=MS.gene44073.t1
Gene Sequence

>MS.gene44073

ATGTGTTTACCTGAAGAGGAAAGAGATAGAGTGAAAGACATGGCACTAGAAGCAGTGGTTTATCCACAAACACAAGATCCTTTTAGTTATGGAATCAAAGATTTTTACAACTTCAACTTCAACACTTTTGTTGCAAAAGAACAACAAGAACAGAGATCTTTCAGTTTTGTAGAAAACCAAACAGAAAATAATTGTCCTCCTTATGTAGATTGGAATAACAATGGTTCCACTTTTTCACCACCCCATTTGAATGAAGTTCAAGAAACCACTACTGATCCAAGTAGTAATACTATTACTAATAACACTCAAAACTTTCATGCTTCACCCTCTGTGAACACAGTTATTCGTCCGAAAAGGCGCAGAGCTAGAAGCAGAAAAAACAAAGAAGAAATTGAGAATCAGAGAATGACTCACATTGCTGTTGAGCGTAATAGAAGAAAGCAGATGAATGACTATCTTTCTATTCTTCGCTCTCTAATGCCAGATTCTTACATCCAAAGGGTACTTACTACTTACATAACATCACTTAGAATATATGTTTAGATTAACAGTGAGTTTAGTAGAATCACGGCGTGTCACTTTGATTTTAACATAAACTTCACTTTAGAGTTTTAAAAAAATCACTGTGATTTCGTCAAACTCATCGTGATTATAACATGCAGTTACATGTTCTTGGTACTCACATGCCGAACTTTAGATTACCAGAGCTCCCTTCTTCTAGAAACTAGAGGGCTAAGACAAACAAAAAACTGAGTGTGTTTGTTTTTTTGTTGTTGGTGAATGCAGGGTGATCAAGCTTCTATAATTGGAGGTGCTATTAACTTTGTTAAAGAGCTTGAGCACAAGTTTCATTTTCTTGGTACTAAGAAAGAAAGAGAAGTGAAATCTGATGAAGCTGGTGGATCAAACAACATGCCATTTTCTGAATTCTTTTCATTTCCACAGTATTCAACAAGTGGTAGTGTGTGTGATAATTCTAATTCTGCAGCTACTATTGGTGAAAAAGTTGGTGAGATTCAATCTTGCATTGCTGACATAGAAGTGACAATGGTGGAAAACCATGCAAATCTTAAAATAAGATCAAGAAAGAGGCCAAAACAGCTCTTGAAAATGGTATCTGGTTTGCAAAGCATGCGTCTCACAATCTTGCATTTAAATGTTACTACTACTGGTGAAATTGTTCTTTACTCTCTCAGTGTTAAGGTTTGTGCTTGTTATTTCTTTTCACTTTTTCTTGTTGCTTTAGATTTCTTTGAACAATTTTTGGAAGTGCTTAATTAAAGTGAAAATGCATTGAATTTTTTTTTTTATTTAGGTTGAAGATGATTGCAAGTTGGGATCAGTGGATGATATAGCTTCAGCTGTATACCAGATGGTCAATAGGATTCAACAAGAGGCAATGTTGAATTAA

Protein sequence

>MS.gene44073.t1

MCLPEEERDRVKDMALEAVVYPQTQDPFSYGIKDFYNFNFNTFVAKEQQEQRSFSFVENQTENNCPPYVDWNNNGSTFSPPHLNEVQETTTDPSSNTITNNTQNFHASPSVNTVIRPKRRRARSRKNKEEIENQRMTHIAVERNRRKQMNDYLSILRSLMPDSYIQRGDQASIIGGAINFVKELEHKFHFLGTKKEREVKSDEAGGSNNMPFSEFFSFPQYSTSGSVCDNSNSAATIGEKVGEIQSCIADIEVTMVENHANLKIRSRKRPKQLLKMVSGLQSMRLTILHLNVTTTGEIVLYSLSVKVEDDCKLGSVDDIASAVYQMVNRIQQEAMLN