AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene058722


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene058722.t1 MTR_7g079870 97.674 172 3 1 1 171 1 172 4.39e-122 341
MS.gene058722.t1 MTR_7g021660 41.139 158 79 5 1 156 1 146 2.49e-28 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene058722.t1 AT5G16490 48.052 154 64 6 1 152 1 140 6.67e-31 109
MS.gene058722.t1 AT1G27380 34.416 154 69 4 1 129 1 147 2.05e-16 72.8

Find 42 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGGAGATGTTTCATGTTT+TGG 0.253272 7.4:+26263134 None:intergenic
GATGAAATGGACATGGAAAT+AGG 0.297095 7.4:-26263296 MS.gene058722:CDS
GTCATTCTTCCTTTCTCAGC+TGG 0.335866 7.4:-26264849 MS.gene058722:CDS
TTGAAGGATAGGTTAGGCTT+TGG 0.378556 7.4:+26263954 None:intergenic
GGACTTAGAAGAAGATGAAA+TGG 0.383098 7.4:-26263309 MS.gene058722:CDS
AGAGAATCCCATCCCCTCAT+TGG 0.414199 7.4:+26263200 None:intergenic
TCAATTAATCAAGCAATAGA+AGG 0.417530 7.4:+26263101 None:intergenic
GCCTTTGAACAACTTGTTGA+AGG 0.426359 7.4:+26263938 None:intergenic
ATGAAATGGACATGGAAATA+GGG 0.448347 7.4:-26263295 MS.gene058722:CDS
GAGGATTCAGAGACTTTGTC+TGG 0.450700 7.4:-26264017 MS.gene058722:CDS
AATAGAAGGCATGATGTTGA+TGG 0.460773 7.4:+26263115 None:intergenic
AACATGTGACACACATTGGT+TGG 0.460995 7.4:-26263256 MS.gene058722:CDS
TGAACAACTTGTTGAAGGAT+AGG 0.476710 7.4:+26263943 None:intergenic
TGTGGTGAATTAGTCTCTGC+AGG 0.479443 7.4:+26264771 None:intergenic
GAGAATCCCATCCCCTCATT+GGG 0.490983 7.4:+26263201 None:intergenic
ATAAGATTAGAAGGATCTAA+AGG 0.496998 7.4:-26264044 MS.gene058722:intron
CTCATGACCCAATGAGGGGA+TGG 0.511835 7.4:-26263208 MS.gene058722:CDS
GAGGCTACAGAGAGAAGCTC+AGG 0.512955 7.4:+26263170 None:intergenic
AGAAAGTATGAGACAGAGAA+TGG 0.521813 7.4:-26264880 None:intergenic
TCCTTCAACAAGTTGTTCAA+AGG 0.523718 7.4:-26263939 MS.gene058722:CDS
GTCACATGTTGTACATCTGT+TGG 0.530235 7.4:+26263269 None:intergenic
TCACATGTTGTACATCTGTT+GGG 0.533947 7.4:+26263270 None:intergenic
GAGATACAACCAGCTGAGAA+AGG 0.537814 7.4:+26264840 None:intergenic
TCTGAGGCTAGTGTTGCTGT+TGG 0.544954 7.4:-26264819 MS.gene058722:CDS
AAAGTATGAAGAATTCTTTG+AGG 0.549357 7.4:-26263992 MS.gene058722:CDS
ACATGTGACACACATTGGTT+GGG 0.559436 7.4:-26263255 MS.gene058722:CDS
TCATGACCCAATGAGGGGAT+GGG 0.567190 7.4:-26263207 MS.gene058722:CDS
CTCAGCTGGTTGTATCTCTG+AGG 0.578716 7.4:-26264835 MS.gene058722:CDS
ATAGAAGGCATGATGTTGAT+GGG 0.591363 7.4:+26263116 None:intergenic
AACTTGTTGAAGGATAGGTT+AGG 0.593453 7.4:+26263948 None:intergenic
GCTACAGAGAGAAGCTCAGG+AGG 0.604067 7.4:+26263173 None:intergenic
TGGGTCATGAGCAGCACATG+AGG 0.609467 7.4:+26263220 None:intergenic
GTGACACACATTGGTTGGGA+TGG 0.614285 7.4:-26263251 MS.gene058722:CDS
TGCTGCTCATGACCCAATGA+GGG 0.614602 7.4:-26263213 MS.gene058722:CDS
TAATTCAGTGGAGAAAGAAG+AGG 0.620308 7.4:-26263330 MS.gene058722:intron
GTATGAGACAGAGAATGGAA+AGG 0.630032 7.4:-26264875 MS.gene058722:CDS
AGAAGAAGATGAAATGGACA+TGG 0.630572 7.4:-26263303 MS.gene058722:CDS
AGAAGGATCTAAAGGAGTCG+AGG 0.632435 7.4:-26264036 MS.gene058722:CDS
AAGAGACTTATTGCATCATG+TGG 0.639239 7.4:+26264753 None:intergenic
GTGCTGCTCATGACCCAATG+AGG 0.658635 7.4:-26263214 MS.gene058722:CDS
GCTGCTCATGACCCAATGAG+GGG 0.751010 7.4:-26263212 MS.gene058722:CDS
GTACAACATGTGACACACAT+TGG 0.753481 7.4:-26263260 MS.gene058722:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATAATAAAAATAAAATTGT+AGG - chr7.4:26264534-26264553 MS.gene058722:intron 10.0%
!! TCTTTGTAAATAAAAATATA+TGG - chr7.4:26264581-26264600 MS.gene058722:intron 10.0%
!!! ATTCTAAAAATGTTTATTTA+GGG + chr7.4:26264258-26264277 None:intergenic 10.0%
!! AATATATGTTTAATAGAGAA+TGG + chr7.4:26263704-26263723 None:intergenic 15.0%
!!! CATTCTAAAAATGTTTATTT+AGG + chr7.4:26264259-26264278 None:intergenic 15.0%
!!! TTCTCTAATTTTTAATTAGT+TGG - chr7.4:26263845-26263864 MS.gene058722:intron 15.0%
!!! TTTTTCTTTTTTGAAAGTTA+CGG + chr7.4:26263814-26263833 None:intergenic 15.0%
!!! TTTTTTTATGTTTAATTCAG+TGG - chr7.4:26264640-26264659 MS.gene058722:intron 15.0%
!! ATGTATAAAAAAAAATGTCG+TGG - chr7.4:26263758-26263777 MS.gene058722:intron 20.0%
!! TACTAGCTAAATAAAACTAA+GGG + chr7.4:26263336-26263355 None:intergenic 20.0%
!! TGTATAAAAAAAAATGTCGT+GGG - chr7.4:26263759-26263778 MS.gene058722:intron 20.0%
!! TTACTAGCTAAATAAAACTA+AGG + chr7.4:26263337-26263356 None:intergenic 20.0%
!!! ATAAAATTGGGTTTAAGATA+AGG + chr7.4:26264401-26264420 None:intergenic 20.0%
! AAAGTATGAAGAATTCTTTG+AGG - chr7.4:26263990-26264009 MS.gene058722:CDS 25.0%
! ATAAGATTAGAAGGATCTAA+AGG - chr7.4:26263938-26263957 MS.gene058722:CDS 25.0%
! ATACAATAAATTTGACCATC+GGG + chr7.4:26263661-26263680 None:intergenic 25.0%
! CATACAATAAATTTGACCAT+CGG + chr7.4:26263662-26263681 None:intergenic 25.0%
! GATATCATAGTAAAAGAGAT+AGG + chr7.4:26263255-26263274 None:intergenic 25.0%
! GATGATATGATAAGATTAGA+AGG - chr7.4:26263929-26263948 MS.gene058722:CDS 25.0%
! GTATAAAAAAAAATGTCGTG+GGG - chr7.4:26263760-26263779 MS.gene058722:intron 25.0%
! TGAATTTAGTCATTCGATAA+AGG - chr7.4:26263421-26263440 MS.gene058722:intron 25.0%
! TGTTTAATAGAGAATGGAAA+AGG + chr7.4:26263698-26263717 None:intergenic 25.0%
!! AAGAACTTTTCTCAATTGTT+TGG - chr7.4:26264070-26264089 MS.gene058722:intron 25.0%
!! ATGGAAGTCTTAATTTTTCA+TGG - chr7.4:26264600-26264619 MS.gene058722:intron 25.0%
!! GTTTTCTCATACTAATTTTG+TGG - chr7.4:26264111-26264130 MS.gene058722:intron 25.0%
!! TAAACCCAATTTTATAGAGT+CGG - chr7.4:26264406-26264425 MS.gene058722:intron 25.0%
!! TTTAAGATAAGGAAAGTTAG+AGG + chr7.4:26264390-26264409 None:intergenic 25.0%
ATGAAATGGACATGGAAATA+GGG - chr7.4:26264687-26264706 MS.gene058722:intron 30.0%
CATTCCGACTCTATAAAATT+GGG + chr7.4:26264413-26264432 None:intergenic 30.0%
CTCGATCATCTCAATATATA+AGG - chr7.4:26264290-26264309 MS.gene058722:intron 30.0%
GAAGAAATACGTGTCAATAA+TGG - chr7.4:26264330-26264349 MS.gene058722:intron 30.0%
TACGGAACGAAATAAAAACA+CGG + chr7.4:26264200-26264219 None:intergenic 30.0%
TATCAATCAACTTCATCCAA+CGG + chr7.4:26263579-26263598 None:intergenic 30.0%
TCATCTCAATATATAAGGTG+TGG - chr7.4:26264295-26264314 MS.gene058722:intron 30.0%
TCTCATACCTATACTTGTTT+GGG + chr7.4:26263736-26263755 None:intergenic 30.0%
TTCTCATACCTATACTTGTT+TGG + chr7.4:26263737-26263756 None:intergenic 30.0%
TTGCGATCAAAACTTCTATA+CGG + chr7.4:26264218-26264237 None:intergenic 30.0%
AAGAGACTTATTGCATCATG+TGG + chr7.4:26263232-26263251 None:intergenic 35.0%
AGAAGAAGATGAAATGGACA+TGG - chr7.4:26264679-26264698 MS.gene058722:intron 35.0%
AGATAAGGAAAGTTAGAGGT+AGG + chr7.4:26264386-26264405 None:intergenic 35.0%
ATAAGGAAAGTTAGAGGTAG+GGG + chr7.4:26264384-26264403 None:intergenic 35.0%
CCATTCCGACTCTATAAAAT+TGG + chr7.4:26264414-26264433 None:intergenic 35.0%
CTCATACCTATACTTGTTTG+GGG + chr7.4:26263735-26263754 None:intergenic 35.0%
GATAAGGAAAGTTAGAGGTA+GGG + chr7.4:26264385-26264404 None:intergenic 35.0%
GATGAAATGGACATGGAAAT+AGG - chr7.4:26264686-26264705 MS.gene058722:intron 35.0%
GGACTTAGAAGAAGATGAAA+TGG - chr7.4:26264673-26264692 MS.gene058722:intron 35.0%
TAATTCAGTGGAGAAAGAAG+AGG - chr7.4:26264652-26264671 MS.gene058722:intron 35.0%
TAGTCATTCGATAAAGGACT+TGG - chr7.4:26263427-26263446 MS.gene058722:intron 35.0%
TATGACAACATACCACCATA+TGG + chr7.4:26263508-26263527 None:intergenic 35.0%
TCACATGTTGTACATCTGTT+GGG + chr7.4:26264715-26264734 None:intergenic 35.0%
TCATACCTATACTTGTTTGG+GGG + chr7.4:26263734-26263753 None:intergenic 35.0%
TCCTTCAACAAGTTGTTCAA+AGG - chr7.4:26264043-26264062 MS.gene058722:intron 35.0%
TTGAGATGATCGAGACTAAA+AGG + chr7.4:26264284-26264303 None:intergenic 35.0%
! AATAGAAGGCATGATGTTGA+TGG + chr7.4:26264870-26264889 None:intergenic 35.0%
! ATAGAAGGCATGATGTTGAT+GGG + chr7.4:26264869-26264888 None:intergenic 35.0%
! ATGGGAGATGTTTCATGTTT+TGG + chr7.4:26264851-26264870 None:intergenic 35.0%
! CCAATTTTATAGAGTCGGAA+TGG - chr7.4:26264411-26264430 MS.gene058722:intron 35.0%
!! AACTTGTTGAAGGATAGGTT+AGG + chr7.4:26264037-26264056 None:intergenic 35.0%
!! TGAACAACTTGTTGAAGGAT+AGG + chr7.4:26264042-26264061 None:intergenic 35.0%
!! TTTTGGCTGTAAAGATTGAG+AGG + chr7.4:26264834-26264853 None:intergenic 35.0%
AAAGTTAGAGGTAGGGGAAA+TGG + chr7.4:26264378-26264397 None:intergenic 40.0%
AACATGTGACACACATTGGT+TGG - chr7.4:26264726-26264745 MS.gene058722:intron 40.0%
GTACAACATGTGACACACAT+TGG - chr7.4:26264722-26264741 MS.gene058722:intron 40.0%
GTCACATGTTGTACATCTGT+TGG + chr7.4:26264716-26264735 None:intergenic 40.0%
TTCTTCCCCCAAACAAGTAT+AGG - chr7.4:26263726-26263745 MS.gene058722:intron 40.0%
TTGAAGGATAGGTTAGGCTT+TGG + chr7.4:26264031-26264050 None:intergenic 40.0%
! ACATGTGACACACATTGGTT+GGG - chr7.4:26264727-26264746 MS.gene058722:intron 40.0%
!! AAGAAAGTGTTGCCATATGG+TGG - chr7.4:26263493-26263512 MS.gene058722:intron 40.0%
!! CTGCAGGTTTTGATCTTCTT+GGG + chr7.4:26263198-26263217 None:intergenic 40.0%
!! GCCTTTGAACAACTTGTTGA+AGG + chr7.4:26264047-26264066 None:intergenic 40.0%
!! TCTGCAGGTTTTGATCTTCT+TGG + chr7.4:26263199-26263218 None:intergenic 40.0%
!! TGCAAGAAAGTGTTGCCATA+TGG - chr7.4:26263490-26263509 MS.gene058722:intron 40.0%
!!! AACGATGTATTTTGACCCGA+TGG - chr7.4:26263643-26263662 MS.gene058722:intron 40.0%
AGAAGGATCTAAAGGAGTCG+AGG - chr7.4:26263946-26263965 MS.gene058722:CDS 45.0%
AGTCGGAATGGTGAGAAGAT+GGG - chr7.4:26264423-26264442 MS.gene058722:intron 45.0%
GAGATACAACCAGCTGAGAA+AGG + chr7.4:26263145-26263164 None:intergenic 45.0%
GAGGATTCAGAGACTTTGTC+TGG - chr7.4:26263965-26263984 MS.gene058722:CDS 45.0%
GTCATTCTTCCTTTCTCAGC+TGG - chr7.4:26263133-26263152 MS.gene058722:CDS 45.0%
! TCAACTTCATCCAACGGACT+CGG + chr7.4:26263573-26263592 None:intergenic 45.0%
! TGTGGTGAATTAGTCTCTGC+AGG + chr7.4:26263214-26263233 None:intergenic 45.0%
!! GGTTTTGATCTTCTTGGGTG+TGG + chr7.4:26263193-26263212 None:intergenic 45.0%
!! AAAAGATATAAATTAATATA+TGG + chr7.4:26264138-26264157 None:intergenic 5.0%
!!! ATTGTATTTTAAATTTTATT+TGG - chr7.4:26263606-26263625 MS.gene058722:intron 5.0%
AGAGAATCCCATCCCCTCAT+TGG + chr7.4:26264785-26264804 None:intergenic 50.0%
AGGACTTGGATTCTCTCCCA+CGG - chr7.4:26263441-26263460 MS.gene058722:intron 50.0%
CTCAGCTGGTTGTATCTCTG+AGG - chr7.4:26263147-26263166 MS.gene058722:CDS 50.0%
GAGAATCCCATCCCCTCATT+GGG + chr7.4:26264784-26264803 None:intergenic 50.0%
GAGTCGGAATGGTGAGAAGA+TGG - chr7.4:26264422-26264441 MS.gene058722:intron 50.0%
GATTCTCTCCCACGGTACAT+CGG - chr7.4:26263449-26263468 MS.gene058722:intron 50.0%
TCATGACCCAATGAGGGGAT+GGG - chr7.4:26264775-26264794 MS.gene058722:CDS 50.0%
TGCTGCTCATGACCCAATGA+GGG - chr7.4:26264769-26264788 MS.gene058722:CDS 50.0%
TTGGTGAGTATGCAAGCGTG+TGG - chr7.4:26264089-26264108 MS.gene058722:intron 50.0%
! GTGACACACATTGGTTGGGA+TGG - chr7.4:26264731-26264750 MS.gene058722:intron 50.0%
! TCTGAGGCTAGTGTTGCTGT+TGG - chr7.4:26263163-26263182 MS.gene058722:CDS 50.0%
! TTGTTGCACCGATGTACCGT+GGG + chr7.4:26263460-26263479 None:intergenic 50.0%
! TTTGTTGCACCGATGTACCG+TGG + chr7.4:26263461-26263480 None:intergenic 50.0%
CTCATGACCCAATGAGGGGA+TGG - chr7.4:26264774-26264793 MS.gene058722:CDS 55.0%
GAGAGAAGATCCGAGTCCGT+TGG - chr7.4:26263560-26263579 MS.gene058722:intron 55.0%
GAGGCTACAGAGAGAAGCTC+AGG + chr7.4:26264815-26264834 None:intergenic 55.0%
GCTACAGAGAGAAGCTCAGG+AGG + chr7.4:26264812-26264831 None:intergenic 55.0%
GCTGCTCATGACCCAATGAG+GGG - chr7.4:26264770-26264789 MS.gene058722:CDS 55.0%
TGGGTCATGAGCAGCACATG+AGG + chr7.4:26264765-26264784 None:intergenic 55.0%
! GTGCTGCTCATGACCCAATG+AGG - chr7.4:26264768-26264787 MS.gene058722:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 26263109 26264895 26263109 ID=MS.gene058722
chr7.4 mRNA 26263109 26264895 26263109 ID=MS.gene058722.t1;Parent=MS.gene058722
chr7.4 exon 26264760 26264895 26264760 ID=MS.gene058722.t1.exon1;Parent=MS.gene058722.t1
chr7.4 CDS 26264760 26264895 26264760 ID=cds.MS.gene058722.t1;Parent=MS.gene058722.t1
chr7.4 exon 26263913 26264056 26263913 ID=MS.gene058722.t1.exon2;Parent=MS.gene058722.t1
chr7.4 CDS 26263913 26264056 26263913 ID=cds.MS.gene058722.t1;Parent=MS.gene058722.t1
chr7.4 exon 26263109 26263344 26263109 ID=MS.gene058722.t1.exon3;Parent=MS.gene058722.t1
chr7.4 CDS 26263109 26263344 26263109 ID=cds.MS.gene058722.t1;Parent=MS.gene058722.t1
Gene Sequence

>MS.gene058722

ATGAGACAGAGAATGGAAAGGCTTGTCATTCTTCCTTTCTCAGCTGGTTGTATCTCTGAGGCTAGTGTTGCTGTTGGTGTTCCACACCCAAGAAGATCAAAACCTGCAGAGACTAATTCACCACATGATGCAATAAGTCTCTTCCTATCTCTTTTACTATGATATCAACAATCATATATTACATATGCTAATTTCTATCACTACAATAATTCTTTGCATTAATTCCCTTAGTTTTATTTAGCTAGTAAAATAAAATAAGAGACACACAAACACTCTTGATTATAGATCGATACACACATTAAATTATGAATTTGAATTTAGTCATTCGATAAAGGACTTGGATTCTCTCCCACGGTACATCGGTGCAACAAAAGTTTCTCGTGCAAGAAAGTGTTGCCATATGGTGGTATGTTGTCATATTTAAAAATAAATTGTTGCATCATTGATCTGTGAGAGAAGATCCGAGTCCGTTGGATGAAGTTGATTGATATTACTAGATTGTATTTTAAATTTTATTTGGAGAATGAAAATATGAACGATGTATTTTGACCCGATGGTCAAATTTATTGTATGCATCAATAGTGCACCTTTTCCATTCTCTATTAAACATATATTTTTTCTTCCCCCAAACAAGTATAGGTATGAGAAAATGTATAAAAAAAAATGTCGTGGGGAAATATTTTGCATTTGATATTATTTTTTCCGTAACTTTCAAAAAAGAAAAAGATATTATTTTTTCTCTAATTTTTAATTAGTTGGTTCTAATCACGATATGTTTAAATTTATATGTATATGTTTATTTATGATCTATTACTAATTAGATGATATGATAAGATTAGAAGGATCTAAAGGAGTCGAGGATTCAGAGACTTTGTCTGGTGAAAGTATGAAGAATTCTTTGAGGTTACTTGATGTTGTTCCAAAGCCTAACCTATCCTTCAACAAGTTGTTCAAAGGCTTCAAGAACTTTTCTCAATTGTTTGGTGAGTATGCAAGCGTGTGGTTTTCTCATACTAATTTTGTGGTCCATATATTAATTTATATCTTTTTTATAAGTTAATTTATCTCTTTAGTATATATAATATACTCCGTGTTTTTATTTCGTTCCGTATAGAAGTTTTGATCGCAAGTTTTTCTAAAAATGATCCCTAAATAAACATTTTTAGAATGAACCTTTTAGTCTCGATCATCTCAATATATAAGGTGTGGTGTGTATGACTAGAAGAAATACGTGTCAATAATGGTGTATAAACGTTTAACTAGTCTCCATTTCCCCTACCTCTAACTTTCCTTATCTTAAACCCAATTTTATAGAGTCGGAATGGTGAGAAGATGGGAAAAAGATGAATGTGAATTATAGTCAATTCGACATTATTGATCTTACGCGACAATACTAACATGAATTTTTTATTTTTATATACATGTCATAATAAAAATAAAATTGTAGGAATTAAAATCGAAAATTTATTATTTCTTTGTAAATAAAAATATATGGAAGTCTTAATTTTTCATGGAATTCAATTTTTTTTTTTTTTTTTATGTTTAATTCAGTGGAGAAAGAAGAGGACTTAGAAGAAGATGAAATGGACATGGAAATAGGGTGCCCAACAGATGTACAACATGTGACACACATTGGTTGGGATGGTGTTACAACCTCATGTGCTGCTCATGACCCAATGAGGGGATGGGATTCTCTCATTCCTCCTGAGCTTCTCTCTGTAGCCTCTCAATCTTTACAGCCAAAACATGAAACATCTCCCATCAACATCATGCCTTCTATTGCTTGA

Protein sequence

>MS.gene058722.t1

MRQRMERLVILPFSAGCISEASVAVGVPHPRRSKPAETNSPHDAIKGSKGVEDSETLSGESMKNSLRLLDVVPKPNLSFNKLFKGFKNFSQLFVEKEEDLEEDEMDMEIGCPTDVQHVTHIGWDGVTTSCAAHDPMRGWDSLIPPELLSVASQSLQPKHETSPINIMPSIA