AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene006210

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006210.t1 MTR_0558s0020 86.058 208 28 1 147 353 1 208 4.26e-128 369
MS.gene006210.t1 MTR_1g083640 78.924 223 31 1 147 353 1 223 2.92e-126 364
MS.gene006210.t1 MTR_2g014100 80.556 216 33 1 147 353 1 216 2.24e-124 358
MS.gene006210.t1 MTR_3g008240 82.759 203 34 1 147 348 1 203 1.23e-118 341
MS.gene006210.t1 MTR_4g040430 81.683 202 33 1 147 348 1 198 1.17e-116 336
MS.gene006210.t1 MTR_5g071590 73.034 178 35 2 147 311 1 178 9.57e-90 267
MS.gene006210.t1 MTR_8g446020 66.184 207 31 1 147 353 1 168 4.08e-88 266
MS.gene006210.t1 MTR_0337s0040 65.865 208 31 2 147 353 1 169 9.22e-86 259
MS.gene006210.t1 MTR_6g090505 81.818 143 26 0 211 353 1 143 7.53e-80 248
MS.gene006210.t1 MTR_1g055240 85.470 117 17 0 237 353 3 119 8.65e-69 213
MS.gene006210.t1 MTR_0019s0290 77.778 126 28 0 228 353 9 134 7.26e-66 205
MS.gene006210.t1 MTR_1281s0010 78.704 108 23 0 165 272 1 108 1.21e-56 180
MS.gene006210.t1 MTR_4g008820 67.227 119 38 1 128 245 106 224 7.67e-40 149
MS.gene006210.t1 MTR_8g046060 63.281 128 35 4 110 225 51 178 1.21e-33 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 61 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGAGAAAAGCGATCTTGTT+AGG 0.317886 1.4:-77395289 None:intergenic
TTTAAGTCCGAAAATCAAAA+AGG 0.371320 1.4:-77396822 None:intergenic
GTGAATAACGTCGGAGAGAA+AGG 0.392004 1.4:-77395571 None:intergenic
TTCTCATACTCAACAAGAAC+TGG 0.395633 1.4:-77396531 None:intergenic
AGCTGGAATATATTTGAAGT+TGG 0.404118 1.4:+77396590 MS.gene006210:CDS
TTAGAACACGTGTGCAATAT+CGG 0.410415 1.4:-77395235 None:intergenic
CAAGGACATGTGTTATAATC+TGG 0.413968 1.4:+77395184 None:intergenic
ATAACACTGGATTCTCTGTT+AGG 0.417808 1.4:+77396373 MS.gene006210:CDS
TAAAGAATCATGGAGGTCTT+TGG 0.421610 1.4:+77396302 MS.gene006210:CDS
TTTCTGAATTGCACGAATCA+AGG 0.424507 1.4:-77395435 None:intergenic
CGAGAAGTAAATGAAGTTCA+AGG 0.430014 1.4:+77396708 MS.gene006210:CDS
TTTCTCACCGTTTCCGTCAC+CGG 0.430974 1.4:+77395304 MS.gene006210:CDS
CCATGATTCTTTATCACTAA+AGG 0.442634 1.4:-77396292 None:intergenic
TGAATGTCTATAAGATATAT+AGG 0.445219 1.4:+77396622 MS.gene006210:CDS
CGTTATGCTTGTAACAAAGA+AGG 0.449439 1.4:+77396456 MS.gene006210:CDS
ATCTGAGAGTGGACAATTGA+CGG 0.452529 1.4:+77396227 MS.gene006210:CDS
GCTTTAATAAATTCTAAAGC+TGG 0.457187 1.4:+77396738 MS.gene006210:CDS
CTCAAGTAGCGCAAATGCTC+TGG 0.460440 1.4:-77396678 None:intergenic
GCTTTAGAATTTATTAAAGC+AGG 0.461801 1.4:-77396735 None:intergenic
ACAAAATAAGAAATCGGATA+AGG 0.469178 1.4:+77396422 MS.gene006210:CDS
TGAGAAAAGCGATCTTGTTA+GGG 0.471595 1.4:-77395288 None:intergenic
TTAAAACCAACACTTTCCTC+TGG 0.473076 1.4:-77396567 None:intergenic
TTTAATTATGCATATAACAC+TGG 0.485542 1.4:+77396360 MS.gene006210:CDS
CAATTCACAAAATAAGAAAT+CGG 0.490263 1.4:+77396416 MS.gene006210:CDS
GAGAACATCTTATGAAGTGA+TGG 0.499875 1.4:+77396770 MS.gene006210:CDS
AACGGTGAGAATCGAGGTGC+CGG 0.515310 1.4:-77395492 None:intergenic
TTCACTCCGACGTATTTCTC+CGG 0.519990 1.4:+77395589 MS.gene006210:CDS
CACGTCGGAGAAGCGAAGAA+AGG 0.520105 1.4:-77395541 None:intergenic
TGTCTATAAGATATATAGGT+GGG 0.523740 1.4:+77396626 MS.gene006210:CDS
CACGTCGGAACGGCAAGAAA+CGG 0.524911 1.4:-77395352 None:intergenic
AACGACGCCGGTGACGGAAA+CGG 0.526717 1.4:-77395311 None:intergenic
GGTGAATCACGTCGGAGAGA+AGG 0.529438 1.4:-77395413 None:intergenic
CAAGTTGCAGCAGCGAGAAA+CGG 0.533204 1.4:-77395510 None:intergenic
CCTTTAGTGATAAAGAATCA+TGG 0.533415 1.4:+77396292 MS.gene006210:CDS
GTGAATCACGTCGGAGAGAA+GGG 0.536667 1.4:-77395412 None:intergenic
TTCTGAATTGCACGAATCAA+GGG 0.538180 1.4:-77395434 None:intergenic
TAACAAAGAAGGTTTCAAGA+AGG 0.538422 1.4:+77396467 MS.gene006210:CDS
AACAAAGAAGGTTTCAAGAA+GGG 0.545537 1.4:+77396468 MS.gene006210:CDS
AAATGCTCTGGTTTATGTAA+TGG 0.552634 1.4:-77396666 None:intergenic
TAACGTCGGAGAAGCGAGCA+AGG 0.562201 1.4:-77395383 None:intergenic
TGAAAATTCAGTTATTGATG+CGG 0.565546 1.4:+77396251 MS.gene006210:CDS
GGCTGAGAATCACGTCGGAA+CGG 0.580107 1.4:-77395362 None:intergenic
GAAGTGATGGGTCAAGGAGT+TGG 0.580260 1.4:+77396783 MS.gene006210:CDS
TCTTATGAAGTGATGGGTCA+AGG 0.589029 1.4:+77396777 MS.gene006210:CDS
GGGTCAAGGAGTTGGTGGCA+CGG 0.591884 1.4:+77396791 MS.gene006210:CDS
TCGTGAAACGACGCCGGTGA+CGG 0.598129 1.4:-77395317 None:intergenic
AGAACATCTTATGAAGTGAT+GGG 0.601988 1.4:+77396771 MS.gene006210:CDS
ATATCAACTTCATCTGAGAG+TGG 0.614980 1.4:+77396216 MS.gene006210:CDS
AGAACTGGACTGTCACATGT+TGG 0.620791 1.4:-77396516 None:intergenic
GTGATGGGTCAAGGAGTTGG+TGG 0.627058 1.4:+77396786 MS.gene006210:CDS
GCGATTCAGAAATTCATCGC+CGG 0.632392 1.4:+77395473 MS.gene006210:CDS
ATGTCTATAAGATATATAGG+TGG 0.643489 1.4:+77396625 MS.gene006210:CDS
GCGAGAAACGGTGAGAATCG+AGG 0.668358 1.4:-77395498 None:intergenic
TCGTGATCGTGAAACGACGC+CGG 0.673306 1.4:-77395323 None:intergenic
GAGAAGGGTGAAAATAACGT+CGG 0.709240 1.4:-77395397 None:intergenic
AACTCACCGGAGAAATACGT+CGG 0.711593 1.4:-77395595 None:intergenic
TACGTCGGAGTGAATAACGT+CGG 0.712291 1.4:-77395580 None:intergenic
GAATCAAGGGTGAATCACGT+CGG 0.714908 1.4:-77395421 None:intergenic
GAGAAAGGTGAGAATCACGT+CGG 0.723440 1.4:-77395556 None:intergenic
AGCAAGGCTGAGAATCACGT+CGG 0.725394 1.4:-77395367 None:intergenic
TTAGTGATAAAGAATCATGG+AGG 0.769153 1.4:+77396295 MS.gene006210:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTCAATTTATCATATCTAA+TGG + chr1.4:77396145-77396164 MS.gene006210:intron 15.0%
!!! GAATCATTTAAAATAATTGT+TGG + chr1.4:77395974-77395993 MS.gene006210:intron 15.0%
!! CAATTCACAAAATAAGAAAT+CGG + chr1.4:77396416-77396435 MS.gene006210:CDS 20.0%
!! TGAATGTCTATAAGATATAT+AGG + chr1.4:77396622-77396641 MS.gene006210:CDS 20.0%
!! TTTAATTATGCATATAACAC+TGG + chr1.4:77396360-77396379 MS.gene006210:CDS 20.0%
! AAAAACTATGCTAAAACCAT+TGG - chr1.4:77396109-77396128 None:intergenic 25.0%
! ACAAAATAAGAAATCGGATA+AGG + chr1.4:77396422-77396441 MS.gene006210:CDS 25.0%
! ATGTCTATAAGATATATAGG+TGG + chr1.4:77396625-77396644 MS.gene006210:CDS 25.0%
! CATATAAATGAATAACTCAC+CGG - chr1.4:77395611-77395630 None:intergenic 25.0%
! TGAAAATTCAGTTATTGATG+CGG + chr1.4:77396251-77396270 MS.gene006210:CDS 25.0%
! TGTCTATAAGATATATAGGT+GGG + chr1.4:77396626-77396645 MS.gene006210:CDS 25.0%
!!! CTTATTTTGTGAATTGTTCT+TGG - chr1.4:77396412-77396431 None:intergenic 25.0%
!!! GCTTTAATAAATTCTAAAGC+TGG + chr1.4:77396738-77396757 MS.gene006210:CDS 25.0%
!!! GCTTTAGAATTTATTAAAGC+AGG - chr1.4:77396738-77396757 None:intergenic 25.0%
AACAAAGAAGGTTTCAAGAA+GGG + chr1.4:77396468-77396487 MS.gene006210:CDS 30.0%
AGAACATCTTATGAAGTGAT+GGG + chr1.4:77396771-77396790 MS.gene006210:CDS 30.0%
CCATGATTCTTTATCACTAA+AGG - chr1.4:77396295-77396314 None:intergenic 30.0%
CCTTTAGTGATAAAGAATCA+TGG + chr1.4:77396292-77396311 MS.gene006210:CDS 30.0%
TAACAAAGAAGGTTTCAAGA+AGG + chr1.4:77396467-77396486 MS.gene006210:CDS 30.0%
TTAGTGATAAAGAATCATGG+AGG + chr1.4:77396295-77396314 MS.gene006210:CDS 30.0%
! AAATGCTCTGGTTTATGTAA+TGG - chr1.4:77396669-77396688 None:intergenic 30.0%
! AGCTGGAATATATTTGAAGT+TGG + chr1.4:77396590-77396609 MS.gene006210:CDS 30.0%
!! GCTTTAAAACTGAAGTAAAC+TGG + chr1.4:77395762-77395781 MS.gene006210:intron 30.0%
ATAACACTGGATTCTCTGTT+AGG + chr1.4:77396373-77396392 MS.gene006210:CDS 35.0%
ATATCAACTTCATCTGAGAG+TGG + chr1.4:77396216-77396235 MS.gene006210:CDS 35.0%
ATTGTTGGAGTATGAGTGTT+AGG + chr1.4:77395989-77396008 MS.gene006210:intron 35.0%
CGAGAAGTAAATGAAGTTCA+AGG + chr1.4:77396708-77396727 MS.gene006210:CDS 35.0%
CGTTATGCTTGTAACAAAGA+AGG + chr1.4:77396456-77396475 MS.gene006210:CDS 35.0%
GAAAGCTAAAGAAAAACCAG+AGG + chr1.4:77396551-77396570 MS.gene006210:CDS 35.0%
GAGAACATCTTATGAAGTGA+TGG + chr1.4:77396770-77396789 MS.gene006210:CDS 35.0%
GAGTTGTACTCCAAAATCAT+TGG - chr1.4:77396066-77396085 None:intergenic 35.0%
GCTAAATGCTACAAAACTGA+TGG + chr1.4:77395669-77395688 MS.gene006210:intron 35.0%
GTCTGCTTAATCCTAAAAAC+AGG + chr1.4:77396493-77396512 MS.gene006210:CDS 35.0%
TAAAGAATCATGGAGGTCTT+TGG + chr1.4:77396302-77396321 MS.gene006210:CDS 35.0%
TGAGAAAAGCGATCTTGTTA+GGG - chr1.4:77395291-77395310 None:intergenic 35.0%
TTAAAACCAACACTTTCCTC+TGG - chr1.4:77396570-77396589 None:intergenic 35.0%
TTAGAACACGTGTGCAATAT+CGG - chr1.4:77395238-77395257 None:intergenic 35.0%
TTCTCATACTCAACAAGAAC+TGG - chr1.4:77396534-77396553 None:intergenic 35.0%
TTCTGAATTGCACGAATCAA+GGG - chr1.4:77395437-77395456 None:intergenic 35.0%
TTGTTGGAGTATGAGTGTTA+GGG + chr1.4:77395990-77396009 MS.gene006210:intron 35.0%
TTTCTGAATTGCACGAATCA+AGG - chr1.4:77395438-77395457 None:intergenic 35.0%
!!! GAAAGTGTTGGTTTTAAAGC+TGG + chr1.4:77396573-77396592 MS.gene006210:CDS 35.0%
!!! GTGTTTGTTGCTGTTTTCAA+TGG + chr1.4:77396188-77396207 MS.gene006210:intron 35.0%
ATCTGAGAGTGGACAATTGA+CGG + chr1.4:77396227-77396246 MS.gene006210:CDS 40.0%
CTCACCAAAATCATTTCCAC+AGG + chr1.4:77396040-77396059 MS.gene006210:intron 40.0%
GAGAAGGGTGAAAATAACGT+CGG - chr1.4:77395400-77395419 None:intergenic 40.0%
GTGAGAAAAGCGATCTTGTT+AGG - chr1.4:77395292-77395311 None:intergenic 40.0%
! GAAAAACCAGAGGAAAGTGT+TGG + chr1.4:77396561-77396580 MS.gene006210:CDS 40.0%
! TTGGCCTGTGGAAATGATTT+TGG - chr1.4:77396047-77396066 None:intergenic 40.0%
! TTTCCACAGGCCAATGATTT+TGG + chr1.4:77396053-77396072 MS.gene006210:intron 40.0%
!! TCACATGTTGGCCTGTTTTT+AGG - chr1.4:77396507-77396526 None:intergenic 40.0%
!! TCTTATGAAGTGATGGGTCA+AGG + chr1.4:77396777-77396796 MS.gene006210:CDS 40.0%
AAACCATATCCACAGGCCAA+TGG + chr1.4:77396090-77396109 MS.gene006210:intron 45.0%
AACTCACCGGAGAAATACGT+CGG - chr1.4:77395598-77395617 None:intergenic 45.0%
AGAACTGGACTGTCACATGT+TGG - chr1.4:77396519-77396538 None:intergenic 45.0%
CTCACCAAAACCATATCCAC+AGG + chr1.4:77396083-77396102 MS.gene006210:intron 45.0%
GAATCAAGGGTGAATCACGT+CGG - chr1.4:77395424-77395443 None:intergenic 45.0%
GAGAAAGGTGAGAATCACGT+CGG - chr1.4:77395559-77395578 None:intergenic 45.0%
GCGATTCAGAAATTCATCGC+CGG + chr1.4:77395473-77395492 MS.gene006210:CDS 45.0%
GTGAATAACGTCGGAGAGAA+AGG - chr1.4:77395574-77395593 None:intergenic 45.0%
TACGTCGGAGTGAATAACGT+CGG - chr1.4:77395583-77395602 None:intergenic 45.0%
TTCACTCCGACGTATTTCTC+CGG + chr1.4:77395589-77395608 MS.gene006210:CDS 45.0%
! AAACCATTGGCCTGTGGATA+TGG - chr1.4:77396096-77396115 None:intergenic 45.0%
! ACTCCAAAATCATTGGCCTG+TGG - chr1.4:77396059-77396078 None:intergenic 45.0%
! ATGCTAAAACCATTGGCCTG+TGG - chr1.4:77396102-77396121 None:intergenic 45.0%
! TTGGCCTGTGGATATGGTTT+TGG - chr1.4:77396090-77396109 None:intergenic 45.0%
AGCAAGGCTGAGAATCACGT+CGG - chr1.4:77395370-77395389 None:intergenic 50.0%
CAAGTTGCAGCAGCGAGAAA+CGG - chr1.4:77395513-77395532 None:intergenic 50.0%
CTCAAGTAGCGCAAATGCTC+TGG - chr1.4:77396681-77396700 None:intergenic 50.0%
GTGAATCACGTCGGAGAGAA+GGG - chr1.4:77395415-77395434 None:intergenic 50.0%
TTTCTCACCGTTTCCGTCAC+CGG + chr1.4:77395304-77395323 MS.gene006210:CDS 50.0%
!! GAAGTGATGGGTCAAGGAGT+TGG + chr1.4:77396783-77396802 MS.gene006210:CDS 50.0%
AACGGTGAGAATCGAGGTGC+CGG - chr1.4:77395495-77395514 None:intergenic 55.0%
CACGTCGGAACGGCAAGAAA+CGG - chr1.4:77395355-77395374 None:intergenic 55.0%
CACGTCGGAGAAGCGAAGAA+AGG - chr1.4:77395544-77395563 None:intergenic 55.0%
GCGAGAAACGGTGAGAATCG+AGG - chr1.4:77395501-77395520 None:intergenic 55.0%
GGCTGAGAATCACGTCGGAA+CGG - chr1.4:77395365-77395384 None:intergenic 55.0%
GGTGAATCACGTCGGAGAGA+AGG - chr1.4:77395416-77395435 None:intergenic 55.0%
TAACGTCGGAGAAGCGAGCA+AGG - chr1.4:77395386-77395405 None:intergenic 55.0%
TCGTGATCGTGAAACGACGC+CGG - chr1.4:77395326-77395345 None:intergenic 55.0%
!! GTGATGGGTCAAGGAGTTGG+TGG + chr1.4:77396786-77396805 MS.gene006210:CDS 55.0%
TCGTGAAACGACGCCGGTGA+CGG - chr1.4:77395320-77395339 None:intergenic 60.0%
!! AACGACGCCGGTGACGGAAA+CGG - chr1.4:77395314-77395333 None:intergenic 60.0%
!! GGGTCAAGGAGTTGGTGGCA+CGG + chr1.4:77396791-77396810 MS.gene006210:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 77395191 77396830 77395191 ID=MS.gene006210
chr1.4 mRNA 77395191 77396830 77395191 ID=MS.gene006210.t1;Parent=MS.gene006210
chr1.4 exon 77395191 77395610 77395191 ID=MS.gene006210.t1.exon1;Parent=MS.gene006210.t1
chr1.4 CDS 77395191 77395610 77395191 ID=cds.MS.gene006210.t1;Parent=MS.gene006210.t1
chr1.4 exon 77396189 77396830 77396189 ID=MS.gene006210.t1.exon2;Parent=MS.gene006210.t1
chr1.4 CDS 77396189 77396830 77396189 ID=cds.MS.gene006210.t1;Parent=MS.gene006210.t1
Gene Sequence

>MS.gene006210

ATGTGTTATAATCTGGTGCTTCAGCTCAAACATATCACAACAGTCCGATATTGCACACGTGTTCTAATCTTGAGCTTTAGATGCTACAGTGTTTCGTCCCTAACAAGATCGCTTTTCTCACCGTTTCCGTCACCGGCGTCGTTTCACGATCACGATTCTCACCGTTTCTTGCCGTTCCGACGTGATTCTCAGCCTTGCTCGCTTCTCCGACGTTATTTTCACCCTTCTCTCCGACGTGATTCACCCTTGATTCGTGCAATTCAGAAATTCATCTTGATTCGTGCGATTCAGAAATTCATCGCCGGCACCTCGATTCTCACCGTTTCTCGCTGCTGCAACTTGATTCTCATCCTTTCTTCGCTTCTCCGACGTGATTCTCACCTTTCTCTCCGACGTTATTCACTCCGACGTATTTCTCCGGTGAGTTATTCATTTATATGATTCAGTCTGTTAATTCGATGCAATCTGTGATATTTTTGCTAAATGCTACAAAACTGATGGTTGAATCATTGAAAATAAATTATTGTTGATTATATAAAATTACTGTTGAATCATTGAATTGAAAACTGATGCTTTAAAACTGAAGTAAACTGGATCATTGCAAATTATTGTTGTAGTAAGAATTTTACTTGATTGAATCATTGCAATGATTGAATCATTGCAATATGTGATATTTTAGTTCAGTTGATTACATCAGTTAATTTGATTCAATCTGTGATGTTTTTAACTCAATGTGAGTATTCAGCTGTGATTTTTTAACTCAATGCTATAAAACTGATGATTGAATCATTTAAAATAATTGTTGGAGTATGAGTGTTAGGGATAATTTGATAGCAATTTAGCTTATTACTCACCAAAATCATTTCCACAGGCCAATGATTTTGGAGTACAACTCACCAAAACCATATCCACAGGCCAATGGTTTTAGCATAGTTTTTCAGAGTTTTTCAGTAGTTTCAATTTATCATATCTAATGGTTTTTTTTTTGTTCTTAATAGTGTTTGTTGCTGTTTTCAATGGATTTGATATCAACTTCATCTGAGAGTGGACAATTGACGGTTGAAAATTCAGTTATTGATGCGGATAGTTCTCAATGTTACTCCTTTAGTGATAAAGAATCATGGAGGTCTTTGGTCTTTAAATCTATAAAAGAGATTGAAGATTTTTATTTTAATTATGCATATAACACTGGATTCTCTGTTAGGAGTATGTTGAAGTCCAAGAACAATTCACAAAATAAGAAATCGGATAAGGTACATTATGTGCGTTATGCTTGTAACAAAGAAGGTTTCAAGAAGGGAAGTCTGCTTAATCCTAAAAACAGGCCAACATGTGACAGTCCAGTTCTTGTTGAGTATGAGAAAGCTAAAGAAAAACCAGAGGAAAGTGTTGGTTTTAAAGCTGGAATATATTTGAAGTTGGATGAAGCGTTGAATGTCTATAAGATATATAGGTGGGAAGTTGATCACTGTCATCCATTACATAAACCAGAGCATTTGCGCTACTTGAGATCATTTCGAGAAGTAAATGAAGTTCAAGGACAACCTGCTTTAATAAATTCTAAAGCTGGAATGTCGATGAGAACATCTTATGAAGTGATGGGTCAAGGAGTTGGTGGCACGGAGAATCTTCCTTTTTGA
Protein sequence

>MS.gene006210.t1

MCYNLVLQLKHITTVRYCTRVLILSFRCYSVSSLTRSLFSPFPSPASFHDHDSHRFLPFRRDSQPCSLLRRYFHPSLRRDSPLIRAIQKFILIRAIQKFIAGTSILTVSRCCNLILILSSLLRRDSHLSLRRYSLRRISPCLLLFSMDLISTSSESGQLTVENSVIDADSSQCYSFSDKESWRSLVFKSIKEIEDFYFNYAYNTGFSVRSMLKSKNNSQNKKSDKVHYVRYACNKEGFKKGSLLNPKNRPTCDSPVLVEYEKAKEKPEESVGFKAGIYLKLDEALNVYKIYRWEVDHCHPLHKPEHLRYLRSFREVNEVQGQPALINSKAGMSMRTSYEVMGQGVGGTENLPF