AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52262

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52262.t1 MTR_7g077650 74.545 275 62 3 1 268 99 372 1.31e-140 400
MS.gene52262.t1 MTR_7g077660 74.359 273 61 5 2 268 99 368 1.46e-137 392
MS.gene52262.t1 MTR_7g077620 66.176 272 83 4 2 266 101 370 7.36e-123 355
MS.gene52262.t1 MTR_7g076110 54.839 279 111 6 4 268 36 313 4.78e-97 287
MS.gene52262.t1 MTR_7g076100 58.824 238 87 5 39 268 66 300 1.49e-87 263
MS.gene52262.t1 MTR_1g108740 46.442 267 118 12 6 266 97 344 3.61e-58 189
MS.gene52262.t1 MTR_5g038260 42.244 303 128 11 2 268 92 383 8.87e-55 181
MS.gene52262.t1 MTR_5g038230 42.336 274 93 10 2 244 90 329 1.23e-49 167
MS.gene52262.t1 MTR_1g064570 37.231 325 131 16 2 268 91 400 3.12e-43 151
MS.gene52262.t1 MTR_5g082770 44.651 215 90 7 4 204 88 287 3.41e-43 149
MS.gene52262.t1 MTR_7g076130 56.911 123 49 2 71 190 27 148 9.05e-40 135
MS.gene52262.t1 MTR_5g082780 38.793 232 108 10 15 232 1 212 4.48e-34 123
MS.gene52262.t1 MTR_1g016150 50.575 87 39 3 6 89 106 191 1.08e-18 82.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 50 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTATATTGTTAATGATTT+AGG 0.039594 7.4:-28473777 MS.gene52262:CDS
AAAGACCAAGCCAATCATTT+TGG 0.213196 7.4:-28474238 MS.gene52262:CDS
TTTATATTGTTAATGATTTA+GGG 0.247410 7.4:-28473776 MS.gene52262:CDS
CCATGATAACGACGTAGTTT+TGG 0.306817 7.4:+28474035 None:intergenic
AATGACCAAACTTGAGAGTT+TGG 0.311921 7.4:-28473883 MS.gene52262:CDS
AATTACAACTTTCCTACAAC+TGG 0.317321 7.4:-28473710 MS.gene52262:CDS
GTCTTCCAAACTCTCAAGTT+TGG 0.322441 7.4:+28473878 None:intergenic
GTTGCAGCAATTTACAAGTT+TGG 0.322860 7.4:-28474275 MS.gene52262:CDS
GGAGGTACACTATACTTAAA+AGG 0.322941 7.4:+28474377 None:intergenic
TTGTAGGAAAGTTGTAATTT+TGG 0.337038 7.4:+28473714 None:intergenic
CCATGGTTGGCTTGCATTAG+TGG 0.344716 7.4:-28474429 MS.gene52262:CDS
GGGTTCTACCACAACTTCAT+TGG 0.363398 7.4:-28473674 MS.gene52262:CDS
TTCGAGAGGTGGCAGACTAA+TGG 0.384467 7.4:+28474355 None:intergenic
AGCCTCTTGTTTCTCCAAGT+TGG 0.414433 7.4:-28473811 MS.gene52262:CDS
AAAACGTTGCATCCAGTTGT+AGG 0.414803 7.4:+28473698 None:intergenic
AATCATTGACCGGAGAAATA+TGG 0.417114 7.4:-28473995 MS.gene52262:CDS
TTGTTTCTCCAAGTTGGAAA+AGG 0.437802 7.4:-28473805 MS.gene52262:CDS
TCGAGAGGTGGCAGACTAAT+GGG 0.438780 7.4:+28474356 None:intergenic
ACTAGCCATCTTCTCATAGT+AGG 0.443005 7.4:+28474073 None:intergenic
GGTTCTACCACAACTTCATT+GGG 0.443765 7.4:-28473673 MS.gene52262:CDS
AGGAGGATTGTTTAGCTTGA+AGG 0.455047 7.4:+28474124 None:intergenic
GTTTGGGCTGTAGCCATGGT+TGG 0.500900 7.4:-28474442 MS.gene52262:CDS
CTACGCGAATCCAAAATGAT+TGG 0.502017 7.4:+28474228 None:intergenic
TAATCACTTGGATTTGTCAC+GGG 0.505018 7.4:+28474302 None:intergenic
CCAAAACTACGTCGTTATCA+TGG 0.509352 7.4:-28474035 MS.gene52262:CDS
TCTCATCAACCATATTTCTC+CGG 0.510997 7.4:+28473986 None:intergenic
CGAATCCAAAATGATTGGCT+TGG 0.520142 7.4:+28474233 None:intergenic
CCAGTTCCAATTTGAAAACG+TGG 0.529346 7.4:+28473931 None:intergenic
CAGTTCCAATTTGAAAACGT+GGG 0.532083 7.4:+28473932 None:intergenic
ACCTCTCGAATCTGTTTCCA+AGG 0.534304 7.4:-28474342 MS.gene52262:CDS
GAGATCTTTAACGTCAAGGA+TGG 0.538671 7.4:-28473750 MS.gene52262:CDS
GTCAGCAGACAAGGTAACCT+TGG 0.544724 7.4:+28474325 None:intergenic
GTTAGAGATCTTTAACGTCA+AGG 0.568886 7.4:-28473754 MS.gene52262:CDS
TGTCACGGGGTCAGCAGACA+AGG 0.572198 7.4:+28474316 None:intergenic
TTGGAACTGGATGCCGAGAG+TGG 0.572302 7.4:-28473918 MS.gene52262:CDS
ATGAGAAGATGCTTAATCGA+CGG 0.575214 7.4:-28473969 MS.gene52262:CDS
GGATCATTTGAGTCATCAGA+AGG 0.579857 7.4:+28474104 None:intergenic
ATAATCACTTGGATTTGTCA+CGG 0.582648 7.4:+28474301 None:intergenic
GTTTAGCTTGAAGGATACAA+TGG 0.589118 7.4:+28474133 None:intergenic
GCTGCAACCACATAATCACT+TGG 0.591162 7.4:+28474290 None:intergenic
TTCCAACTTGGAGAAACAAG+AGG 0.597328 7.4:+28473809 None:intergenic
GACAAATCCAAGTGATTATG+TGG 0.609021 7.4:-28474297 MS.gene52262:CDS
GCTCAATCCCAATGAAGTTG+TGG 0.625686 7.4:+28473666 None:intergenic
CCACTAATGCAAGCCAACCA+TGG 0.628857 7.4:+28474429 None:intergenic
TCATTTGAGTCATCAGAAGG+AGG 0.630870 7.4:+28474107 None:intergenic
TTGGAAACAGATTCGAGAGG+TGG 0.643460 7.4:+28474344 None:intergenic
AGTTCCAATTTGAAAACGTG+GGG 0.649411 7.4:+28473933 None:intergenic
AATCACTTGGATTTGTCACG+GGG 0.664381 7.4:+28474303 None:intergenic
AGAGGTGGCAGACTAATGGG+AGG 0.733529 7.4:+28474359 None:intergenic
ACCTTGGAAACAGATTCGAG+AGG 0.760909 7.4:+28474341 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATATTGTTAATGATTT+AGG - chr7.4:28474343-28474362 MS.gene52262:CDS 10.0%
!! TTTATATTGTTAATGATTTA+GGG - chr7.4:28474344-28474363 MS.gene52262:CDS 10.0%
!!! ACGAATATTGTGTTTTATAA+AGG - chr7.4:28473935-28473954 MS.gene52262:CDS 20.0%
! TTCTCATAGTAGGAAAAATT+AGG + chr7.4:28474040-28474059 None:intergenic 25.0%
!! TATTGTGTTTTATAAAGGCA+TGG - chr7.4:28473940-28473959 MS.gene52262:CDS 25.0%
!! TATTTTGTGAAATCATTGAC+CGG - chr7.4:28474115-28474134 MS.gene52262:CDS 25.0%
!! TTGTAGGAAAGTTGTAATTT+TGG + chr7.4:28474409-28474428 None:intergenic 25.0%
!!! ATTTTATTTGTCAGAAGTGT+TGG - chr7.4:28474268-28474287 MS.gene52262:CDS 25.0%
AATTACAACTTTCCTACAAC+TGG - chr7.4:28474410-28474429 MS.gene52262:CDS 30.0%
ATAATCACTTGGATTTGTCA+CGG + chr7.4:28473822-28473841 None:intergenic 30.0%
! AATTGAATCCTTTTCCAACT+TGG + chr7.4:28474326-28474345 None:intergenic 30.0%
! TTTTTCCTACTATGAGAAGA+TGG - chr7.4:28474042-28474061 MS.gene52262:CDS 30.0%
!!! CGTAGTTTTGGAATCATATA+TGG + chr7.4:28474076-28474095 None:intergenic 30.0%
AATCATTGACCGGAGAAATA+TGG - chr7.4:28474125-28474144 MS.gene52262:CDS 35.0%
AATGACCAAACTTGAGAGTT+TGG - chr7.4:28474237-28474256 MS.gene52262:CDS 35.0%
AGTTCCAATTTGAAAACGTG+GGG + chr7.4:28474190-28474209 None:intergenic 35.0%
ATGAGAAGATGCTTAATCGA+CGG - chr7.4:28474151-28474170 MS.gene52262:CDS 35.0%
CAGTTCCAATTTGAAAACGT+GGG + chr7.4:28474191-28474210 None:intergenic 35.0%
GACAAATCCAAGTGATTATG+TGG - chr7.4:28473823-28473842 MS.gene52262:CDS 35.0%
GTTAGAGATCTTTAACGTCA+AGG - chr7.4:28474366-28474385 MS.gene52262:CDS 35.0%
GTTGCAGCAATTTACAAGTT+TGG - chr7.4:28473845-28473864 MS.gene52262:CDS 35.0%
TAATCACTTGGATTTGTCAC+GGG + chr7.4:28473821-28473840 None:intergenic 35.0%
TCTCATCAACCATATTTCTC+CGG + chr7.4:28474137-28474156 None:intergenic 35.0%
! AAAGACCAAGCCAATCATTT+TGG - chr7.4:28473882-28473901 MS.gene52262:CDS 35.0%
! GGAGGTACACTATACTTAAA+AGG + chr7.4:28473746-28473765 None:intergenic 35.0%
! TTGTTTCTCCAAGTTGGAAA+AGG - chr7.4:28474315-28474334 MS.gene52262:CDS 35.0%
!! GTTTAGCTTGAAGGATACAA+TGG + chr7.4:28473990-28474009 None:intergenic 35.0%
!! TTGTTCAAGTTTTCCACTCT+CGG + chr7.4:28474218-28474237 None:intergenic 35.0%
AAAACGTTGCATCCAGTTGT+AGG + chr7.4:28474425-28474444 None:intergenic 40.0%
AATCACTTGGATTTGTCACG+GGG + chr7.4:28473820-28473839 None:intergenic 40.0%
ACTAGCCATCTTCTCATAGT+AGG + chr7.4:28474050-28474069 None:intergenic 40.0%
CCAAAACTACGTCGTTATCA+TGG - chr7.4:28474085-28474104 MS.gene52262:CDS 40.0%
CCAGTTCCAATTTGAAAACG+TGG + chr7.4:28474192-28474211 None:intergenic 40.0%
CTACGCGAATCCAAAATGAT+TGG + chr7.4:28473895-28473914 None:intergenic 40.0%
GAGATCTTTAACGTCAAGGA+TGG - chr7.4:28474370-28474389 MS.gene52262:CDS 40.0%
GGATCATTTGAGTCATCAGA+AGG + chr7.4:28474019-28474038 None:intergenic 40.0%
GGTTCTACCACAACTTCATT+GGG - chr7.4:28474447-28474466 MS.gene52262:CDS 40.0%
GTCTTCCAAACTCTCAAGTT+TGG + chr7.4:28474245-28474264 None:intergenic 40.0%
TCATTTGAGTCATCAGAAGG+AGG + chr7.4:28474016-28474035 None:intergenic 40.0%
TTCCAACTTGGAGAAACAAG+AGG + chr7.4:28474314-28474333 None:intergenic 40.0%
! ACAACTGGATGCAACGTTTT+TGG - chr7.4:28474425-28474444 MS.gene52262:CDS 40.0%
! CAAACCCCACGTTTTCAAAT+TGG - chr7.4:28474183-28474202 MS.gene52262:CDS 40.0%
! CAACTGGATGCAACGTTTTT+GGG - chr7.4:28474426-28474445 MS.gene52262:CDS 40.0%
! CCACGTTTTCAAATTGGAAC+TGG - chr7.4:28474189-28474208 MS.gene52262:CDS 40.0%
! CGAATCCAAAATGATTGGCT+TGG + chr7.4:28473890-28473909 None:intergenic 40.0%
!! AGGAGGATTGTTTAGCTTGA+AGG + chr7.4:28473999-28474018 None:intergenic 40.0%
!! CCATGATAACGACGTAGTTT+TGG + chr7.4:28474088-28474107 None:intergenic 40.0%
ACCTCTCGAATCTGTTTCCA+AGG - chr7.4:28473778-28473797 MS.gene52262:CDS 45.0%
ACCTTGGAAACAGATTCGAG+AGG + chr7.4:28473782-28473801 None:intergenic 45.0%
GCTGCAACCACATAATCACT+TGG + chr7.4:28473833-28473852 None:intergenic 45.0%
GGGTTCTACCACAACTTCAT+TGG - chr7.4:28474446-28474465 MS.gene52262:CDS 45.0%
TTGGAAACAGATTCGAGAGG+TGG + chr7.4:28473779-28473798 None:intergenic 45.0%
! AGCCTCTTGTTTCTCCAAGT+TGG - chr7.4:28474309-28474328 MS.gene52262:CDS 45.0%
!! TTTTGTTTGGGCTGTAGCCA+TGG - chr7.4:28473674-28473693 MS.gene52262:CDS 45.0%
CCACTAATGCAAGCCAACCA+TGG + chr7.4:28473694-28473713 None:intergenic 50.0%
GTCAGCAGACAAGGTAACCT+TGG + chr7.4:28473798-28473817 None:intergenic 50.0%
TCGAGAGGTGGCAGACTAAT+GGG + chr7.4:28473767-28473786 None:intergenic 50.0%
TTCGAGAGGTGGCAGACTAA+TGG + chr7.4:28473768-28473787 None:intergenic 50.0%
!! CCATGGTTGGCTTGCATTAG+TGG - chr7.4:28473691-28473710 MS.gene52262:CDS 50.0%
AGAGGTGGCAGACTAATGGG+AGG + chr7.4:28473764-28473783 None:intergenic 55.0%
GTTTGGGCTGTAGCCATGGT+TGG - chr7.4:28473678-28473697 MS.gene52262:CDS 55.0%
TTGGAACTGGATGCCGAGAG+TGG - chr7.4:28474202-28474221 MS.gene52262:CDS 55.0%
TGTCACGGGGTCAGCAGACA+AGG + chr7.4:28473807-28473826 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 28473668 28474474 28473668 ID=MS.gene52262
chr7.4 mRNA 28473668 28474474 28473668 ID=MS.gene52262.t1;Parent=MS.gene52262
chr7.4 exon 28473668 28474474 28473668 ID=MS.gene52262.t1.exon1;Parent=MS.gene52262.t1
chr7.4 CDS 28473668 28474474 28473668 ID=cds.MS.gene52262.t1;Parent=MS.gene52262.t1
Gene Sequence

>MS.gene52262

ATGAAATTTTGTTTGGGCTGTAGCCATGGTTGGCTTGCATTAGTGGATGATAACGATGTCATTACTCTAGTGAATCCTTTTAAGTATAGTGTACCTCCCATTAGTCTGCCACCTCTCGAATCTGTTTCCAAGGTTACCTTGTCTGCTGACCCCGTGACAAATCCAAGTGATTATGTGGTTGCAGCAATTTACAAGTTTGGTTATCTCGCTTTCAAAAGACCAAGCCAATCATTTTGGATTCGCGTAGACACAAATGAATTTACTTTCACGAATATTGTGTTTTATAAAGGCATGGTATTTGCTGATAGCTGCAGAGATACCATTGTATCCTTCAAGCTAAACAATCCTCCTTCTGATGACTCAAATGATCCTAATTTTTCCTACTATGAGAAGATGGCTAGTACTCCATATATGATTCCAAAACTACGTCGTTATCATGGACTTGCTTATTTTGTGAAATCATTGACCGGAGAAATATGGTTGATGAGAAGATGCTTAATCGACGGTTTTTCACTCAAACCCCACGTTTTCAAATTGGAACTGGATGCCGAGAGTGGAAAACTTGAACAAATGACCAAACTTGAGAGTTTGGAAGACAACATTTTATTTGTCAGAAGTGTTGGTGATTCAATTTCTGTGTCAGCCTCTTGTTTCTCCAAGTTGGAAAAGGATTCAATTTATATTGTTAATGATTTAGGGTTAGAGATCTTTAACGTCAAGGATGGAAGCTTTCAGAGACCAAAATTACAACTTTCCTACAACTGGATGCAACGTTTTTGGGTTCTACCACAACTTCATTGGGATTGA
Protein sequence

>MS.gene52262.t1

MKFCLGCSHGWLALVDDNDVITLVNPFKYSVPPISLPPLESVSKVTLSADPVTNPSDYVVAAIYKFGYLAFKRPSQSFWIRVDTNEFTFTNIVFYKGMVFADSCRDTIVSFKLNNPPSDDSNDPNFSYYEKMASTPYMIPKLRRYHGLAYFVKSLTGEIWLMRRCLIDGFSLKPHVFKLELDAESGKLEQMTKLESLEDNILFVRSVGDSISVSASCFSKLEKDSIYIVNDLGLEIFNVKDGSFQRPKLQLSYNWMQRFWVLPQLHWD