AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053599


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053599.t1 MTR_4g093150 92.958 213 8 1 31 236 1 213 8.40e-140 390
MS.gene053599.t1 MTR_2g009770 52.903 155 72 1 61 214 98 252 4.65e-36 129
MS.gene053599.t1 MTR_1g054835 36.585 123 76 1 78 198 42 164 3.65e-13 68.6
MS.gene053599.t1 MTR_1g070350 34.167 120 77 1 73 192 509 626 2.13e-12 66.6
MS.gene053599.t1 MTR_5g078300 38.750 80 49 0 91 170 612 691 1.22e-11 64.3
MS.gene053599.t1 MTR_4g107310 31.250 208 122 7 43 234 262 464 3.38e-11 62.8
MS.gene053599.t1 MTR_0168s0060 33.333 132 85 1 75 203 307 438 6.06e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053599.t1 AT5G16720 37.000 100 63 0 99 198 360 459 3.72e-15 74.7
MS.gene053599.t1 AT1G70750 34.783 115 72 1 96 207 410 524 2.91e-14 72.0
MS.gene053599.t1 AT1G74830 37.500 96 60 0 99 194 305 400 3.37e-14 71.6
MS.gene053599.t1 AT1G18265 52.273 88 42 0 89 176 183 270 4.87e-14 70.1
MS.gene053599.t1 AT5G06560 35.000 100 65 0 99 198 74 173 2.48e-12 66.2

Find 53 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAATCCCATCTTTGGAAAA+TGG 0.168151 4.3:-21085943 MS.gene053599:CDS
TGAGTCGAAGAATTGGTATT+AGG 0.240330 4.3:+21085913 None:intergenic
TCCCACAATTCGTTTATGTT+TGG 0.317458 4.3:-21085995 MS.gene053599:CDS
GAAGAACTCAAGCAATATCT+TGG 0.374861 4.3:-21085511 MS.gene053599:CDS
GAGTCGAAGAATTGGTATTA+GGG 0.386407 4.3:+21085914 None:intergenic
TGATGAAGTGATCGAGTCTT+TGG 0.389665 4.3:-21085599 MS.gene053599:CDS
AAATCCCATCTTTGGAAAAT+GGG 0.392542 4.3:-21085942 MS.gene053599:CDS
GAAAGCTAATGCGGCGTTTG+CGG 0.398717 4.3:-21085764 MS.gene053599:CDS
AAGAACTCAAGCAATATCTT+GGG 0.416257 4.3:-21085510 MS.gene053599:CDS
TCTCTTCTGAGTCGAAGAAT+TGG 0.418771 4.3:+21085906 None:intergenic
GAAGAGATTGAATGGTCGTT+TGG 0.421960 4.3:-21085890 MS.gene053599:CDS
ATGTTTGGAAAACTTTGTTT+TGG 0.423857 4.3:-21085980 MS.gene053599:CDS
GTGTGTTGGAAGAGCAGTTG+AGG 0.428235 4.3:-21085543 MS.gene053599:CDS
TTCCAAACATAAACGAATTG+TGG 0.432068 4.3:+21085993 None:intergenic
TCCAAACATAAACGAATTGT+GGG 0.444313 4.3:+21085994 None:intergenic
AAGCAATATCTTGGGGAGGA+TGG 0.455312 4.3:-21085502 MS.gene053599:CDS
AGGCAATGGCGATGATTCTC+AGG 0.455510 4.3:-21085699 MS.gene053599:CDS
TGAATGGTCGTTTGGAAGAT+CGG 0.461435 4.3:-21085882 MS.gene053599:CDS
GGCTTCTTCATCTGCGGAAG+AGG 0.462933 4.3:-21085719 MS.gene053599:CDS
GTAGTTAGCTCTTCTGAAAA+CGG 0.463530 4.3:-21085415 MS.gene053599:CDS
GGCGTTTGCGGAGCTTGATA+AGG 0.464641 4.3:-21085752 MS.gene053599:CDS
TCAAGATTCTTCACTTCGGT+TGG 0.466081 4.3:-21086062 MS.gene053599:CDS
TCTCGAGGCATGAATCTCAT+AGG 0.486643 4.3:-21085567 MS.gene053599:CDS
TGTGTTGGAAGAGCAGTTGA+GGG 0.487289 4.3:-21085542 MS.gene053599:CDS
AGCAATATCTTGGGGAGGAT+GGG 0.488013 4.3:-21085501 MS.gene053599:CDS
AAGCTGATGTTAGTAGAGAT+AGG 0.499821 4.3:-21085465 MS.gene053599:CDS
GAAAGATGATAGTGAAATGC+AGG 0.502055 4.3:-21085851 MS.gene053599:CDS
TCGACTCAGAAGAGATTGAA+TGG 0.516087 4.3:-21085898 MS.gene053599:CDS
TTCATCTGCGGAAGAGGCAA+TGG 0.519311 4.3:-21085713 MS.gene053599:CDS
TACTAACATCAGCTTCAAGT+TGG 0.521972 4.3:+21085473 None:intergenic
CACAACCTTGGAAACTTACA+AGG 0.522214 4.3:+21085384 None:intergenic
AGCGAATCAATTCCGCAGAA+TGG 0.525489 4.3:-21085644 MS.gene053599:CDS
TGGTCGTTTGGAAGATCGGT+TGG 0.527702 4.3:-21085878 MS.gene053599:CDS
TCAAACACCTCATCCACATC+AGG 0.540118 4.3:+21085826 None:intergenic
TGTTTCAAGATTCTTCACTT+CGG 0.555363 4.3:-21086066 MS.gene053599:CDS
AAGTGATCGAGTCTTTGGAA+TGG 0.572333 4.3:-21085594 MS.gene053599:CDS
TGAATCTCATAGGAGTGTGT+TGG 0.573968 4.3:-21085557 MS.gene053599:CDS
GTTTGGAAGATCGGTTGGAA+AGG 0.591359 4.3:-21085873 MS.gene053599:CDS
TTGCGGAGCTTGATAAGGAA+CGG 0.610513 4.3:-21085747 MS.gene053599:CDS
GCAGGTTCCTGATGTGGATG+AGG 0.610761 4.3:-21085833 MS.gene053599:CDS
CTTTGGAATGGACGATCTCG+AGG 0.612708 4.3:-21085582 MS.gene053599:CDS
AGTTGATAAAGATTGAGCGC+AGG 0.614343 4.3:-21085786 MS.gene053599:CDS
ACCTTGGAAACTTACAAGGT+CGG 0.615530 4.3:+21085388 None:intergenic
ACTTCTGTTCAGCCATTCTG+CGG 0.620830 4.3:+21085632 None:intergenic
TGAAATGCAGGTTCCTGATG+TGG 0.621860 4.3:-21085839 MS.gene053599:CDS
AAAATCACAGAGAAAACGTA+GGG 0.635297 4.3:+21086026 None:intergenic
GCTTCAGAGTGAGAAGAGCT+CGG 0.636966 4.3:-21085677 MS.gene053599:CDS
GCTTGATAAGGAACGGACAG+CGG 0.649607 4.3:-21085740 MS.gene053599:CDS
TGAGCGCAGGAAAGCTAATG+CGG 0.653423 4.3:-21085773 MS.gene053599:CDS
AGAACTCAAGCAATATCTTG+GGG 0.655002 4.3:-21085509 MS.gene053599:CDS
ACTCAAGCAATATCTTGGGG+AGG 0.657753 4.3:-21085506 MS.gene053599:CDS
GACAGCGGCTTCTTCATCTG+CGG 0.673445 4.3:-21085725 MS.gene053599:CDS
CAAAATCACAGAGAAAACGT+AGG 0.688372 4.3:+21086025 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAAGAAAAAAATCCCATCTT+TGG - chr4.3:21085536-21085555 MS.gene053599:CDS 25.0%
!!! ATGTTTGGAAAACTTTGTTT+TGG - chr4.3:21085506-21085525 MS.gene053599:CDS 25.0%
AAAATCACAGAGAAAACGTA+GGG + chr4.3:21085463-21085482 None:intergenic 30.0%
AAGAACTCAAGCAATATCTT+GGG - chr4.3:21085976-21085995 MS.gene053599:CDS 30.0%
TCCAAACATAAACGAATTGT+GGG + chr4.3:21085495-21085514 None:intergenic 30.0%
TGTTTCAAGATTCTTCACTT+CGG - chr4.3:21085420-21085439 MS.gene053599:CDS 30.0%
TTCCAAACATAAACGAATTG+TGG + chr4.3:21085496-21085515 None:intergenic 30.0%
! AAAATCCCATCTTTGGAAAA+TGG - chr4.3:21085543-21085562 MS.gene053599:CDS 30.0%
! AAATCCCATCTTTGGAAAAT+GGG - chr4.3:21085544-21085563 MS.gene053599:CDS 30.0%
AAGCTGATGTTAGTAGAGAT+AGG - chr4.3:21086021-21086040 MS.gene053599:CDS 35.0%
AGAACTCAAGCAATATCTTG+GGG - chr4.3:21085977-21085996 MS.gene053599:CDS 35.0%
CAAAATCACAGAGAAAACGT+AGG + chr4.3:21085464-21085483 None:intergenic 35.0%
GAAGAACTCAAGCAATATCT+TGG - chr4.3:21085975-21085994 MS.gene053599:CDS 35.0%
GAGTCGAAGAATTGGTATTA+GGG + chr4.3:21085575-21085594 None:intergenic 35.0%
TACTAACATCAGCTTCAAGT+TGG + chr4.3:21086016-21086035 None:intergenic 35.0%
TCCCACAATTCGTTTATGTT+TGG - chr4.3:21085491-21085510 MS.gene053599:CDS 35.0%
TGAGTCGAAGAATTGGTATT+AGG + chr4.3:21085576-21085595 None:intergenic 35.0%
! CTACGTTTTCTCTGTGATTT+TGG - chr4.3:21085462-21085481 MS.gene053599:CDS 35.0%
! GAAAGATGATAGTGAAATGC+AGG - chr4.3:21085635-21085654 MS.gene053599:CDS 35.0%
! GTAGTTAGCTCTTCTGAAAA+CGG - chr4.3:21086071-21086090 MS.gene053599:CDS 35.0%
GAAGAGATTGAATGGTCGTT+TGG - chr4.3:21085596-21085615 MS.gene053599:CDS 40.0%
TCAAGATTCTTCACTTCGGT+TGG - chr4.3:21085424-21085443 MS.gene053599:CDS 40.0%
TCGACTCAGAAGAGATTGAA+TGG - chr4.3:21085588-21085607 MS.gene053599:CDS 40.0%
TCTCTTCTGAGTCGAAGAAT+TGG + chr4.3:21085583-21085602 None:intergenic 40.0%
TGAATGGTCGTTTGGAAGAT+CGG - chr4.3:21085604-21085623 MS.gene053599:CDS 40.0%
TGATGAAGTGATCGAGTCTT+TGG - chr4.3:21085887-21085906 MS.gene053599:CDS 40.0%
! AAGTGATCGAGTCTTTGGAA+TGG - chr4.3:21085892-21085911 MS.gene053599:CDS 40.0%
! CACTTCGGTTGGCATTTTAA+GGG - chr4.3:21085435-21085454 MS.gene053599:CDS 40.0%
! GAGACCCATTTTCCAAAGAT+GGG + chr4.3:21085551-21085570 None:intergenic 40.0%
! TCACTTCGGTTGGCATTTTA+AGG - chr4.3:21085434-21085453 MS.gene053599:CDS 40.0%
! TGAATCTCATAGGAGTGTGT+TGG - chr4.3:21085929-21085948 MS.gene053599:CDS 40.0%
! TGAGACCCATTTTCCAAAGA+TGG + chr4.3:21085552-21085571 None:intergenic 40.0%
!! AGTTGATAAAGATTGAGCGC+AGG - chr4.3:21085700-21085719 MS.gene053599:CDS 40.0%
AAGCAATATCTTGGGGAGGA+TGG - chr4.3:21085984-21086003 MS.gene053599:CDS 45.0%
ACTCAAGCAATATCTTGGGG+AGG - chr4.3:21085980-21085999 MS.gene053599:CDS 45.0%
ACTTCTGTTCAGCCATTCTG+CGG + chr4.3:21085857-21085876 None:intergenic 45.0%
AGCAATATCTTGGGGAGGAT+GGG - chr4.3:21085985-21086004 MS.gene053599:CDS 45.0%
AGCGAATCAATTCCGCAGAA+TGG - chr4.3:21085842-21085861 MS.gene053599:CDS 45.0%
GTTTGGAAGATCGGTTGGAA+AGG - chr4.3:21085613-21085632 MS.gene053599:CDS 45.0%
TCAAACACCTCATCCACATC+AGG + chr4.3:21085663-21085682 None:intergenic 45.0%
TCTCGAGGCATGAATCTCAT+AGG - chr4.3:21085919-21085938 MS.gene053599:CDS 45.0%
TGAAATGCAGGTTCCTGATG+TGG - chr4.3:21085647-21085666 MS.gene053599:CDS 45.0%
TGTGTTGGAAGAGCAGTTGA+GGG - chr4.3:21085944-21085963 MS.gene053599:CDS 45.0%
TTGCGGAGCTTGATAAGGAA+CGG - chr4.3:21085739-21085758 MS.gene053599:CDS 45.0%
AGGCAATGGCGATGATTCTC+AGG - chr4.3:21085787-21085806 MS.gene053599:CDS 50.0%
GAAAGCTAATGCGGCGTTTG+CGG - chr4.3:21085722-21085741 MS.gene053599:CDS 50.0%
GCTTCAGAGTGAGAAGAGCT+CGG - chr4.3:21085809-21085828 MS.gene053599:CDS 50.0%
GCTTGATAAGGAACGGACAG+CGG - chr4.3:21085746-21085765 MS.gene053599:CDS 50.0%
GTGTGTTGGAAGAGCAGTTG+AGG - chr4.3:21085943-21085962 MS.gene053599:CDS 50.0%
TGAGCGCAGGAAAGCTAATG+CGG - chr4.3:21085713-21085732 MS.gene053599:CDS 50.0%
TGGTCGTTTGGAAGATCGGT+TGG - chr4.3:21085608-21085627 MS.gene053599:CDS 50.0%
TTCATCTGCGGAAGAGGCAA+TGG - chr4.3:21085773-21085792 MS.gene053599:CDS 50.0%
!! CTTTGGAATGGACGATCTCG+AGG - chr4.3:21085904-21085923 MS.gene053599:CDS 50.0%
GACAGCGGCTTCTTCATCTG+CGG - chr4.3:21085761-21085780 MS.gene053599:CDS 55.0%
GCAGGTTCCTGATGTGGATG+AGG - chr4.3:21085653-21085672 MS.gene053599:CDS 55.0%
GGCGTTTGCGGAGCTTGATA+AGG - chr4.3:21085734-21085753 MS.gene053599:CDS 55.0%
GGCTTCTTCATCTGCGGAAG+AGG - chr4.3:21085767-21085786 MS.gene053599:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 21085399 21086109 21085399 ID=MS.gene053599
chr4.3 mRNA 21085399 21086109 21085399 ID=MS.gene053599.t1;Parent=MS.gene053599
chr4.3 exon 21085399 21086109 21085399 ID=MS.gene053599.t1.exon1;Parent=MS.gene053599.t1
chr4.3 CDS 21085399 21086109 21085399 ID=cds.MS.gene053599.t1;Parent=MS.gene053599.t1
Gene Sequence

>MS.gene053599

ATGTTTTTGATGTTAGGCTTTTGTTTCAAGATTCTTCACTTCGGTTGGCATTTTAAGGGTGCCCTACGTTTTCTCTGTGATTTTGGACGCATTCCCACAATTCGTTTATGTTTGGAAAACTTTGTTTTGGAAGTTTCTAAGAAAAAAATCCCATCTTTGGAAAATGGGTCTCACCCTAATACCAATTCTTCGACTCAGAAGAGATTGAATGGTCGTTTGGAAGATCGGTTGGAAAGGAAAGATGATAGTGAAATGCAGGTTCCTGATGTGGATGAGGTGTTTGATGTAATCACTCTGAGAAAGTTGATAAAGATTGAGCGCAGGAAAGCTAATGCGGCGTTTGCGGAGCTTGATAAGGAACGGACAGCGGCTTCTTCATCTGCGGAAGAGGCAATGGCGATGATTCTCAGGCTTCAGAGTGAGAAGAGCTCGGCTGAAATTCAAGCGAATCAATTCCGCAGAATGGCTGAACAGAAGTTAGAGTATGATGATGAAGTGATCGAGTCTTTGGAATGGACGATCTCGAGGCATGAATCTCATAGGAGTGTGTTGGAAGAGCAGTTGAGGGTTTATAGAGAAGAACTCAAGCAATATCTTGGGGAGGATGGGATAAACCAACTTGAAGCTGATGTTAGTAGAGATAGGAGTTTTGAGAATGAAGCAGTTGATTCTGTAGTTAGCTCTTCTGAAAACGGATCACCGACCTTGTAA

Protein sequence

>MS.gene053599.t1

MFLMLGFCFKILHFGWHFKGALRFLCDFGRIPTIRLCLENFVLEVSKKKIPSLENGSHPNTNSSTQKRLNGRLEDRLERKDDSEMQVPDVDEVFDVITLRKLIKIERRKANAAFAELDKERTAASSSAEEAMAMILRLQSEKSSAEIQANQFRRMAEQKLEYDDEVIESLEWTISRHESHRSVLEEQLRVYREELKQYLGEDGINQLEADVSRDRSFENEAVDSVVSSSENGSPTL