AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene45444

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene45444.t1 MTR_1g057400 94.258 209 12 0 1 209 1 209 3.05e-151 418
MS.gene45444.t1 MTR_7g106000 59.524 210 78 4 2 209 22 226 8.64e-84 248
MS.gene45444.t1 MTR_7g105970 55.721 201 85 2 8 208 29 225 5.25e-78 233
MS.gene45444.t1 MTR_7g106010 55.610 205 87 3 7 209 25 227 1.05e-76 230
MS.gene45444.t1 MTR_7g106030 55.721 201 85 2 11 209 33 231 1.91e-73 222
MS.gene45444.t1 MTR_1g057290 47.573 206 107 1 5 209 12 217 6.66e-49 159
MS.gene45444.t1 MTR_1g057270 39.796 196 111 4 16 209 52 242 6.75e-42 142
MS.gene45444.t1 MTR_4g119428 38.614 202 113 5 11 206 41 237 1.59e-39 136
MS.gene45444.t1 MTR_7g105870 39.267 191 111 2 17 206 39 225 9.19e-31 112
MS.gene45444.t1 MTR_1g057300 57.143 112 43 3 1 111 1 108 3.38e-27 100
MS.gene45444.t1 MTR_2g011350 30.899 178 113 5 32 209 35 202 3.14e-21 87.4
MS.gene45444.t1 MTR_6g471090 29.787 188 113 8 8 190 5 178 2.46e-18 80.1
MS.gene45444.t1 MTR_6g071410 30.811 185 113 8 15 190 2 180 4.20e-18 79.3
MS.gene45444.t1 MTR_6g070890 30.811 185 113 8 15 190 2 180 4.20e-18 79.3
MS.gene45444.t1 MTR_6g070900 28.649 185 117 8 15 190 2 180 5.84e-16 73.6
MS.gene45444.t1 MTR_6g071400 28.649 185 117 8 15 190 2 180 5.84e-16 73.6
MS.gene45444.t1 MTR_6g471080 28.947 190 107 9 10 190 5 175 6.13e-13 65.5
MS.gene45444.t1 MTR_1g105570 22.886 201 139 7 9 209 46 230 2.67e-11 61.2
MS.gene45444.t1 MTR_7g106050 25.510 196 131 6 3 196 10 192 9.20e-11 59.3
MS.gene45444.t1 MTR_2g086790 22.989 174 118 4 21 183 19 187 9.98e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene45444.t1 AT2G35980 36.453 203 121 3 10 209 30 227 8.20e-43 144
MS.gene45444.t1 AT2G35460 35.354 198 122 2 14 209 45 238 1.06e-41 141
MS.gene45444.t1 AT5G06320 37.306 193 116 3 17 209 44 231 1.58e-37 130
MS.gene45444.t1 AT3G11650 35.500 200 122 4 12 209 45 239 5.09e-36 127
MS.gene45444.t1 AT1G61760 25.000 168 120 3 20 187 43 204 4.93e-16 73.9
MS.gene45444.t1 AT5G53730 27.222 180 121 5 34 209 40 213 1.32e-15 72.8
MS.gene45444.t1 AT4G05220 21.693 189 139 4 21 209 46 225 1.19e-13 67.8
MS.gene45444.t1 AT3G11660 26.047 215 145 6 1 208 1 208 1.43e-13 67.0
MS.gene45444.t1 AT1G32270 29.139 151 98 3 42 190 1 144 2.89e-13 67.8
MS.gene45444.t1 AT1G32270 29.139 151 98 3 42 190 1 144 4.50e-13 67.4

Find 45 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGTGTGATGTAAATTTCTA+AGG 0.241378 1.3:-42202332 None:intergenic
GTCTCATAATCCTTATATTC+TGG 0.303690 1.3:-42202844 MS.gene45444:CDS
AACATCTTCTGCCGCGGTTG+TGG 0.309180 1.3:+42202924 None:intergenic
GTCGTCGTTGTAGTTGAATT+TGG 0.331563 1.3:+42202769 None:intergenic
TGAAATTATACTTTGATATG+AGG 0.341974 1.3:-42202466 MS.gene45444:CDS
ACATCTTCTGCCGCGGTTGT+GGG 0.356163 1.3:+42202925 None:intergenic
TTTAGACTTGGTGATTATAT+TGG 0.359682 1.3:-42202443 MS.gene45444:CDS
GGACAACGAGCCAGAATATA+AGG 0.361089 1.3:+42202834 None:intergenic
TTCTTTGACACTGAATTTGA+AGG 0.387330 1.3:+42202802 None:intergenic
TTATATTGGTCCACATACTA+AGG 0.447899 1.3:-42202429 MS.gene45444:CDS
GACTAGGTTTGCTTCAACAA+AGG 0.454451 1.3:-42202639 MS.gene45444:CDS
TTAGTTCCATTAGCAACAAA+AGG 0.456789 1.3:+42202380 None:intergenic
ATGCGTCTTACGAAGGGACT+AGG 0.465204 1.3:-42202655 MS.gene45444:CDS
CATCTTCTGCCGCGGTTGTG+GGG 0.481542 1.3:+42202926 None:intergenic
CCAGAGAAAACACCACTCAT+AGG 0.486502 1.3:+42202569 None:intergenic
TCGAGCTCTTAGTGTATTGT+CGG 0.489123 1.3:+42202594 None:intergenic
TGTGGTTTATGATCGTGATC+AGG 0.495393 1.3:-42202537 MS.gene45444:CDS
TGAATTTGAAGGTTTGAGGT+TGG 0.499247 1.3:+42202813 None:intergenic
CAACCTCGTACTCAACTTCA+CGG 0.507914 1.3:-42202729 MS.gene45444:CDS
ACACTGAATTTGAAGGTTTG+AGG 0.515810 1.3:+42202809 None:intergenic
TTAATGTTACCCTTAGTATG+TGG 0.518350 1.3:+42202419 None:intergenic
AGTTGAGTACGAGGTTGTAA+TGG 0.520447 1.3:+42202735 None:intergenic
GTTTCCATATTATGCCGAAA+AGG 0.522769 1.3:+42202894 None:intergenic
TGAGTACGAGGTTGTAATGG+AGG 0.524265 1.3:+42202738 None:intergenic
TTTCTCTGGGCAACGTGTTG+TGG 0.548150 1.3:-42202555 MS.gene45444:CDS
ATGGTCATGCGTCTTACGAA+GGG 0.569573 1.3:-42202661 MS.gene45444:CDS
GATGGTCATGCGTCTTACGA+AGG 0.573273 1.3:-42202662 MS.gene45444:CDS
CGTGTGATGTAAATTTCTAA+GGG 0.574936 1.3:-42202331 None:intergenic
CTTCAACAAAGGTTGTAACA+TGG 0.577415 1.3:-42202628 MS.gene45444:CDS
GAAATTTACATCACACGTGG+TGG 0.578702 1.3:+42202337 None:intergenic
GAAGCAAAACCCCACAACCG+CGG 0.582202 1.3:-42202935 MS.gene45444:CDS
GAGTACGAGGTTGTAATGGA+GGG 0.597384 1.3:+42202739 None:intergenic
TATATTGGTCCACATACTAA+GGG 0.600116 1.3:-42202428 MS.gene45444:CDS
GAGGTTGTAATGGAGGGTGT+TGG 0.602071 1.3:+42202745 None:intergenic
GTAGCAATCATCGTTCTCGT+TGG 0.605038 1.3:-42202866 MS.gene45444:CDS
ATCTACTACGATGTAATCGA+TGG 0.611885 1.3:-42202680 MS.gene45444:CDS
AAATTTACATCACACGTGGT+GGG 0.616840 1.3:+42202338 None:intergenic
TTTGAACGTGATAAGAAAGA+CGG 0.617561 1.3:-42202506 MS.gene45444:CDS
CTAAGGGTAACATTAAGTGT+AGG 0.622130 1.3:-42202412 MS.gene45444:CDS
TTTGATATGAGGTTTAGACT+TGG 0.636469 1.3:-42202455 MS.gene45444:CDS
AGCAACAACATCTTCTGCCG+CGG 0.641568 1.3:+42202918 None:intergenic
AAGAGCTCGAATCCTATGAG+TGG 0.682861 1.3:-42202581 MS.gene45444:CDS
GGGCCGTGAAGTTGAGTACG+AGG 0.683761 1.3:+42202726 None:intergenic
CGAGAACGATGATTGCTACG+AGG 0.746688 1.3:+42202870 None:intergenic
TTAGAAATTTACATCACACG+TGG 0.754009 1.3:+42202334 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAAATTATACTTTGATATG+AGG - chr1.3:42202809-42202828 MS.gene45444:CDS 20.0%
!!! TAGATGTTGAGTTTTTTGTT+TGG + chr1.3:42202580-42202599 None:intergenic 25.0%
!!! TGAGTTTTTTGTTTGGATTA+CGG + chr1.3:42202573-42202592 None:intergenic 25.0%
!!! TTTAGACTTGGTGATTATAT+TGG - chr1.3:42202832-42202851 MS.gene45444:CDS 25.0%
GTCTCATAATCCTTATATTC+TGG - chr1.3:42202431-42202450 MS.gene45444:CDS 30.0%
TATATTGGTCCACATACTAA+GGG - chr1.3:42202847-42202866 MS.gene45444:CDS 30.0%
TTAATGTTACCCTTAGTATG+TGG + chr1.3:42202859-42202878 None:intergenic 30.0%
TTAGAAATTTACATCACACG+TGG + chr1.3:42202944-42202963 None:intergenic 30.0%
TTAGTTCCATTAGCAACAAA+AGG + chr1.3:42202898-42202917 None:intergenic 30.0%
TTATATTGGTCCACATACTA+AGG - chr1.3:42202846-42202865 MS.gene45444:CDS 30.0%
TTCTTTGACACTGAATTTGA+AGG + chr1.3:42202476-42202495 None:intergenic 30.0%
TTTGAACGTGATAAGAAAGA+CGG - chr1.3:42202769-42202788 MS.gene45444:CDS 30.0%
TTTGATATGAGGTTTAGACT+TGG - chr1.3:42202820-42202839 MS.gene45444:CDS 30.0%
! TTTTGTTGCTAATGGAACTA+AGG - chr1.3:42202897-42202916 MS.gene45444:CDS 30.0%
!!! GAGTTTTTTGTTTGGATTAC+GGG + chr1.3:42202572-42202591 None:intergenic 30.0%
AAATTTACATCACACGTGGT+GGG + chr1.3:42202940-42202959 None:intergenic 35.0%
ACACTGAATTTGAAGGTTTG+AGG + chr1.3:42202469-42202488 None:intergenic 35.0%
ATCTACTACGATGTAATCGA+TGG - chr1.3:42202595-42202614 MS.gene45444:CDS 35.0%
CTAAGGGTAACATTAAGTGT+AGG - chr1.3:42202863-42202882 MS.gene45444:CDS 35.0%
CTTCAACAAAGGTTGTAACA+TGG - chr1.3:42202647-42202666 MS.gene45444:CDS 35.0%
GTTTCCATATTATGCCGAAA+AGG + chr1.3:42202384-42202403 None:intergenic 35.0%
! GATGTTCCTTTTGTTGCTAA+TGG - chr1.3:42202889-42202908 MS.gene45444:CDS 35.0%
! TGAATTTGAAGGTTTGAGGT+TGG + chr1.3:42202465-42202484 None:intergenic 35.0%
AGTTGAGTACGAGGTTGTAA+TGG + chr1.3:42202543-42202562 None:intergenic 40.0%
GAAATTTACATCACACGTGG+TGG + chr1.3:42202941-42202960 None:intergenic 40.0%
GTCGTCGTTGTAGTTGAATT+TGG + chr1.3:42202509-42202528 None:intergenic 40.0%
TCGAGCTCTTAGTGTATTGT+CGG + chr1.3:42202684-42202703 None:intergenic 40.0%
TGTGGTTTATGATCGTGATC+AGG - chr1.3:42202738-42202757 MS.gene45444:CDS 40.0%
! AGATGTTGTTGCTGCCTTTT+CGG - chr1.3:42202367-42202386 MS.gene45444:CDS 40.0%
! CTATGAGTGGTGTTTTCTCT+GGG - chr1.3:42202707-42202726 MS.gene45444:CDS 40.0%
! GACTAGGTTTGCTTCAACAA+AGG - chr1.3:42202636-42202655 MS.gene45444:CDS 40.0%
AAGAGCTCGAATCCTATGAG+TGG - chr1.3:42202694-42202713 MS.gene45444:CDS 45.0%
ATGGTCATGCGTCTTACGAA+GGG - chr1.3:42202614-42202633 MS.gene45444:CDS 45.0%
CAACCTCGTACTCAACTTCA+CGG - chr1.3:42202546-42202565 MS.gene45444:CDS 45.0%
CCAGAGAAAACACCACTCAT+AGG + chr1.3:42202709-42202728 None:intergenic 45.0%
GGACAACGAGCCAGAATATA+AGG + chr1.3:42202444-42202463 None:intergenic 45.0%
GTAGCAATCATCGTTCTCGT+TGG - chr1.3:42202409-42202428 MS.gene45444:CDS 45.0%
TGAGTACGAGGTTGTAATGG+AGG + chr1.3:42202540-42202559 None:intergenic 45.0%
! CCTATGAGTGGTGTTTTCTC+TGG - chr1.3:42202706-42202725 MS.gene45444:CDS 45.0%
! GAGTACGAGGTTGTAATGGA+GGG + chr1.3:42202539-42202558 None:intergenic 45.0%
! GCTGCCTTTTCGGCATAATA+TGG - chr1.3:42202377-42202396 MS.gene45444:CDS 45.0%
AGCAACAACATCTTCTGCCG+CGG + chr1.3:42202360-42202379 None:intergenic 50.0%
ATGCGTCTTACGAAGGGACT+AGG - chr1.3:42202620-42202639 MS.gene45444:CDS 50.0%
CGAGAACGATGATTGCTACG+AGG + chr1.3:42202408-42202427 None:intergenic 50.0%
GATGGTCATGCGTCTTACGA+AGG - chr1.3:42202613-42202632 MS.gene45444:CDS 50.0%
TTTCTCTGGGCAACGTGTTG+TGG - chr1.3:42202720-42202739 MS.gene45444:CDS 50.0%
! GAGGTTGTAATGGAGGGTGT+TGG + chr1.3:42202533-42202552 None:intergenic 50.0%
AACATCTTCTGCCGCGGTTG+TGG + chr1.3:42202354-42202373 None:intergenic 55.0%
ACATCTTCTGCCGCGGTTGT+GGG + chr1.3:42202353-42202372 None:intergenic 55.0%
GAAGCAAAACCCCACAACCG+CGG - chr1.3:42202340-42202359 MS.gene45444:CDS 55.0%
CATCTTCTGCCGCGGTTGTG+GGG + chr1.3:42202352-42202371 None:intergenic 60.0%
GGGCCGTGAAGTTGAGTACG+AGG + chr1.3:42202552-42202571 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 42202334 42202963 42202334 ID=MS.gene45444
chr1.3 mRNA 42202334 42202963 42202334 ID=MS.gene45444.t1;Parent=MS.gene45444
chr1.3 exon 42202334 42202963 42202334 ID=MS.gene45444.t1.exon1;Parent=MS.gene45444.t1
chr1.3 CDS 42202334 42202963 42202334 ID=cds.MS.gene45444.t1;Parent=MS.gene45444.t1
Gene Sequence

>MS.gene45444

ATGGCAGAAGCAAAACCCCACAACCGCGGCAGAAGATGTTGTTGCTGCCTTTTCGGCATAATATGGAAACTCCTCGTAGCAATCATCGTTCTCGTTGGTCTCATAATCCTTATATTCTGGCTCGTTGTCCAACCTCAAACCTTCAAATTCAGTGTCAAAGAAGCAAAACTCACCAAATTCAACTACAACGACGACACCAACACCCTCCATTACAACCTCGTACTCAACTTCACGGCCCGTAATCCAAACAAAAAACTCAACATCTACTACGATGTAATCGATGGTCATGCGTCTTACGAAGGGACTAGGTTTGCTTCAACAAAGGTTGTAACATGGTTAAATTCATTCCGACAATACACTAAGAGCTCGAATCCTATGAGTGGTGTTTTCTCTGGGCAACGTGTTGTGGTTTATGATCGTGATCAGGTTTCTGACTTTGAACGTGATAAGAAAGACGGAGTTTTTCATATTAATGTGAAATTATACTTTGATATGAGGTTTAGACTTGGTGATTATATTGGTCCACATACTAAGGGTAACATTAAGTGTAGGCTTGATGTTCCTTTTGTTGCTAATGGAACTAAGGTCATGAAAGCATTTGAACCCACCACGTGTGATGTAAATTTCTAA
Protein sequence

>MS.gene45444.t1

MAEAKPHNRGRRCCCCLFGIIWKLLVAIIVLVGLIILIFWLVVQPQTFKFSVKEAKLTKFNYNDDTNTLHYNLVLNFTARNPNKKLNIYYDVIDGHASYEGTRFASTKVVTWLNSFRQYTKSSNPMSGVFSGQRVVVYDRDQVSDFERDKKDGVFHINVKLYFDMRFRLGDYIGPHTKGNIKCRLDVPFVANGTKVMKAFEPTTCDVNF