AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0614530

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0614530 MtrunA17_Chr4g0050581 91.803 183 9 2 1 181 1 179 4.26e-109 309
Msa0614530 MtrunA17_Chr2g0278961 55.901 161 49 6 5 161 6 148 2.66e-45 147
Msa0614530 MtrunA17_Chr2g0278951 54.118 170 55 7 5 169 6 157 3.06e-45 147
Msa0614530 MtrunA17_Chr8g0378161 33.684 190 98 9 9 175 5 189 2.68e-21 86.3
Msa0614530 MtrunA17_Chr3g0103131 42.553 94 48 4 39 128 42 133 1.33e-12 62.4
Msa0614530 MtrunA17_Chr2g0328581 41.026 78 41 2 45 122 65 137 3.37e-12 62.4
Msa0614530 MtrunA17_Chr2g0282741 41.250 80 42 3 53 130 2 78 4.90e-12 63.2
Msa0614530 MtrunA17_Chr5g0399201 45.455 66 35 1 56 121 13 77 1.39e-11 62.0
Msa0614530 MtrunA17_Chr2g0333221 41.667 84 42 3 54 135 69 147 1.94e-11 61.6
Msa0614530 MtrunA17_Chr7g0253281 33.333 150 88 4 1 146 3 144 2.41e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0614530 AT4G13830.2 38.462 130 68 4 55 175 66 192 1.28e-21 87.4
Msa0614530 AT4G13830.1 47.222 72 36 2 55 126 66 135 4.64e-14 66.6
Msa0614530 AT4G13830.3 47.222 72 36 2 55 126 66 135 7.02e-14 66.6
Msa0614530 AT3G62600.1 46.753 77 35 3 53 127 24 96 1.01e-11 62.8
Msa0614530 AT2G20560.1 37.500 80 45 3 53 130 2 78 1.83e-11 62.0
Msa0614530 AT1G28210.1 40.426 94 49 4 55 147 48 135 2.84e-11 61.6
Msa0614530 AT1G28210.3 40.426 94 49 4 55 147 48 135 2.92e-11 61.6
Msa0614530 AT1G28210.2 40.426 94 49 4 55 147 48 135 4.13e-11 61.2
Msa0614530 AT5G59610.2 33.871 124 57 4 19 123 19 136 6.95e-11 59.7
Msa0614530 AT4G28480.2 36.905 84 48 3 53 134 2 82 7.42e-11 60.1
Msa0614530 AT4G28480.1 36.905 84 48 3 53 134 2 82 7.58e-11 60.1

Find 28 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACAATATGATAGTGAATT+AGG 0.232905 4_2:+63594881 Msa0614530:CDS
GTAGAAATTTGATCCATTCT+TGG 0.275553 4_2:-63594678 None:intergenic
TTTAGTTGATTCCTCTTTCA+TGG 0.279301 4_2:-63594804 None:intergenic
AATGCTTAGGCTTGAGGTTA+AGG 0.338721 4_2:-63594543 None:intergenic
AGTAGACGTATGGGACAAAA+AGG 0.403585 4_2:+63595001 Msa0614530:CDS
ATATTGTAAATGATGAGATA+TGG 0.436536 4_2:+63594933 Msa0614530:CDS
AAGTGGTTGAGTTGAAGAAA+AGG 0.458554 4_2:+63594975 Msa0614530:CDS
ATGATGAGATATGGAGAAGT+AGG 0.468838 4_2:+63594942 Msa0614530:CDS
AAATTTCTACAAAATGTTGT+CGG 0.490774 4_2:+63594691 Msa0614530:CDS
AAAGAGAGCTTATAGATCAA+TGG 0.492226 4_2:+63594745 Msa0614530:CDS
GAAAAGGTCTAGTAGACGTA+TGG 0.496414 4_2:+63594991 Msa0614530:CDS
GCTTTGAATTTGAAATGCTT+AGG 0.497473 4_2:-63594556 None:intergenic
TCATGATCCTTCCATGAAAG+AGG 0.504521 4_2:+63594793 Msa0614530:CDS
ATTTGAAATGCTTAGGCTTG+AGG 0.508030 4_2:-63594549 None:intergenic
GTTGATTCCTCTTTCATGGA+AGG 0.513452 4_2:-63594800 None:intergenic
GAATCCGAAAAGCGCGACAA+TGG 0.529224 4_2:+63594715 Msa0614530:CDS
GAAGGATCATGACACACATC+AGG 0.542719 4_2:-63594782 None:intergenic
CTAGTGGAAGAAACCAAGAA+TGG 0.557604 4_2:+63594665 Msa0614530:CDS
TCATATTGTTCACGAAGCAT+AGG 0.565520 4_2:-63594869 None:intergenic
GGACACAAAGCATGAAAGAT+CGG 0.571745 4_2:+63595047 Msa0614530:CDS
GGTCTTGGGGTAGCAGAATG+AGG 0.576046 4_2:+63595026 Msa0614530:CDS
AAAAGGTCTAGTAGACGTAT+GGG 0.582302 4_2:+63594992 Msa0614530:CDS
GTGTAGAGCAACAAAGCTAG+TGG 0.596500 4_2:+63594649 Msa0614530:CDS
GATTACTAGAGAGTTGTGGA+AGG 0.607019 4_2:-63594589 None:intergenic
AGATGATTACTAGAGAGTTG+TGG 0.607411 4_2:-63594593 None:intergenic
AAGTAGGTGGCAAGAACAAG+TGG 0.619538 4_2:+63594958 Msa0614530:CDS
ATGAGATATGGAGAAGTAGG+TGG 0.638622 4_2:+63594945 Msa0614530:CDS
GTTGCAAAGTGTACATGACA+AGG 0.688927 4_2:-63594620 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTTCTACAAAATGTTGT+CGG + chr4_2:63594691-63594710 Msa0614530:CDS 20.0%
!! ATATTGTAAATGATGAGATA+TGG + chr4_2:63594933-63594952 Msa0614530:CDS 20.0%
!! GAACAATATGATAGTGAATT+AGG + chr4_2:63594881-63594900 Msa0614530:CDS 25.0%
! GCTTTGAATTTGAAATGCTT+AGG - chr4_2:63594559-63594578 None:intergenic 30.0%
GTAGAAATTTGATCCATTCT+TGG - chr4_2:63594681-63594700 None:intergenic 30.0%
AAAGAGAGCTTATAGATCAA+TGG + chr4_2:63594745-63594764 Msa0614530:CDS 30.0%
! TTTAGTTGATTCCTCTTTCA+TGG - chr4_2:63594807-63594826 None:intergenic 30.0%
! ATTTGAAATGCTTAGGCTTG+AGG - chr4_2:63594552-63594571 None:intergenic 35.0%
AGATGATTACTAGAGAGTTG+TGG - chr4_2:63594596-63594615 None:intergenic 35.0%
TCATATTGTTCACGAAGCAT+AGG - chr4_2:63594872-63594891 None:intergenic 35.0%
ATGATGAGATATGGAGAAGT+AGG + chr4_2:63594942-63594961 Msa0614530:CDS 35.0%
!! AAGTGGTTGAGTTGAAGAAA+AGG + chr4_2:63594975-63594994 Msa0614530:CDS 35.0%
AAAAGGTCTAGTAGACGTAT+GGG + chr4_2:63594992-63595011 Msa0614530:CDS 35.0%
AATGCTTAGGCTTGAGGTTA+AGG - chr4_2:63594546-63594565 None:intergenic 40.0%
GATTACTAGAGAGTTGTGGA+AGG - chr4_2:63594592-63594611 None:intergenic 40.0%
GTTGCAAAGTGTACATGACA+AGG - chr4_2:63594623-63594642 None:intergenic 40.0%
CTAGTGGAAGAAACCAAGAA+TGG + chr4_2:63594665-63594684 Msa0614530:CDS 40.0%
TCATGATCCTTCCATGAAAG+AGG + chr4_2:63594793-63594812 Msa0614530:CDS 40.0%
! GTTGATTCCTCTTTCATGGA+AGG - chr4_2:63594803-63594822 None:intergenic 40.0%
ATGAGATATGGAGAAGTAGG+TGG + chr4_2:63594945-63594964 Msa0614530:CDS 40.0%
GAAAAGGTCTAGTAGACGTA+TGG + chr4_2:63594991-63595010 Msa0614530:CDS 40.0%
AGTAGACGTATGGGACAAAA+AGG + chr4_2:63595001-63595020 Msa0614530:CDS 40.0%
GGACACAAAGCATGAAAGAT+CGG + chr4_2:63595047-63595066 Msa0614530:CDS 40.0%
GTGTAGAGCAACAAAGCTAG+TGG + chr4_2:63594649-63594668 Msa0614530:CDS 45.0%
! TCTTCCATTGTCGCGCTTTT+CGG - chr4_2:63594722-63594741 None:intergenic 45.0%
GAAGGATCATGACACACATC+AGG - chr4_2:63594785-63594804 None:intergenic 45.0%
AAGTAGGTGGCAAGAACAAG+TGG + chr4_2:63594958-63594977 Msa0614530:CDS 45.0%
GACGTATGGGACAAAAAGGA+AGG + chr4_2:63595005-63595024 Msa0614530:CDS 45.0%
TGGGACAAAAAGGAAGGTCT+TGG + chr4_2:63595011-63595030 Msa0614530:CDS 45.0%
GGGACAAAAAGGAAGGTCTT+GGG + chr4_2:63595012-63595031 Msa0614530:CDS 45.0%
GGACAAAAAGGAAGGTCTTG+GGG + chr4_2:63595013-63595032 Msa0614530:CDS 45.0%
! GAATCCGAAAAGCGCGACAA+TGG + chr4_2:63594715-63594734 Msa0614530:CDS 50.0%
GGTCTTGGGGTAGCAGAATG+AGG + chr4_2:63595026-63595045 Msa0614530:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 63594530 63595075 63594530 ID=Msa0614530;Name=Msa0614530
chr4_2 mRNA 63594530 63595075 63594530 ID=Msa0614530-mRNA-1;Parent=Msa0614530;Name=Msa0614530-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|181
chr4_2 exon 63594530 63595075 63594530 ID=Msa0614530-mRNA-1:exon:17787;Parent=Msa0614530-mRNA-1
chr4_2 CDS 63594530 63595075 63594530 ID=Msa0614530-mRNA-1:cds;Parent=Msa0614530-mRNA-1
Gene Sequence

>Msa0614530

ATGAATGCTTCATCCTTAACCTCAAGCCTAAGCATTTCAAATTCAAAGCAATTTCATCACCTTCCACAACTCTCTAGTAATCATCTAAGACCTTGTCATGTACACTTTGCAACAATTTCGTGTAGAGCAACAAAGCTAGTGGAAGAAACCAAGAATGGATCAAATTTCTACAAAATGTTGTCGGTGAATCCGAAAAGCGCGACAATGGAAGAAATAAAGAGAGCTTATAGATCAATGGCACTTCAGTATCATCCTGATGTGTGTCATGATCCTTCCATGAAAGAGGAATCAACTAAAATTTTTGTTCGATTAAATGCAGCTTATGAAACTTTGTCAAATCCTATGCTTCGTGAACAATATGATAGTGAATTAGGTTTGAGAAACAACATGATGAATAATAATAATATTGTAAATGATGAGATATGGAGAAGTAGGTGGCAAGAACAAGTGGTTGAGTTGAAGAAAAGGTCTAGTAGACGTATGGGACAAAAAGGAAGGTCTTGGGGTAGCAGAATGAGGACACAAAGCATGAAAGATCGGAACTAA
Protein sequence

>Msa0614530

MNASSLTSSLSISNSKQFHHLPQLSSNHLRPCHVHFATISCRATKLVEETKNGSNFYKMLSVNPKSATMEEIKRAYRSMALQYHPDVCHDPSMKEESTKIFVRLNAAYETLSNPMLREQYDSELGLRNNMMNNNNIVNDEIWRSRWQEQVVELKKRSSRRMGQKGRSWGSRMRTQSMKDRN*