AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64407


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64407.t1 MTR_2g054750 89.286 140 3 1 1 140 1 128 2.84e-86 248
MS.gene64407.t1 MTR_4g113840 77.857 140 31 0 1 140 1 140 3.55e-80 233
MS.gene64407.t1 MTR_4g011190 45.139 144 60 2 6 134 5 144 3.74e-36 121
MS.gene64407.t1 MTR_3g107610 35.758 165 60 4 6 134 5 159 2.78e-28 102
MS.gene64407.t1 MTR_3g107610 34.014 147 47 4 6 114 5 139 1.34e-19 80.1
MS.gene64407.t1 MTR_3g107610 43.617 94 42 4 50 136 5 94 1.02e-13 65.1
MS.gene64407.t1 MTR_6g069400 28.358 134 74 4 1 134 265 376 5.81e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64407.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.14e-64 193
MS.gene64407.t1 AT2G26695 67.626 139 42 2 1 138 1 137 2.14e-64 193
MS.gene64407.t1 AT5G25490 38.182 165 65 5 6 137 5 165 3.47e-32 112
MS.gene64407.t1 AT5G25490 38.182 165 65 5 6 137 5 165 3.47e-32 112
MS.gene64407.t1 AT3G15680 40.909 154 68 6 6 136 5 158 2.38e-30 107
MS.gene64407.t1 AT3G15680 40.909 154 68 6 6 136 5 158 2.38e-30 107
MS.gene64407.t1 AT2G17975 31.544 149 72 6 6 130 7 149 6.87e-14 67.0
MS.gene64407.t1 AT2G17975 31.507 146 84 6 2 140 125 261 7.32e-11 58.5
MS.gene64407.t1 AT2G17975 31.724 145 83 6 3 140 96 231 2.88e-11 59.3

Find 36 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTAGGGTATCCACAATTT+TGG 0.169674 2.4:+35171777 None:intergenic
CAGTTATATCTATAAGTTTC+TGG 0.205304 2.4:+35171740 None:intergenic
GGATCAGGGCCTCCAATCTT+AGG 0.228355 2.4:+35171761 None:intergenic
ACATTTCATACCAAAACTTT+TGG 0.233482 2.4:+35170927 None:intergenic
AATGGTTACTCTTGTGGATT+TGG 0.299384 2.4:-35171617 MS.gene64407:CDS
ATGGATGCCTCTGGTGGATA+TGG 0.313642 2.4:-35171587 MS.gene64407:CDS
TGCAAAACACCCAAAAGTTT+TGG 0.338060 2.4:-35170937 MS.gene64407:intron
TATCTATAAGTTTCTGGATC+AGG 0.344425 2.4:+35171746 None:intergenic
CAGAAACTTATAGATATAAC+TGG 0.359021 2.4:-35171739 MS.gene64407:CDS
TCTTCTTGAAATTTATATGC+TGG 0.441540 2.4:+35171810 None:intergenic
AATTGTGGATACCCTAAGAT+TGG 0.457887 2.4:-35171773 MS.gene64407:CDS
TGAGCTGGTCAGGAGGAGAT+TGG 0.487008 2.4:-35171847 MS.gene64407:CDS
ATCTATAAGTTTCTGGATCA+GGG 0.487320 2.4:+35171747 None:intergenic
GGTGGGAACATGGATGCCTC+TGG 0.491282 2.4:-35171596 MS.gene64407:CDS
ATATAACTGGACTGAAACCT+TGG 0.499509 2.4:-35171726 MS.gene64407:CDS
AACTGGACTGAAACCTTGGC+AGG 0.503471 2.4:-35171722 MS.gene64407:CDS
GATCAGGGCCTCCAATCTTA+GGG 0.508242 2.4:+35171762 None:intergenic
CTGAAACCTTGGCAGGGGAC+TGG 0.517119 2.4:-35171715 MS.gene64407:CDS
AGCATATAAATTTCAAGAAG+AGG 0.527814 2.4:-35171808 MS.gene64407:CDS
CTGGGTGGAAAACTGGTGAC+TGG 0.538853 2.4:-35171544 MS.gene64407:CDS
TTGTGGATTTGGTGGGAACA+TGG 0.541127 2.4:-35171606 MS.gene64407:CDS
GGTTACTCTTGTGGATTTGG+TGG 0.558743 2.4:-35171614 MS.gene64407:CDS
GCATATAAATTTCAAGAAGA+GGG 0.572289 2.4:-35171807 MS.gene64407:CDS
CTGGTGACTGGATATGCACT+AGG 0.573750 2.4:-35171532 MS.gene64407:intron
TGTGGATACCCTAAGATTGG+AGG 0.581161 2.4:-35171770 MS.gene64407:CDS
AGGGATGCATGCCAAAATTG+TGG 0.584842 2.4:-35171788 MS.gene64407:CDS
TCATGTATCAGATATGGCTG+TGG 0.590303 2.4:-35170997 MS.gene64407:intron
GTTACTCTTGTGGATTTGGT+GGG 0.590561 2.4:-35171613 MS.gene64407:CDS
GGGAACATGGATGCCTCTGG+TGG 0.591219 2.4:-35171593 MS.gene64407:CDS
ACTGGACTGAAACCTTGGCA+GGG 0.594678 2.4:-35171721 MS.gene64407:CDS
GCAGGGGACTGGTATTGCAG+TGG 0.597750 2.4:-35171704 MS.gene64407:CDS
GCAATACCAGTCCCCTGCCA+AGG 0.605697 2.4:+35171709 None:intergenic
CTGGACTGAAACCTTGGCAG+GGG 0.627405 2.4:-35171720 MS.gene64407:CDS
AGAACAAGCTGTTATAGATG+TGG 0.633263 2.4:-35171650 MS.gene64407:CDS
ATCAGATCCATATCCACCAG+AGG 0.683350 2.4:+35171580 None:intergenic
TATTGCAGTGGTATGAACTG+TGG 0.711677 2.4:-35171692 MS.gene64407:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAATTATATAAGCATCA+TGG + chr2.4:35171827-35171846 None:intergenic 15.0%
!! ATATAATTAATTCCTATTTC+AGG - chr2.4:35171835-35171854 MS.gene64407:CDS 15.0%
!! TAATTACAAAATATGTGATA+GGG + chr2.4:35171403-35171422 None:intergenic 15.0%
!! TTAATTACAAAATATGTGAT+AGG + chr2.4:35171404-35171423 None:intergenic 15.0%
! AGCATATAAATTTCAAGAAG+AGG - chr2.4:35170875-35170894 MS.gene64407:intron 25.0%
! CAGAAACTTATAGATATAAC+TGG - chr2.4:35170944-35170963 MS.gene64407:CDS 25.0%
! CAGTTATATCTATAAGTTTC+TGG + chr2.4:35170946-35170965 None:intergenic 25.0%
! GCATATAAATTTCAAGAAGA+GGG - chr2.4:35170876-35170895 MS.gene64407:intron 25.0%
! GCATATACTTTAAGTAATGA+AGG + chr2.4:35171786-35171805 None:intergenic 25.0%
! TAATTAATTCCTATTTCAGG+TGG - chr2.4:35171838-35171857 MS.gene64407:CDS 25.0%
! TCTTCTTGAAATTTATATGC+TGG + chr2.4:35170876-35170895 None:intergenic 25.0%
!! ACATTTCATACCAAAACTTT+TGG + chr2.4:35171759-35171778 None:intergenic 25.0%
!! ATCACATATTTTGTAACTGA+GGG - chr2.4:35171186-35171205 MS.gene64407:intron 25.0%
!! CATTTCATACCAAAACTTTT+GGG + chr2.4:35171758-35171777 None:intergenic 25.0%
!! TGCATTTTGTAATTAGACTT+GGG - chr2.4:35171464-35171483 MS.gene64407:intron 25.0%
CGATAAATTTCAAATCTCCT+CGG + chr2.4:35171549-35171568 None:intergenic 30.0%
TTGAAAAATGGTTACTCTTG+TGG - chr2.4:35171060-35171079 MS.gene64407:intron 30.0%
TTGTAATTAGACTTGGGAAA+CGG - chr2.4:35171470-35171489 MS.gene64407:intron 30.0%
! ATCTATAAGTTTCTGGATCA+GGG + chr2.4:35170939-35170958 None:intergenic 30.0%
! CATCACATATTTTGTAACTG+AGG - chr2.4:35171185-35171204 MS.gene64407:intron 30.0%
! CGAGGAGATTTGAAATTTAT+CGG - chr2.4:35171547-35171566 MS.gene64407:CDS 30.0%
! CTGCATTTTGTAATTAGACT+TGG - chr2.4:35171463-35171482 MS.gene64407:intron 30.0%
! TATCTATAAGTTTCTGGATC+AGG + chr2.4:35170940-35170959 None:intergenic 30.0%
! TCACATATTTTGTAACTGAG+GGG - chr2.4:35171187-35171206 MS.gene64407:intron 30.0%
AATGGTTACTCTTGTGGATT+TGG - chr2.4:35171066-35171085 MS.gene64407:intron 35.0%
AATTGTGGATACCCTAAGAT+TGG - chr2.4:35170910-35170929 MS.gene64407:intron 35.0%
AGAACAAGCTGTTATAGATG+TGG - chr2.4:35171033-35171052 MS.gene64407:intron 35.0%
AGATGTGGTGCATTGAAAAA+TGG - chr2.4:35171048-35171067 MS.gene64407:intron 35.0%
ATATAACTGGACTGAAACCT+TGG - chr2.4:35170957-35170976 MS.gene64407:CDS 35.0%
TCTTGTGTAAAAACAGGGTA+AGG - chr2.4:35171282-35171301 MS.gene64407:intron 35.0%
TGCTTCTCATGTATCAGATA+TGG - chr2.4:35171680-35171699 MS.gene64407:CDS 35.0%
! TGCAAAACACCCAAAAGTTT+TGG - chr2.4:35171746-35171765 MS.gene64407:CDS 35.0%
!! TCTTAGGGTATCCACAATTT+TGG + chr2.4:35170909-35170928 None:intergenic 35.0%
!! TGTTTTGCACTTGAAGCATT+CGG + chr2.4:35171735-35171754 None:intergenic 35.0%
!!! TTACCCTGTTTTTACACAAG+AGG + chr2.4:35171283-35171302 None:intergenic 35.0%
ACAGCCTCTTGTGTAAAAAC+AGG - chr2.4:35171276-35171295 MS.gene64407:intron 40.0%
ACGTACAATACACCAAATGG+TGG - chr2.4:35171307-35171326 MS.gene64407:intron 40.0%
CAATCTGAACCACCTGAAAT+AGG + chr2.4:35171850-35171869 None:intergenic 40.0%
CAGCCTCTTGTGTAAAAACA+GGG - chr2.4:35171277-35171296 MS.gene64407:intron 40.0%
CGTACAATACACCAAATGGT+GGG - chr2.4:35171308-35171327 MS.gene64407:intron 40.0%
GCTACGTACAATACACCAAA+TGG - chr2.4:35171304-35171323 MS.gene64407:intron 40.0%
GTTGTTGTCATGTGACTGTA+AGG - chr2.4:35171232-35171251 MS.gene64407:intron 40.0%
TAAGCATCATGGATCTGATG+AGG + chr2.4:35171816-35171835 None:intergenic 40.0%
TATTGCAGTGGTATGAACTG+TGG - chr2.4:35170991-35171010 MS.gene64407:intron 40.0%
TCATGTATCAGATATGGCTG+TGG - chr2.4:35171686-35171705 MS.gene64407:CDS 40.0%
! AAATATGTGATAGGGCATCC+CGG + chr2.4:35171395-35171414 None:intergenic 40.0%
! CAGTTTTACAATTGTCTCCG+AGG - chr2.4:35171529-35171548 MS.gene64407:intron 40.0%
! GTTACTCTTGTGGATTTGGT+GGG - chr2.4:35171070-35171089 MS.gene64407:intron 40.0%
AGGGATGCATGCCAAAATTG+TGG - chr2.4:35170895-35170914 MS.gene64407:intron 45.0%
ATCAGATCCATATCCACCAG+AGG + chr2.4:35171106-35171125 None:intergenic 45.0%
GGTTACTCTTGTGGATTTGG+TGG - chr2.4:35171069-35171088 MS.gene64407:intron 45.0%
TCATGTGACTGTAAGGTCAC+CGG - chr2.4:35171239-35171258 MS.gene64407:intron 45.0%
TGTGGATACCCTAAGATTGG+AGG - chr2.4:35170913-35170932 MS.gene64407:intron 45.0%
TTGTAACTGAGGGGTAACCT+TGG - chr2.4:35171196-35171215 MS.gene64407:intron 45.0%
! TTACACAAGAGGCTGTTTCC+AGG + chr2.4:35171272-35171291 None:intergenic 45.0%
!! TTGTGGATTTGGTGGGAACA+TGG - chr2.4:35171077-35171096 MS.gene64407:intron 45.0%
AACTGGACTGAAACCTTGGC+AGG - chr2.4:35170961-35170980 MS.gene64407:CDS 50.0%
ACTGGACTGAAACCTTGGCA+GGG - chr2.4:35170962-35170981 MS.gene64407:CDS 50.0%
CTGATTGCAATTACCCCCCT+GGG - chr2.4:35171121-35171140 MS.gene64407:intron 50.0%
CTGGTGACTGGATATGCACT+AGG - chr2.4:35171151-35171170 MS.gene64407:intron 50.0%
GATCAGGGCCTCCAATCTTA+GGG + chr2.4:35170924-35170943 None:intergenic 50.0%
TCTGATTGCAATTACCCCCC+TGG - chr2.4:35171120-35171139 MS.gene64407:intron 50.0%
! AGTCACCAGTTTTCCACCCA+GGG + chr2.4:35171140-35171159 None:intergenic 50.0%
! ATGGATGCCTCTGGTGGATA+TGG - chr2.4:35171096-35171115 MS.gene64407:intron 50.0%
! GCTGTTTCCAGGACTTGAAC+CGG + chr2.4:35171261-35171280 None:intergenic 50.0%
ATTGCAATTACCCCCCTGGG+TGG - chr2.4:35171124-35171143 MS.gene64407:intron 55.0%
CAACTTTGCCAGTTGCGCCA+AGG + chr2.4:35171216-35171235 None:intergenic 55.0%
CATACGCAGGGTTTGGGAAG+GGG + chr2.4:35171356-35171375 None:intergenic 55.0%
CTGGACTGAAACCTTGGCAG+GGG - chr2.4:35170963-35170982 MS.gene64407:CDS 55.0%
CTGGGTGGAAAACTGGTGAC+TGG - chr2.4:35171139-35171158 MS.gene64407:intron 55.0%
CTTCCCAAACCCTGCGTATG+CGG - chr2.4:35171356-35171375 MS.gene64407:intron 55.0%
GCATACGCAGGGTTTGGGAA+GGG + chr2.4:35171357-35171376 None:intergenic 55.0%
GGATCAGGGCCTCCAATCTT+AGG + chr2.4:35170925-35170944 None:intergenic 55.0%
TGAGCTGGTCAGGAGGAGAT+TGG - chr2.4:35170836-35170855 MS.gene64407:intron 55.0%
TTCCCAAACCCTGCGTATGC+GGG - chr2.4:35171357-35171376 MS.gene64407:intron 55.0%
! CAGTCACCAGTTTTCCACCC+AGG + chr2.4:35171141-35171160 None:intergenic 55.0%
! GTCACCAGTTTTCCACCCAG+GGG + chr2.4:35171139-35171158 None:intergenic 55.0%
! TCACCAGTTTTCCACCCAGG+GGG + chr2.4:35171138-35171157 None:intergenic 55.0%
!! AAGGTCACCGGTTCAAGTCC+TGG - chr2.4:35171251-35171270 MS.gene64407:intron 55.0%
ACTGAAGCTCCCGCATACGC+AGG + chr2.4:35171369-35171388 None:intergenic 60.0%
AGGGGTAACCTTGGCGCAAC+TGG - chr2.4:35171205-35171224 MS.gene64407:intron 60.0%
ATGCGGGAGCTTCAGTGCAC+CGG - chr2.4:35171373-35171392 MS.gene64407:intron 60.0%
CGCATACGCAGGGTTTGGGA+AGG + chr2.4:35171358-35171377 None:intergenic 60.0%
CTCCCGCATACGCAGGGTTT+GGG + chr2.4:35171362-35171381 None:intergenic 60.0%
CTGAAACCTTGGCAGGGGAC+TGG - chr2.4:35170968-35170987 MS.gene64407:CDS 60.0%
CTGAAGCTCCCGCATACGCA+GGG + chr2.4:35171368-35171387 None:intergenic 60.0%
GCAATACCAGTCCCCTGCCA+AGG + chr2.4:35170977-35170996 None:intergenic 60.0%
GGGAACATGGATGCCTCTGG+TGG - chr2.4:35171090-35171109 MS.gene64407:intron 60.0%
GGTGGGAACATGGATGCCTC+TGG - chr2.4:35171087-35171106 MS.gene64407:intron 60.0%
TACCCCCCTGGGTGGAAAAC+TGG - chr2.4:35171132-35171151 MS.gene64407:intron 60.0%
TGGGAAGGGGTCCCACCATT+TGG + chr2.4:35171322-35171341 None:intergenic 60.0%
! CACCAGTTTTCCACCCAGGG+GGG + chr2.4:35171137-35171156 None:intergenic 60.0%
! GCAGGGGACTGGTATTGCAG+TGG - chr2.4:35170979-35170998 MS.gene64407:CDS 60.0%
GCTCCCGCATACGCAGGGTT+TGG + chr2.4:35171363-35171382 None:intergenic 65.0%
GGACCCCTTCCCAAACCGGT+GGG - chr2.4:35171329-35171348 MS.gene64407:intron 65.0%
GGTGGGACCCCTTCCCAAAC+CGG - chr2.4:35171325-35171344 MS.gene64407:intron 65.0%
GGTTTGGGAAGGGGTCCCAC+CGG + chr2.4:35171326-35171345 None:intergenic 65.0%
TGCGGGAGCTTCAGTGCACC+GGG - chr2.4:35171374-35171393 MS.gene64407:intron 65.0%
!! GGAAGGGGTCCCACCGGTTT+GGG + chr2.4:35171341-35171360 None:intergenic 65.0%
!! GGGTCCCACCGGTTTGGGAA+GGG + chr2.4:35171336-35171355 None:intergenic 65.0%
!! GGTCCCACCGGTTTGGGAAG+GGG + chr2.4:35171335-35171354 None:intergenic 65.0%
GGGACCCCTTCCCAAACCGG+TGG - chr2.4:35171328-35171347 MS.gene64407:intron 70.0%
! GGGAAGGGGTCCCACCGGTT+TGG + chr2.4:35171342-35171361 None:intergenic 70.0%
!! GGGGTCCCACCGGTTTGGGA+AGG + chr2.4:35171337-35171356 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 35170835 35171870 35170835 ID=MS.gene64407
chr2.4 mRNA 35170835 35171870 35170835 ID=MS.gene64407.t1;Parent=MS.gene64407
chr2.4 exon 35171533 35171870 35171533 ID=MS.gene64407.t1.exon1;Parent=MS.gene64407.t1
chr2.4 CDS 35171533 35171870 35171533 ID=cds.MS.gene64407.t1;Parent=MS.gene64407.t1
chr2.4 exon 35170938 35171008 35170938 ID=MS.gene64407.t1.exon2;Parent=MS.gene64407.t1
chr2.4 CDS 35170938 35171008 35170938 ID=cds.MS.gene64407.t1;Parent=MS.gene64407.t1
chr2.4 exon 35170835 35170848 35170835 ID=MS.gene64407.t1.exon3;Parent=MS.gene64407.t1
chr2.4 CDS 35170835 35170848 35170835 ID=cds.MS.gene64407.t1;Parent=MS.gene64407.t1
Gene Sequence

>MS.gene64407

ATGAGCTGGTCAGGAGGAGATTGGATGTGCAATGCTTGCCAGCATATAAATTTCAAGAAGAGGGATGCATGCCAAAATTGTGGATACCCTAAGATTGGAGGCCCTGATCCAGAAACTTATAGATATAACTGGACTGAAACCTTGGCAGGGGACTGGTATTGCAGTGGTATGAACTGTGGAGCTCACAATTATGCTAGCAGAACAAGCTGTTATAGATGTGGTGCATTGAAAAATGGTTACTCTTGTGGATTTGGTGGGAACATGGATGCCTCTGGTGGATATGGATCTGATTGCAATTACCCCCCTGGGTGGAAAACTGGTGACTGGATATGCACTAGGTATTTTCACATCATCACATATTTTGTAACTGAGGGGTAACCTTGGCGCAACTGGCAAAGTTGTTGTCATGTGACTGTAAGGTCACCGGTTCAAGTCCTGGAAACAGCCTCTTGTGTAAAAACAGGGTAAGGCTACGTACAATACACCAAATGGTGGGACCCCTTCCCAAACCGGTGGGACCCCTTCCCAAACCCTGCGTATGCGGGAGCTTCAGTGCACCGGGATGCCCTATCACATATTTTGTAATTAACTTCACTAAAATATGCTGCATTTTCATGTACTGAAGTTGCTGCATTTTGTAATTAGACTTGGGAAACGGAGAAATTATTATTAATAAGAATGATGACACTAATGACAGTTTTACAATTGTCTCCGAGGAGATTTGAAATTTATCGGTCAAGACTACAAAGTCAACTCTCATCTCTGCGCTGACATAAAATAACTCGTTTCATTATATTACATAAAAAGAAATATGAAATATCATAGAAATACATTTTTATTTTCTTTGCTTCTCATGTATCAGATATGGCTGTGGAGTGCACAATTATGCTAGCAGAGCCGAATGCTTCAAGTGCAAAACACCCAAAAGTTTTGGTATGAAATGTTTATCCTTCATTACTTAAAGTATATGCTATTCAACCTCATCAGATCCATGATGCTTATATAATTAATTCCTATTTCAGGTGGTTCAGATTGA

Protein sequence

>MS.gene64407.t1

MSWSGGDWMCNACQHINFKKRDACQNCGYPKIGGPDPETYRYNWTETLAGDWYCSGMNCGAHNYASRTSCYRCGALKNGYSCGFGGNMDASGGYGSDCNYPPGWKTGDWICTRYGCGVHNYASRAECFKCKTPKSFGGSD