AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene008898

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene008898.t1 MTR_8g069080 94.146 205 12 0 12 216 33 237 9.59e-137 384
MS.gene008898.t1 MTR_2g076780 91.262 206 17 1 12 216 1 206 6.21e-129 363
MS.gene008898.t1 MTR_5g032600 45.143 175 87 2 43 215 73 240 2.10e-38 134
MS.gene008898.t1 MTR_3g100650 42.442 172 88 3 47 215 79 242 6.47e-29 109
MS.gene008898.t1 MTR_1g077020 37.500 176 75 4 47 215 8 155 1.70e-28 106
MS.gene008898.t1 MTR_5g020510 37.288 177 91 4 48 215 99 264 1.77e-28 108
MS.gene008898.t1 MTR_4g134580 34.300 207 95 6 47 215 112 315 5.63e-27 106
MS.gene008898.t1 MTR_8g442330 38.182 165 53 4 57 216 14 134 2.98e-25 96.3
MS.gene008898.t1 MTR_5g065440 33.028 218 122 6 18 215 23 236 1.61e-24 97.8
MS.gene008898.t1 MTR_7g010300 36.257 171 99 4 48 215 88 251 3.83e-23 95.5
MS.gene008898.t1 MTR_6g012280 38.012 171 95 5 48 215 91 253 5.13e-22 92.4
MS.gene008898.t1 MTR_3g039810 62.745 51 19 0 47 97 19 69 4.35e-18 76.3
MS.gene008898.t1 MTR_8g467340 61.538 52 18 1 48 97 64 115 4.92e-15 73.2
MS.gene008898.t1 MTR_6g012220 58.000 50 17 1 47 96 20 65 8.89e-15 67.4
MS.gene008898.t1 MTR_6g073013 47.368 57 29 1 48 103 19 75 2.25e-13 66.2
MS.gene008898.t1 MTR_8g069380 56.716 67 20 3 154 216 23 84 3.29e-13 64.3
MS.gene008898.t1 MTR_8g051480 53.731 67 23 4 155 216 36 99 9.40e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene008898.t1 AT2G02540 39.655 174 94 4 47 215 86 253 9.60e-33 120
MS.gene008898.t1 AT2G02540 39.655 174 94 4 47 215 86 253 9.60e-33 120
MS.gene008898.t1 AT4G24660 38.462 169 76 3 47 215 48 188 4.01e-32 117
MS.gene008898.t1 AT4G24660 34.101 217 112 5 1 215 1 188 4.08e-32 116
MS.gene008898.t1 AT5G65410 36.000 225 114 6 1 215 18 222 9.39e-30 112
MS.gene008898.t1 AT1G14440 35.519 183 82 5 47 215 89 249 3.42e-27 105
MS.gene008898.t1 AT1G14440 35.519 183 82 5 47 215 89 249 3.42e-27 105
MS.gene008898.t1 AT2G18350 36.364 176 84 7 45 216 79 230 6.12e-25 99.0
MS.gene008898.t1 AT1G69600 38.506 174 84 6 48 215 31 187 6.82e-25 98.2
MS.gene008898.t1 AT5G15210 33.889 180 82 5 48 215 56 210 9.43e-23 93.2
MS.gene008898.t1 AT1G74660 64.706 51 18 0 47 97 38 88 8.91e-22 86.3
MS.gene008898.t1 AT1G74660 64.706 51 18 0 47 97 38 88 1.55e-21 85.5
MS.gene008898.t1 AT3G50890 31.455 213 101 7 15 215 33 212 1.24e-20 87.0
MS.gene008898.t1 AT1G75240 61.290 62 23 1 47 107 75 136 1.38e-20 88.2
MS.gene008898.t1 AT3G28917 50.000 68 29 2 47 113 32 95 1.27e-17 75.5
MS.gene008898.t1 AT3G28920 33.158 190 89 8 48 216 52 224 2.45e-16 76.3
MS.gene008898.t1 AT5G42780 30.882 204 110 6 18 215 33 211 5.03e-16 74.7
MS.gene008898.t1 AT5G60480 34.118 170 82 5 48 215 37 178 6.27e-16 73.9
MS.gene008898.t1 AT1G18835 58.824 51 18 1 47 97 25 72 9.59e-16 70.1
MS.gene008898.t1 AT5G39760 59.615 52 19 1 48 97 56 107 2.33e-13 68.2

Find 50 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGAGTCGGCTGAGGGAAAC+GGG 0.315201 8.1:-36089895 None:intergenic
CACTTTCCAAGGGGTGATCT+TGG 0.335585 8.1:+36090020 MS.gene008898:CDS
TTTCTCTCCGATGAAAATTT+CGG 0.335714 8.1:-36089827 None:intergenic
AGCATGTGACTGGGACTTCT+AGG 0.339165 8.1:+36089952 MS.gene008898:CDS
AGGGAGTCGGCTGAGGGAAA+CGG 0.388732 8.1:-36089896 None:intergenic
ATTGTTTCAACGTAACTAGT+TGG 0.415917 8.1:-36089609 None:intergenic
ACCGGTTACCAGCATGTGAC+TGG 0.421058 8.1:+36089942 MS.gene008898:CDS
CCCAGTCACATGCTGGTAAC+CGG 0.435647 8.1:-36089943 None:intergenic
TTCTTCATCATGATGATTCG+AGG 0.450499 8.1:-36089637 None:intergenic
TAAGTATCACCATGATAGAT+TGG 0.451827 8.1:-36090059 None:intergenic
GTCGAGAAGGGAGTCGGCTG+AGG 0.453909 8.1:-36089903 None:intergenic
ATTGGAGGCTACGCTCTTGA+TGG 0.454275 8.1:+36089732 MS.gene008898:CDS
GGAGTCGGCTGAGGGAAACG+GGG 0.458116 8.1:-36089894 None:intergenic
TATCAAAAGGAAAGGATGCT+TGG 0.463362 8.1:+36090137 MS.gene008898:CDS
AAGAATCACGCTTCCAGCAT+TGG 0.464419 8.1:+36089714 MS.gene008898:CDS
CAAGTTCACTCATTATCAAA+AGG 0.480127 8.1:+36090124 MS.gene008898:CDS
ATGATGAGGCCCACTTTCCA+AGG 0.481132 8.1:+36090009 MS.gene008898:CDS
TATCATGGTGATACTTATAG+TGG 0.482130 8.1:+36090065 MS.gene008898:CDS
TTCTTCAGTTGTTCATGATG+AGG 0.486893 8.1:+36089995 MS.gene008898:CDS
AAGAGCGTAGCCTCCAATGC+TGG 0.502391 8.1:-36089727 None:intergenic
GCATGTGACTGGGACTTCTA+GGG 0.505358 8.1:+36089953 MS.gene008898:CDS
CAAGATCACCCCTTGGAAAG+TGG 0.509725 8.1:-36090019 None:intergenic
AATGGAAACAAAAGAAAATG+AGG 0.526367 8.1:+36089557 None:intergenic
AATCACGCTTCCAGCATTGG+AGG 0.528529 8.1:+36089717 MS.gene008898:CDS
TCATCATGAACAACTGAAGA+AGG 0.530900 8.1:-36089993 None:intergenic
AAGATCACCCCTTGGAAAGT+GGG 0.533623 8.1:-36090018 None:intergenic
GGCTACGCTCTTGATGGCTG+TGG 0.535093 8.1:+36089738 MS.gene008898:CDS
GAGTCGGCTGAGGGAAACGG+GGG 0.542032 8.1:-36089893 None:intergenic
CCAAGGGGTGATCTTGGAGA+AGG 0.555872 8.1:+36090026 MS.gene008898:CDS
GATACTTATAGTGGTGGAGA+AGG 0.556865 8.1:+36090074 MS.gene008898:CDS
TGATGAGGCCCACTTTCCAA+GGG 0.559791 8.1:+36090010 MS.gene008898:CDS
TAGAAGTCCCAGTCACATGC+TGG 0.560832 8.1:-36089950 None:intergenic
TCACTCATTATCAAAAGGAA+AGG 0.573122 8.1:+36090129 MS.gene008898:CDS
TCTCAAAGCAATAACTTCGA+AGG 0.575954 8.1:+36089672 MS.gene008898:CDS
CCGGTTACCAGCATGTGACT+GGG 0.576238 8.1:+36089943 MS.gene008898:CDS
TCGAGAAGGGAGTCGGCTGA+GGG 0.581880 8.1:-36089902 None:intergenic
ATGGTTCCTTCAATTCCAGC+GGG 0.587215 8.1:-36089771 None:intergenic
AAATGAGGAAGACGTAGTGA+TGG 0.593757 8.1:+36089572 MS.gene008898:CDS
CATGGTGATACTTATAGTGG+TGG 0.595025 8.1:+36090068 MS.gene008898:CDS
GTTGTTGAGCCAATCTATCA+TGG 0.597526 8.1:+36090050 MS.gene008898:CDS
TCAGCCGACTCCCTTCTCGA+CGG 0.603425 8.1:+36089905 MS.gene008898:CDS
CCTTCTCCAAGATCACCCCT+TGG 0.609902 8.1:-36090026 None:intergenic
AAAACCGTCGAGAAGGGAGT+CGG 0.612389 8.1:-36089909 None:intergenic
CATGTGACTGGGACTTCTAG+GGG 0.623678 8.1:+36089954 MS.gene008898:CDS
ATACTTATAGTGGTGGAGAA+GGG 0.640736 8.1:+36090075 MS.gene008898:CDS
GTCACATGCTGGTAACCGGT+CGG 0.647933 8.1:-36089939 None:intergenic
GATGGTTCCTTCAATTCCAG+CGG 0.666037 8.1:-36089772 None:intergenic
AAGGGTCGTCAAAATCAAAG+AGG 0.684157 8.1:+36090093 MS.gene008898:CDS
ATGTGACTGGGACTTCTAGG+GGG 0.700324 8.1:+36089955 MS.gene008898:CDS
GATGAGGCCCACTTTCCAAG+GGG 0.725349 8.1:+36090011 MS.gene008898:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AGCACAATTGAAAAATTCGA+TGG - chr8.1:36089793-36089812 None:intergenic 30.0%
ATTGTTTCAACGTAACTAGT+TGG - chr8.1:36089612-36089631 None:intergenic 30.0%
CAAGTTCACTCATTATCAAA+AGG + chr8.1:36090124-36090143 MS.gene008898:CDS 30.0%
TAAGTATCACCATGATAGAT+TGG - chr8.1:36090062-36090081 None:intergenic 30.0%
TATCATGGTGATACTTATAG+TGG + chr8.1:36090065-36090084 MS.gene008898:CDS 30.0%
TCACTCATTATCAAAAGGAA+AGG + chr8.1:36090129-36090148 MS.gene008898:CDS 30.0%
TTTCTCTCCGATGAAAATTT+CGG - chr8.1:36089830-36089849 None:intergenic 30.0%
! AATTTTCATCGGAGAGAAAA+TGG + chr8.1:36089831-36089850 MS.gene008898:CDS 30.0%
!!! CTTTTGATAATGAGTGAACT+TGG - chr8.1:36090126-36090145 None:intergenic 30.0%
TATCAAAAGGAAAGGATGCT+TGG + chr8.1:36090137-36090156 MS.gene008898:CDS 35.0%
TCATCATGAACAACTGAAGA+AGG - chr8.1:36089996-36090015 None:intergenic 35.0%
TCTCAAAGCAATAACTTCGA+AGG + chr8.1:36089672-36089691 MS.gene008898:CDS 35.0%
TTCTTCAGTTGTTCATGATG+AGG + chr8.1:36089995-36090014 MS.gene008898:CDS 35.0%
TTCTTCATCATGATGATTCG+AGG - chr8.1:36089640-36089659 None:intergenic 35.0%
! ACTGTCACCGAAATTTTCAT+CGG + chr8.1:36089820-36089839 MS.gene008898:CDS 35.0%
! ATACTTATAGTGGTGGAGAA+GGG + chr8.1:36090075-36090094 MS.gene008898:CDS 35.0%
!!! CTTGGTTTTGCTATGAAATC+GGG + chr8.1:36090155-36090174 MS.gene008898:CDS 35.0%
!!! GCTTGGTTTTGCTATGAAAT+CGG + chr8.1:36090154-36090173 MS.gene008898:CDS 35.0%
AAATGAGGAAGACGTAGTGA+TGG + chr8.1:36089572-36089591 MS.gene008898:CDS 40.0%
AAGGGTCGTCAAAATCAAAG+AGG + chr8.1:36090093-36090112 MS.gene008898:CDS 40.0%
AGTTTGAAAAACCGTCGAGA+AGG - chr8.1:36089919-36089938 None:intergenic 40.0%
CATGGTGATACTTATAGTGG+TGG + chr8.1:36090068-36090087 MS.gene008898:CDS 40.0%
GTTGTTGAGCCAATCTATCA+TGG + chr8.1:36090050-36090069 MS.gene008898:CDS 40.0%
GTTTGAAAAACCGTCGAGAA+GGG - chr8.1:36089918-36089937 None:intergenic 40.0%
! GATACTTATAGTGGTGGAGA+AGG + chr8.1:36090074-36090093 MS.gene008898:CDS 40.0%
! TTTTTACCCGCTGGAATTGA+AGG + chr8.1:36089765-36089784 MS.gene008898:CDS 40.0%
!! GTTTTGCTATGAAATCGGGT+TGG + chr8.1:36090159-36090178 MS.gene008898:CDS 40.0%
AACGGGGGTTGTTAAAAGGA+AGG - chr8.1:36089881-36089900 None:intergenic 45.0%
AAGAATCACGCTTCCAGCAT+TGG + chr8.1:36089714-36089733 MS.gene008898:CDS 45.0%
AAGATCACCCCTTGGAAAGT+GGG - chr8.1:36090021-36090040 None:intergenic 45.0%
ACGGGGGTTGTTAAAAGGAA+GGG - chr8.1:36089880-36089899 None:intergenic 45.0%
ATGGTTCCTTCAATTCCAGC+GGG - chr8.1:36089774-36089793 None:intergenic 45.0%
GATGGTTCCTTCAATTCCAG+CGG - chr8.1:36089775-36089794 None:intergenic 45.0%
!! ACGGTTTTTCAAACTCCGAC+CGG + chr8.1:36089924-36089943 MS.gene008898:CDS 45.0%
AAAACCGTCGAGAAGGGAGT+CGG - chr8.1:36089912-36089931 None:intergenic 50.0%
AGCATGTGACTGGGACTTCT+AGG + chr8.1:36089952-36089971 MS.gene008898:CDS 50.0%
ATGATGAGGCCCACTTTCCA+AGG + chr8.1:36090009-36090028 MS.gene008898:CDS 50.0%
ATGTGACTGGGACTTCTAGG+GGG + chr8.1:36089955-36089974 MS.gene008898:CDS 50.0%
ATTGGAGGCTACGCTCTTGA+TGG + chr8.1:36089732-36089751 MS.gene008898:CDS 50.0%
CAAGATCACCCCTTGGAAAG+TGG - chr8.1:36090022-36090041 None:intergenic 50.0%
CACTTTCCAAGGGGTGATCT+TGG + chr8.1:36090020-36090039 MS.gene008898:CDS 50.0%
CATGTGACTGGGACTTCTAG+GGG + chr8.1:36089954-36089973 MS.gene008898:CDS 50.0%
GCATGTGACTGGGACTTCTA+GGG + chr8.1:36089953-36089972 MS.gene008898:CDS 50.0%
GGGAAACGGGGGTTGTTAAA+AGG - chr8.1:36089885-36089904 None:intergenic 50.0%
TAGAAGTCCCAGTCACATGC+TGG - chr8.1:36089953-36089972 None:intergenic 50.0%
TGATGAGGCCCACTTTCCAA+GGG + chr8.1:36090010-36090029 MS.gene008898:CDS 50.0%
! AATCACGCTTCCAGCATTGG+AGG + chr8.1:36089717-36089736 MS.gene008898:CDS 50.0%
ACCGGTTACCAGCATGTGAC+TGG + chr8.1:36089942-36089961 MS.gene008898:CDS 55.0%
CCAAGGGGTGATCTTGGAGA+AGG + chr8.1:36090026-36090045 MS.gene008898:CDS 55.0%
CCCAGTCACATGCTGGTAAC+CGG - chr8.1:36089946-36089965 None:intergenic 55.0%
CCGGTTACCAGCATGTGACT+GGG + chr8.1:36089943-36089962 MS.gene008898:CDS 55.0%
CCTTCTCCAAGATCACCCCT+TGG - chr8.1:36090029-36090048 None:intergenic 55.0%
GATGAGGCCCACTTTCCAAG+GGG + chr8.1:36090011-36090030 MS.gene008898:CDS 55.0%
GTCACATGCTGGTAACCGGT+CGG - chr8.1:36089942-36089961 None:intergenic 55.0%
! AAGAGCGTAGCCTCCAATGC+TGG - chr8.1:36089730-36089749 None:intergenic 55.0%
! TGTGGCGAGTTTTTACCCGC+TGG + chr8.1:36089756-36089775 MS.gene008898:CDS 55.0%
AGGGAGTCGGCTGAGGGAAA+CGG - chr8.1:36089899-36089918 None:intergenic 60.0%
TCGAGAAGGGAGTCGGCTGA+GGG - chr8.1:36089905-36089924 None:intergenic 60.0%
! GGCTACGCTCTTGATGGCTG+TGG + chr8.1:36089738-36089757 MS.gene008898:CDS 60.0%
! TCAGCCGACTCCCTTCTCGA+CGG + chr8.1:36089905-36089924 MS.gene008898:CDS 60.0%
GAGTCGGCTGAGGGAAACGG+GGG - chr8.1:36089896-36089915 None:intergenic 65.0%
GGAGTCGGCTGAGGGAAACG+GGG - chr8.1:36089897-36089916 None:intergenic 65.0%
GGGAGTCGGCTGAGGGAAAC+GGG - chr8.1:36089898-36089917 None:intergenic 65.0%
GTCGAGAAGGGAGTCGGCTG+AGG - chr8.1:36089906-36089925 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 36089558 36090205 36089558 ID=MS.gene008898
chr8.1 mRNA 36089558 36090205 36089558 ID=MS.gene008898.t1;Parent=MS.gene008898
chr8.1 exon 36089558 36090205 36089558 ID=MS.gene008898.t1.exon1;Parent=MS.gene008898.t1
chr8.1 CDS 36089558 36090205 36089558 ID=cds.MS.gene008898.t1;Parent=MS.gene008898.t1
Gene Sequence

>MS.gene008898

ATGGAAACAAAAGAAAATGAGGAAGACGTAGTGATGGCTAATGACAGTGATCCAACTAGTTACGTTGAAACAATTAAAACCTCGAATCATCATGATGAAGAAACTCTAATGAATTCTCAAAGCAATAACTTCGAAGGAAAGTTCAAAGAGTGTAGAAAGAATCACGCTTCCAGCATTGGAGGCTACGCTCTTGATGGCTGTGGCGAGTTTTTACCCGCTGGAATTGAAGGAACCATCGAATTTTTCAATTGTGCTGCGTGTAACTGTCACCGAAATTTTCATCGGAGAGAAAATGGTGTTGTTAATGAAGAGAATATTTCCCTTCCTTTTAACAACCCCCGTTTCCCTCAGCCGACTCCCTTCTCGACGGTTTTTCAAACTCCGACCGGTTACCAGCATGTGACTGGGACTTCTAGGGGGACAACTACTTCTATTCCTTCTTCAGTTGTTCATGATGAGGCCCACTTTCCAAGGGGTGATCTTGGAGAAGGTGTTGTTGAGCCAATCTATCATGGTGATACTTATAGTGGTGGAGAAGGGTCGTCAAAATCAAAGAGGTTCAGATCCAAGTTCACTCATTATCAAAAGGAAAGGATGCTTGGTTTTGCTATGAAATCGGGTTGGAAGATTCCTAAGCAAGATGAAAAT
Protein sequence

>MS.gene008898.t1

METKENEEDVVMANDSDPTSYVETIKTSNHHDEETLMNSQSNNFEGKFKECRKNHASSIGGYALDGCGEFLPAGIEGTIEFFNCAACNCHRNFHRRENGVVNEENISLPFNNPRFPQPTPFSTVFQTPTGYQHVTGTSRGTTTSIPSSVVHDEAHFPRGDLGEGVVEPIYHGDTYSGGEGSSKSKRFRSKFTHYQKERMLGFAMKSGWKIPKQDEN