AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene000897

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000897.t1 MTR_7g112770 96.774 124 4 0 1 124 1 124 1.70e-85 245
MS.gene000897.t1 MTR_1g088450 94.068 118 7 0 7 124 2 119 4.43e-68 201
MS.gene000897.t1 MTR_1g083430 89.600 125 12 1 1 124 1 125 7.98e-68 200
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene000897.t1 AT3G05560 87.097 124 16 0 1 124 1 124 1.08e-66 197
MS.gene000897.t1 AT3G05560 87.097 124 16 0 1 124 1 124 1.08e-66 197
MS.gene000897.t1 AT3G05560 87.097 124 16 0 1 124 1 124 1.08e-66 197
MS.gene000897.t1 AT5G27770 85.841 113 16 0 1 113 1 113 5.66e-51 157
MS.gene000897.t1 AT1G02830 69.231 117 34 1 1 115 1 117 5.86e-44 140

Find 25 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCACCCTTCTTCTTTCCCT+TGG 0.344547 7.4:-3716915 None:intergenic
TCCATGATCTTGTCTTCCAC+TGG 0.448631 7.4:-3716962 None:intergenic
ATCAATGTCGGTGGAAAAGC+TGG 0.478964 7.4:+3717019 MS.gene000897:CDS
GGTGGAAAAGCTGGTGCTCT+TGG 0.491454 7.4:+3717028 MS.gene000897:CDS
CACTGGCTTAGCACAGTCAA+TGG 0.524581 7.4:-3716945 None:intergenic
CATTGCTGAGAACGAGGGAG+AGG 0.527747 7.4:+3718279 MS.gene000897:CDS
TGGTGCCAAGGGAAAGAAGA+AGG 0.529349 7.4:+3716910 MS.gene000897:CDS
CTTGCTCTTCTCACGGGTAA+CGG 0.534877 7.4:-3717062 None:intergenic
ATAGAAGTATCTATGAGCTC+AGG 0.546088 7.4:+3718248 MS.gene000897:CDS
AGTGATCTTGCTCTTCTCAC+GGG 0.552636 7.4:-3717068 None:intergenic
CAGTGATCTTGCTCTTCTCA+CGG 0.553223 7.4:-3717069 None:intergenic
GCCAGTGGAAGACAAGATCA+TGG 0.553292 7.4:+3716961 MS.gene000897:CDS
TAGTAACGCAGCTGGTGCCA+AGG 0.558833 7.4:+3716898 MS.gene000897:CDS
CTTCTCACGGGTAACGGTGA+CGG 0.568235 7.4:-3717056 None:intergenic
AGAAACACAATGTAAGAGAC+TGG 0.568481 7.4:+3718200 MS.gene000897:CDS
ATGAGTCGTAGTAACGCAGC+TGG 0.571019 7.4:+3716890 MS.gene000897:CDS
CTTCAACATTGCTGAGAACG+AGG 0.581013 7.4:+3718273 MS.gene000897:CDS
CTTCAAGAGCGAATCAATGT+CGG 0.599288 7.4:+3717007 MS.gene000897:CDS
CTTGGAAAAGTTACTGTCAG+AGG 0.604590 7.4:-3717095 None:intergenic
CTTAGCACAGTCAATGGTGA+AGG 0.610280 7.4:-3716939 None:intergenic
AGTAACGCAGCTGGTGCCAA+GGG 0.611343 7.4:+3716899 MS.gene000897:CDS
CATTGACTGTGCTAAGCCAG+TGG 0.621872 7.4:+3716946 MS.gene000897:CDS
CAAGAGCGAATCAATGTCGG+TGG 0.638592 7.4:+3717010 MS.gene000897:CDS
GGTGCCAAGGGAAAGAAGAA+GGG 0.657143 7.4:+3716911 MS.gene000897:CDS
TTCAACATTGCTGAGAACGA+GGG 0.691023 7.4:+3718274 MS.gene000897:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAGATAAATGATAGTTAT+GGG - chr7.4:3717849-3717868 None:intergenic 15.0%
!!! GCTTTGATTTAATATTTTAT+TGG + chr7.4:3717174-3717193 MS.gene000897:intron 15.0%
!! AAAGATAAATGATAGAGTAA+TGG - chr7.4:3717794-3717813 None:intergenic 20.0%
!! AAGATAAATGATAGAGTAAT+GGG - chr7.4:3717793-3717812 None:intergenic 20.0%
!! ATACTATATTCTGTAGATAT+AGG - chr7.4:3717947-3717966 None:intergenic 20.0%
!! ATATCTACAGAATATAGTAT+TGG + chr7.4:3717947-3717966 MS.gene000897:intron 20.0%
!! GTAAAGATAAATGATAGTTA+TGG - chr7.4:3717850-3717869 None:intergenic 20.0%
!! TATCTACAGAATATAGTATT+GGG + chr7.4:3717948-3717967 MS.gene000897:intron 20.0%
!!! ACATCTTATTTATAGCTTAT+TGG + chr7.4:3717529-3717548 MS.gene000897:intron 20.0%
!!! TAATAAGTGTTCTTTAAGAT+AGG + chr7.4:3717452-3717471 MS.gene000897:intron 20.0%
!!! TCATTTTGGTTTCAATTTAT+TGG + chr7.4:3717309-3717328 MS.gene000897:intron 20.0%
! AAGTAGTCTCACAAAATTTA+TGG + chr7.4:3717732-3717751 MS.gene000897:intron 25.0%
! AGTACGATAACAACAATATA+AGG + chr7.4:3718036-3718055 MS.gene000897:intron 25.0%
! ATAACTTAGTGCTTATACAA+CGG + chr7.4:3717483-3717502 MS.gene000897:intron 25.0%
! ATTCAGTGAAGATAAGTTAT+TGG + chr7.4:3717221-3717240 MS.gene000897:intron 25.0%
! CAATATAAGGTCTACTTAAT+TGG + chr7.4:3718049-3718068 MS.gene000897:intron 25.0%
!! TTGCTTGGTTGATTTATTTA+TGG + chr7.4:3717261-3717280 MS.gene000897:intron 25.0%
!! TTTCAATTTATTGGTCTGTT+TGG + chr7.4:3717318-3717337 MS.gene000897:intron 25.0%
!!! ATCTGATATTTTGCTGTTTT+TGG + chr7.4:3718077-3718096 MS.gene000897:intron 25.0%
!!! ATGATAGTTGATAGTCATTT+TGG + chr7.4:3717295-3717314 MS.gene000897:intron 25.0%
!!! TCTGATATTTTGCTGTTTTT+GGG + chr7.4:3718078-3718097 MS.gene000897:intron 25.0%
AAGTTATTGGCATGAAATCA+TGG + chr7.4:3717234-3717253 MS.gene000897:intron 30.0%
AATAAGATGTTTACCCAAAC+AGG - chr7.4:3717519-3717538 None:intergenic 30.0%
AGACCTTATGTTATTAGTTG+CGG - chr7.4:3718121-3718140 None:intergenic 30.0%
AGTTATGGGACTGTTAAAAT+TGG - chr7.4:3717835-3717854 None:intergenic 30.0%
GTAAATGAATTATTACCGCT+TGG - chr7.4:3717116-3717135 None:intergenic 30.0%
TCAGCAAACTAATTCATTGA+AGG + chr7.4:3717974-3717993 MS.gene000897:intron 30.0%
TTTCCGCAACTAATAACATA+AGG + chr7.4:3718115-3718134 MS.gene000897:intron 30.0%
! ATAAGTTTTGCGAGACTATT+TGG + chr7.4:3717369-3717388 MS.gene000897:intron 30.0%
! ATTTATTGGTCTGTTTGGAT+TGG + chr7.4:3717323-3717342 MS.gene000897:intron 30.0%
! TAAGTTTTGCGAGACTATTT+GGG + chr7.4:3717370-3717389 MS.gene000897:intron 30.0%
!! GTGTTCTTTAAGATAGGTTA+TGG + chr7.4:3717458-3717477 MS.gene000897:intron 30.0%
AACTTACGAACAAGAGCTTA+TGG + chr7.4:3717395-3717414 MS.gene000897:intron 35.0%
AATTGGCACTATGTATAAGC+TGG - chr7.4:3717818-3717837 None:intergenic 35.0%
AGAAACACAATGTAAGAGAC+TGG + chr7.4:3718200-3718219 MS.gene000897:CDS 35.0%
GCTGTCTGAATAAGCTATAT+TGG + chr7.4:3717652-3717671 MS.gene000897:intron 35.0%
GCTTATTTGAGCTTGTCTAT+GGG + chr7.4:3717345-3717364 MS.gene000897:intron 35.0%
TGAAATCATGGTTCATTGCT+TGG + chr7.4:3717246-3717265 MS.gene000897:intron 35.0%
TGCTTATACAACGGCAATAT+AGG + chr7.4:3717492-3717511 MS.gene000897:intron 35.0%
! AGTAATGGGACTGTTAAGAT+TGG - chr7.4:3717779-3717798 None:intergenic 35.0%
!! ATAGAAGTATCTATGAGCTC+AGG + chr7.4:3718248-3718267 MS.gene000897:CDS 35.0%
CTGTAGATATAGGACGTGTT+AGG - chr7.4:3717937-3717956 None:intergenic 40.0%
CTTCAAGAGCGAATCAATGT+CGG + chr7.4:3717007-3717026 MS.gene000897:CDS 40.0%
CTTGGAAAAGTTACTGTCAG+AGG - chr7.4:3717098-3717117 None:intergenic 40.0%
GGCTTATTTGAGCTTGTCTA+TGG + chr7.4:3717344-3717363 MS.gene000897:intron 40.0%
TTCAACATTGCTGAGAACGA+GGG + chr7.4:3718274-3718293 MS.gene000897:CDS 40.0%
! CAAATCGTTGTTTGCTACTC+TGG + chr7.4:3717135-3717154 MS.gene000897:intron 40.0%
! CTGACAGTAACTTTTCCAAG+CGG + chr7.4:3717098-3717117 MS.gene000897:CDS 40.0%
ACGGCAATATAGGTCCTGTT+TGG + chr7.4:3717502-3717521 MS.gene000897:intron 45.0%
AGTGATCTTGCTCTTCTCAC+GGG - chr7.4:3717071-3717090 None:intergenic 45.0%
ATCAATGTCGGTGGAAAAGC+TGG + chr7.4:3717019-3717038 MS.gene000897:CDS 45.0%
CAGTGATCTTGCTCTTCTCA+CGG - chr7.4:3717072-3717091 None:intergenic 45.0%
CGGCAATATAGGTCCTGTTT+GGG + chr7.4:3717503-3717522 MS.gene000897:intron 45.0%
CTTAGCACAGTCAATGGTGA+AGG - chr7.4:3716942-3716961 None:intergenic 45.0%
CTTCAACATTGCTGAGAACG+AGG + chr7.4:3718273-3718292 MS.gene000897:CDS 45.0%
TCCATGATCTTGTCTTCCAC+TGG - chr7.4:3716965-3716984 None:intergenic 45.0%
ATGAGTCGTAGTAACGCAGC+TGG + chr7.4:3716890-3716909 MS.gene000897:CDS 50.0%
CAAGAGCGAATCAATGTCGG+TGG + chr7.4:3717010-3717029 MS.gene000897:CDS 50.0%
CTTGCTCTTCTCACGGGTAA+CGG - chr7.4:3717065-3717084 None:intergenic 50.0%
GCCAGTGGAAGACAAGATCA+TGG + chr7.4:3716961-3716980 MS.gene000897:CDS 50.0%
GGTGCCAAGGGAAAGAAGAA+GGG + chr7.4:3716911-3716930 MS.gene000897:CDS 50.0%
TGCACCCTTCTTCTTTCCCT+TGG - chr7.4:3716918-3716937 None:intergenic 50.0%
! CATTGACTGTGCTAAGCCAG+TGG + chr7.4:3716946-3716965 MS.gene000897:CDS 50.0%
! TGGTGCCAAGGGAAAGAAGA+AGG + chr7.4:3716910-3716929 MS.gene000897:CDS 50.0%
!! CACTGGCTTAGCACAGTCAA+TGG - chr7.4:3716948-3716967 None:intergenic 50.0%
CATTGCTGAGAACGAGGGAG+AGG + chr7.4:3718279-3718298 MS.gene000897:CDS 55.0%
GGTGGAAAAGCTGGTGCTCT+TGG + chr7.4:3717028-3717047 MS.gene000897:CDS 55.0%
! AGTAACGCAGCTGGTGCCAA+GGG + chr7.4:3716899-3716918 MS.gene000897:CDS 55.0%
! CTTCTCACGGGTAACGGTGA+CGG - chr7.4:3717059-3717078 None:intergenic 55.0%
! TAGTAACGCAGCTGGTGCCA+AGG + chr7.4:3716898-3716917 MS.gene000897:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 3716890 3718312 3716890 ID=MS.gene000897
chr7.4 mRNA 3716890 3718312 3716890 ID=MS.gene000897.t1;Parent=MS.gene000897
chr7.4 exon 3716890 3717119 3716890 ID=MS.gene000897.t1.exon1;Parent=MS.gene000897.t1
chr7.4 CDS 3716890 3717119 3716890 ID=cds.MS.gene000897.t1;Parent=MS.gene000897.t1
chr7.4 exon 3718168 3718312 3718168 ID=MS.gene000897.t1.exon2;Parent=MS.gene000897.t1
chr7.4 CDS 3718168 3718312 3718168 ID=cds.MS.gene000897.t1;Parent=MS.gene000897.t1
Gene Sequence

>MS.gene000897

ATGAGTCGTAGTAACGCAGCTGGTGCCAAGGGAAAGAAGAAGGGTGCAACCTTCACCATTGACTGTGCTAAGCCAGTGGAAGACAAGATCATGGACATTGCTTCACTTGAGAAGTTTCTTCAAGAGCGAATCAATGTCGGTGGAAAAGCTGGTGCTCTTGGTGATTCCGTCACCGTTACCCGTGAGAAGAGCAAGATCACTGTTACCTCTGACAGTAACTTTTCCAAGCGGTAATAATTCATTTACAAATCGTTGTTTGCTACTCTGGTTTTATCTCTTATGTTGCTTTGATTTAATATTTTATTGGTCATTACTTTGTTGATTTAGTTATATTCAGTGAAGATAAGTTATTGGCATGAAATCATGGTTCATTGCTTGGTTGATTTATTTATGGATGAATATTTTATGATAGTTGATAGTCATTTTGGTTTCAATTTATTGGTCTGTTTGGATTGGCTTATTTGAGCTTGTCTATGGGCATAAGTTTTGCGAGACTATTTGGGATAACTTACGAACAAGAGCTTATGGCACTCTTAGCTTACATAAACACTTTTAGCTTACTTAATAAGTGTTCTTTAAGATAGGTTATGGAAATAACTTAGTGCTTATACAACGGCAATATAGGTCCTGTTTGGGTAAACATCTTATTTATAGCTTATTGGTCAAGCGCTTAGCTTATCACAAATAAGCGCTTGTGCATCAGCTATTTTAAAAAAAAAGTTAAATCAATGTTAAATTGTTTGTGTATTTGCTATGTTATAAGCTGTCTGAATAAGCTATATTGGTGTACATCTGAAAATAAGTTTAAATCAGCTTATGAAGCTGTTTTCATAAGTTCTCTCAAGTAGTCTCACAAAATTTATGGCTGTAGATAAGCTCAATTAAGCCAATCTTAACAGTCCCATTACTCTATCATTTATCTTTACCAGCTTATACATAGTGCCAATTTTAACAGTCCCATAACTATCATTTATCTTTACTAGCTTATACATAGTGCTTATTATGATAAGCACTTATGCTATAAGTCGCAAATAAGCTGTCTATCCTAACACGTCCTATATCTACAGAATATAGTATTGGGCTATCAGCAAACTAATTCATTGAAGGTTATTTTGTTTATTTTGATTTTTTCTGAATGTAATGTATAGTACGATAACAACAATATAAGGTCTACTTAATTGGACGAGATCTGATATTTTGCTGTTTTTGGGCTTATTTAATTTGATTTCCGCAACTAATAACATAAGGTCTACTTGTTTAACATCTCACTGATTGTAGATACTTGAAGTATTTGACAAAGAAGTACTTGAAGAAACACAATGTAAGAGACTGGCTCAGAGTGATTGCTTCAAACAAAGATAGAAGTATCTATGAGCTCAGGTACTTCAACATTGCTGAGAACGAGGGAGAGGAAGAAGATTAA
Protein sequence

>MS.gene000897.t1

MSRSNAAGAKGKKKGATFTIDCAKPVEDKIMDIASLEKFLQERINVGGKAGALGDSVTVTREKSKITVTSDSNFSKRYLKYLTKKYLKKHNVRDWLRVIASNKDRSIYELRYFNIAENEGEEED