AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073012

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073012.t1 MTR_3g109310 90.857 175 12 1 1 175 125 295 6.02e-116 330
MS.gene073012.t1 MTR_3g110010 82.540 126 22 0 6 131 633 758 1.37e-59 197
MS.gene073012.t1 MTR_3g109982 81.746 126 23 0 6 131 649 774 4.78e-59 196
MS.gene073012.t1 MTR_1g008990 61.017 177 60 7 1 175 170 339 4.24e-53 172
MS.gene073012.t1 MTR_1g008990 73.684 76 20 0 1 76 170 245 8.32e-24 94.4
MS.gene073012.t1 MTR_1g080920 52.778 108 47 2 1 108 209 312 1.68e-19 84.7
MS.gene073012.t1 MTR_7g115120 58.537 82 34 0 2 83 195 276 4.05e-18 80.9
MS.gene073012.t1 MTR_7g115140 47.945 73 38 0 2 74 134 206 8.30e-14 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073012.t1 AT5G24800 46.591 176 74 7 1 175 121 277 2.62e-36 127
MS.gene073012.t1 AT5G28770 53.465 101 43 2 1 101 152 248 7.04e-19 82.0
MS.gene073012.t1 AT5G28770 53.465 101 43 2 1 101 145 241 7.38e-19 82.0
MS.gene073012.t1 AT5G28770 58.667 75 31 0 1 75 152 226 2.56e-15 71.6
MS.gene073012.t1 AT4G02640 46.316 95 48 1 1 95 222 313 1.64e-12 65.1
MS.gene073012.t1 AT4G02640 49.398 83 42 0 1 83 222 304 1.64e-12 65.1
MS.gene073012.t1 AT4G02640 49.398 83 42 0 1 83 216 298 1.86e-12 64.7
MS.gene073012.t1 AT4G02640 49.398 83 42 0 1 83 216 298 1.92e-12 64.7

Find 37 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATGAGTTGTGTAACTATT+TGG 0.238588 3.4:+94269896 MS.gene073012:CDS
AATTCAAATCTTGCTGGGTT+TGG 0.297271 3.4:+94269820 MS.gene073012:CDS
TCTTGCTGGGTTTGGAAACT+TGG 0.301540 3.4:+94269828 MS.gene073012:CDS
AACACTACACAAACAGTTTA+CGG 0.338361 3.4:+94269429 MS.gene073012:CDS
GTGTAACTATTTGGCCTTAA+GGG 0.360767 3.4:+94269905 MS.gene073012:CDS
TGCCTCATACGGTGGTGTTC+CGG 0.376655 3.4:+94269786 MS.gene073012:CDS
GTGCACAATTCAAATCTTGC+TGG 0.391606 3.4:+94269814 MS.gene073012:CDS
ATTTCCCTGCTGGACATTGA+TGG 0.397970 3.4:-94269761 None:intergenic
TGATGTGGTGACAGAGCTTC+TGG 0.398710 3.4:-94269641 None:intergenic
TGTGTAACTATTTGGCCTTA+AGG 0.401972 3.4:+94269904 MS.gene073012:CDS
TTTGAATTGTGCACGCCAAC+CGG 0.414397 3.4:-94269805 None:intergenic
GGTGAAGTTAGCTGAGGATA+TGG 0.427027 3.4:+94269615 MS.gene073012:intron
AACCGGAACACCACCGTATG+AGG 0.428469 3.4:-94269788 None:intergenic
TTTGTCTGAACTTGAGTCTC+AGG 0.431765 3.4:+94269103 MS.gene073012:CDS
CCCTGCTGGACATTGATGGT+TGG 0.492984 3.4:-94269757 None:intergenic
TGCACAATTCAAATCTTGCT+GGG 0.493012 3.4:+94269815 MS.gene073012:CDS
ATGAGGCACTATTTCCCTGC+TGG 0.505822 3.4:-94269771 None:intergenic
GCCAACCATCAATGTCCAGC+AGG 0.512549 3.4:+94269756 MS.gene073012:CDS
CACAACTCATAGCATTGCTT+AGG 0.535820 3.4:-94269885 None:intergenic
TGTAGAAGCTTTGAGAGCTA+AGG 0.540256 3.4:+94269507 MS.gene073012:CDS
TACAATGATGTCGTCGACAA+CGG 0.542670 3.4:+94269859 MS.gene073012:CDS
TTTGACAGAAATACCTTCTG+AGG 0.545576 3.4:-94268947 None:intergenic
AAACTGATTGTTTAGTGATG+TGG 0.571542 3.4:-94269656 None:intergenic
CAGGGAAATAGTGCCTCATA+CGG 0.576934 3.4:+94269775 MS.gene073012:CDS
TCATACGGTGGTGTTCCGGT+TGG 0.585749 3.4:+94269790 MS.gene073012:CDS
TTGATATGAAACGCCTCAGA+AGG 0.589092 3.4:+94268934 None:intergenic
TACTATTCAACAATTTCATG+AGG 0.600013 3.4:+94269453 MS.gene073012:CDS
GCGAGTCAACCAAGAGGTCA+AGG 0.603161 3.4:+94269063 MS.gene073012:CDS
GGAAATAGTGCCTCATACGG+TGG 0.626744 3.4:+94269778 MS.gene073012:CDS
TTAGTAGTCATGTTGAGTTG+TGG 0.648094 3.4:-94269709 None:intergenic
CCAACCATCAATGTCCAGCA+GGG 0.666005 3.4:+94269757 MS.gene073012:CDS
ATAATAGGTGAAGTTAGCTG+AGG 0.671237 3.4:+94269609 MS.gene073012:intron
GTAGTCATGTTGAGTTGTGG+CGG 0.676620 3.4:-94269706 None:intergenic
CAAATTGCGAGTCAACCAAG+AGG 0.697375 3.4:+94269057 MS.gene073012:CDS
TTGGCGAAACATGTGGCATG+CGG 0.727060 3.4:-94269738 None:intergenic
AGTCAACCAAGAGGTCAAGG+TGG 0.727607 3.4:+94269066 MS.gene073012:CDS
TTGATGGTTGGCGAAACATG+TGG 0.736785 3.4:-94269745 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAACATATACTATTATAAT+AGG + chr3.4:94269594-94269613 MS.gene073012:intron 10.0%
!! ACAACACTTCTAATTATATA+TGG + chr3.4:94268986-94269005 MS.gene073012:intron 20.0%
! TACTATTCAACAATTTCATG+AGG + chr3.4:94269453-94269472 MS.gene073012:CDS 25.0%
! TGAGAGATCAAAATTCAAAT+GGG - chr3.4:94269382-94269401 None:intergenic 25.0%
!!! AATTTTGTTTCTGGAATTGT+AGG + chr3.4:94269153-94269172 MS.gene073012:intron 25.0%
!!! GAAGTCATTAATTTTGTTTC+TGG + chr3.4:94269144-94269163 MS.gene073012:intron 25.0%
AAACTGATTGTTTAGTGATG+TGG - chr3.4:94269659-94269678 None:intergenic 30.0%
AACACTACACAAACAGTTTA+CGG + chr3.4:94269429-94269448 MS.gene073012:CDS 30.0%
CTATGAGTTGTGTAACTATT+TGG + chr3.4:94269896-94269915 MS.gene073012:CDS 30.0%
CTGAGAGATCAAAATTCAAA+TGG - chr3.4:94269383-94269402 None:intergenic 30.0%
GTCACTGAAATAGAAATAGT+AGG - chr3.4:94269250-94269269 None:intergenic 30.0%
TGATATAATGATTCGTGACA+TGG + chr3.4:94269020-94269039 MS.gene073012:intron 30.0%
! TAATTCTGAGAGCAAATTCT+AGG + chr3.4:94269221-94269240 MS.gene073012:intron 30.0%
!! CATTTGAATTTTGATCTCTC+AGG + chr3.4:94269381-94269400 MS.gene073012:intron 30.0%
AATTCAAATCTTGCTGGGTT+TGG + chr3.4:94269820-94269839 MS.gene073012:CDS 35.0%
ATAATAGGTGAAGTTAGCTG+AGG + chr3.4:94269609-94269628 MS.gene073012:intron 35.0%
CACAATTTGATATCTCATGC+AGG + chr3.4:94269183-94269202 MS.gene073012:intron 35.0%
TGCACAATTCAAATCTTGCT+GGG + chr3.4:94269815-94269834 MS.gene073012:CDS 35.0%
TTTGACAGAAATACCTTCTG+AGG - chr3.4:94268950-94268969 None:intergenic 35.0%
! CAGGTAACTAATCAGTGTTT+TGG + chr3.4:94269122-94269141 MS.gene073012:intron 35.0%
! TTAGTAGTCATGTTGAGTTG+TGG - chr3.4:94269712-94269731 None:intergenic 35.0%
!! CTACATCTGATTTTAGCACA+CGG - chr3.4:94269492-94269511 None:intergenic 35.0%
!! TTGTTTCTGGAATTGTAGGT+AGG + chr3.4:94269157-94269176 MS.gene073012:intron 35.0%
ATTCGTGACATGGTTTCAGA+AGG + chr3.4:94269030-94269049 MS.gene073012:intron 40.0%
CACAACTCATAGCATTGCTT+AGG - chr3.4:94269888-94269907 None:intergenic 40.0%
GTGCACAATTCAAATCTTGC+TGG + chr3.4:94269814-94269833 MS.gene073012:CDS 40.0%
TACAATGATGTCGTCGACAA+CGG + chr3.4:94269859-94269878 MS.gene073012:CDS 40.0%
TTCGTGACATGGTTTCAGAA+GGG + chr3.4:94269031-94269050 MS.gene073012:intron 40.0%
TTTGTCTGAACTTGAGTCTC+AGG + chr3.4:94269103-94269122 MS.gene073012:CDS 40.0%
!! TCAGGTTGAAAAACTGTCAC+TGG + chr3.4:94269399-94269418 MS.gene073012:intron 40.0%
!! TGTAGAAGCTTTGAGAGCTA+AGG + chr3.4:94269507-94269526 MS.gene073012:CDS 40.0%
ATTTCCCTGCTGGACATTGA+TGG - chr3.4:94269764-94269783 None:intergenic 45.0%
CAAATTGCGAGTCAACCAAG+AGG + chr3.4:94269057-94269076 MS.gene073012:CDS 45.0%
CAGGGAAATAGTGCCTCATA+CGG + chr3.4:94269775-94269794 MS.gene073012:CDS 45.0%
GGTGAAGTTAGCTGAGGATA+TGG + chr3.4:94269615-94269634 MS.gene073012:intron 45.0%
TCTTGCTGGGTTTGGAAACT+TGG + chr3.4:94269828-94269847 MS.gene073012:CDS 45.0%
TTTGAATTGTGCACGCCAAC+CGG - chr3.4:94269808-94269827 None:intergenic 45.0%
! GTAGTCATGTTGAGTTGTGG+CGG - chr3.4:94269709-94269728 None:intergenic 45.0%
! TTGATGGTTGGCGAAACATG+TGG - chr3.4:94269748-94269767 None:intergenic 45.0%
! TTTTCTCCACCTTGACCTCT+TGG - chr3.4:94269075-94269094 None:intergenic 45.0%
AGTCAACCAAGAGGTCAAGG+TGG + chr3.4:94269066-94269085 MS.gene073012:CDS 50.0%
CCAACCATCAATGTCCAGCA+GGG + chr3.4:94269757-94269776 MS.gene073012:CDS 50.0%
GGAAATAGTGCCTCATACGG+TGG + chr3.4:94269778-94269797 MS.gene073012:CDS 50.0%
TGATGTGGTGACAGAGCTTC+TGG - chr3.4:94269644-94269663 None:intergenic 50.0%
TTGGCGAAACATGTGGCATG+CGG - chr3.4:94269741-94269760 None:intergenic 50.0%
! ATGAGGCACTATTTCCCTGC+TGG - chr3.4:94269774-94269793 None:intergenic 50.0%
AACCGGAACACCACCGTATG+AGG - chr3.4:94269791-94269810 None:intergenic 55.0%
GCCAACCATCAATGTCCAGC+AGG + chr3.4:94269756-94269775 MS.gene073012:CDS 55.0%
GCGAGTCAACCAAGAGGTCA+AGG + chr3.4:94269063-94269082 MS.gene073012:CDS 55.0%
TCATACGGTGGTGTTCCGGT+TGG + chr3.4:94269790-94269809 MS.gene073012:CDS 55.0%
TGCCTCATACGGTGGTGTTC+CGG + chr3.4:94269786-94269805 MS.gene073012:CDS 55.0%
! CCCTGCTGGACATTGATGGT+TGG - chr3.4:94269760-94269779 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 94268939 94269924 94268939 ID=MS.gene073012
chr3.4 mRNA 94268939 94269924 94268939 ID=MS.gene073012.t1;Parent=MS.gene073012
chr3.4 exon 94268939 94268955 94268939 ID=MS.gene073012.t1.exon1;Parent=MS.gene073012.t1
chr3.4 CDS 94268939 94268955 94268939 ID=cds.MS.gene073012.t1;Parent=MS.gene073012.t1
chr3.4 exon 94269049 94269124 94269049 ID=MS.gene073012.t1.exon2;Parent=MS.gene073012.t1
chr3.4 CDS 94269049 94269124 94269049 ID=cds.MS.gene073012.t1;Parent=MS.gene073012.t1
chr3.4 exon 94269403 94269528 94269403 ID=MS.gene073012.t1.exon3;Parent=MS.gene073012.t1
chr3.4 CDS 94269403 94269528 94269403 ID=cds.MS.gene073012.t1;Parent=MS.gene073012.t1
chr3.4 exon 94269616 94269924 94269616 ID=MS.gene073012.t1.exon4;Parent=MS.gene073012.t1
chr3.4 CDS 94269616 94269924 94269616 ID=cds.MS.gene073012.t1;Parent=MS.gene073012.t1
Gene Sequence

>MS.gene073012

ATGAAACGCCTCAGAAGGTATTTCTGTCAAATTAAAGCACTTTAAATACAACACTTCTAATTATATATGGTTTTCAAATGATGATATAATGATTCGTGACATGGTTTCAGAAGGGTTTCAAATTGCGAGTCAACCAAGAGGTCAAGGTGGAGAAAACAAGCACATTTGTCTGAACTTGAGTCTCAGGTAACTAATCAGTGTTTTGGAAGTCATTAATTTTGTTTCTGGAATTGTAGGTAGGTTACACAATTTGATATCTCATGCAGGATTTTGAAAGTTAGTTAATTCTGAGAGCAAATTCTAGGAAGCCTACTATTTCTATTTCAGTGACTGAATTAGTCATTTCATTTGTTGATTAAATTTGTTTGTTTTTCAAATTGAAGCATAATCTTTTGTGAGATGTATAACAGCTAAACAACATAAGTCATAATCACTTTCTTCCCATTTGAATTTTGATCTCTCAGGTTGAAAAACTGTCACTGGAAAATGCAACACTACACAAACAGTTTACGGATACTATTCAACAATTTCATGAGGCTGATACAAATAACCGTGTGCTAAAATCAGATGTAGAAGCTTTGAGAGCTAAGGTATACAGTGAGTTTATTCTATAATTATGCATACAAAAATAAATATCAATGATTGAAGAAATTAATTAACATATACTATTATAATAGGTGAAGTTAGCTGAGGATATGGTCACCAGAAGCTCTGTCACCACATCACTAAACAATCAGTTTCTTCATAATCAATGTCAAATGAGCACACCGCCACAACTCAACATGACTACTAATATTCGCCGCATGCCACATGTTTCGCCAACCATCAATGTCCAGCAGGGAAATAGTGCCTCATACGGTGGTGTTCCGGTTGGCGTGCACAATTCAAATCTTGCTGGGTTTGGAAACTTGGACATGACTTACAATGATGTCGTCGACAACGGAGTCCTAAGCAATGCTATGAGTTGTGTAACTATTTGGCCTTAA
Protein sequence

>MS.gene073012.t1

MKRLRRRVSNCESTKRSRWRKQAHLSELESQVEKLSLENATLHKQFTDTIQQFHEADTNNRVLKSDVEALRAKVKLAEDMVTRSSVTTSLNNQFLHNQCQMSTPPQLNMTTNIRRMPHVSPTINVQQGNSASYGGVPVGVHNSNLAGFGNLDMTYNDVVDNGVLSNAMSCVTIWP