AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78488

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78488.t1 MTR_5g043480 95.000 120 6 0 1 120 124 243 8.64e-85 247
MS.gene78488.t1 MTR_5g043480 95.000 120 6 0 1 120 194 313 1.40e-83 246
MS.gene78488.t1 MTR_5g043480 96.364 55 2 0 1 55 124 178 6.33e-34 117
MS.gene78488.t1 MTR_5g043480 96.364 55 2 0 1 55 214 268 1.07e-32 116
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78488.t1 AT2G03390 78.261 115 24 1 2 116 107 220 1.45e-67 203
MS.gene78488.t1 AT2G03390 78.261 115 24 1 2 116 217 330 2.84e-66 203
MS.gene78488.t1 AT2G03390 78.261 115 24 1 2 116 217 330 2.84e-66 203
MS.gene78488.t1 AT2G03390 79.630 54 11 0 2 55 217 270 8.42e-27 100
MS.gene78488.t1 AT2G03390 79.630 54 11 0 2 55 217 270 8.42e-27 100
MS.gene78488.t1 AT2G03390 76.190 42 10 0 2 43 217 258 2.32e-18 78.2
MS.gene78488.t1 AT2G03390 76.190 42 10 0 2 43 217 258 2.32e-18 78.2

Find 33 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTCCCGCAGTTGCTTAAT+AGG 0.261631 5.2:+67729833 None:intergenic
CTTACTTTGTCTGGTTTGTC+AGG 0.358622 5.2:+67729997 None:intergenic
ATAGATGCACTTACTTTGTC+TGG 0.369403 5.2:+67729988 None:intergenic
TTCCCTCCATCTTCGTCACT+TGG 0.379098 5.2:+67729773 None:intergenic
TCTCCCGCAGTTGCTTAATA+GGG 0.393158 5.2:+67729834 None:intergenic
AAAGTAAAGCATAAAATGTT+TGG 0.407562 5.2:-67731354 None:intergenic
CCTCCATCTTCGTCACTTGG+TGG 0.409997 5.2:+67729776 None:intergenic
CCATATGCCACCAGTAGATC+TGG 0.419863 5.2:+67730653 None:intergenic
GAACTTGATTCACTGCATAC+TGG 0.426333 5.2:+67731120 None:intergenic
TATGCAGTGAATCAAGTTCA+TGG 0.439684 5.2:-67731116 MS.gene78488:CDS
GCTAATCAAACCTGATAAAA+CGG 0.469627 5.2:+67731048 None:intergenic
CTCCATCTTCGTCACTTGGT+GGG 0.473073 5.2:+67729777 None:intergenic
CCAGATCTACTGGTGGCATA+TGG 0.477740 5.2:-67730653 MS.gene78488:intron
TTCGTCACTTGGTGGGTCAA+AGG 0.495368 5.2:+67729784 None:intergenic
TCGTCACTTGGTGGGTCAAA+GGG 0.504592 5.2:+67729785 None:intergenic
TTCTATGGAATGGATTCAGC+TGG 0.505006 5.2:-67729866 MS.gene78488:CDS
TAGAACAGAAAAGACATGTA+GGG 0.523219 5.2:+67729884 None:intergenic
GCGTACTGAACCAGATCTAC+TGG 0.524216 5.2:-67730663 MS.gene78488:CDS
CATCCCTATTAAGCAACTGC+GGG 0.535038 5.2:-67729837 MS.gene78488:CDS
TAGAGCTATAATCGTAGGAA+TGG 0.538085 5.2:-67731145 MS.gene78488:CDS
CAGTGAATCAAGTTCATGGA+TGG 0.538216 5.2:-67731112 MS.gene78488:CDS
GTGGGTCAAAGGGTATTTCG+TGG 0.539921 5.2:+67729795 None:intergenic
ATAGAACAGAAAAGACATGT+AGG 0.565791 5.2:+67729883 None:intergenic
GGCTATAGAGCTATAATCGT+AGG 0.576059 5.2:-67731150 MS.gene78488:CDS
GACCCACCAAGTGACGAAGA+TGG 0.585639 5.2:-67729779 MS.gene78488:CDS
CACCAAGTGACGAAGATGGA+GGG 0.603276 5.2:-67729775 MS.gene78488:CDS
TCAAAGGGTATTTCGTGGCG+CGG 0.632604 5.2:+67729800 None:intergenic
AGAACAGAAAAGACATGTAG+GGG 0.640432 5.2:+67729885 None:intergenic
AACCTGATAAAACGGTTGAG+TGG 0.641728 5.2:+67731056 None:intergenic
CCACCAAGTGACGAAGATGG+AGG 0.644237 5.2:-67729776 MS.gene78488:CDS
TCATCCCTATTAAGCAACTG+CGG 0.646965 5.2:-67729838 MS.gene78488:CDS
TACTGAACCAGATCTACTGG+TGG 0.678822 5.2:-67730660 MS.gene78488:CDS
CAAGTTAAGAAGTTGTCTCG+TGG 0.688846 5.2:-67731081 MS.gene78488:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAAGTAATAATATTAAT+TGG + chr5.2:67730966-67730985 None:intergenic 10.0%
!!! TTTTTTTTTTTTTTTGAACA+AGG + chr5.2:67729889-67729908 None:intergenic 10.0%
!! ATGAATTGTAAATGTATTTA+TGG - chr5.2:67730297-67730316 MS.gene78488:intron 15.0%
!! CTTATAGAGTTAAAATTATT+CGG + chr5.2:67730146-67730165 None:intergenic 15.0%
!! TACAATAACAAAAACATATA+AGG + chr5.2:67730337-67730356 None:intergenic 15.0%
!!! AATAATATTAATTGGTTCAA+TGG + chr5.2:67730958-67730977 None:intergenic 15.0%
!!! TAATAATTTGTTGTATTGAT+AGG + chr5.2:67729795-67729814 None:intergenic 15.0%
!!! TGTTATTTATGTTCTTTAAT+TGG - chr5.2:67731163-67731182 MS.gene78488:intron 15.0%
!!! TTTGTTATTGTATTAATAAC+TGG - chr5.2:67730345-67730364 MS.gene78488:intron 15.0%
!! TAATTAGCAACATATTGATA+AGG - chr5.2:67729822-67729841 MS.gene78488:CDS 20.0%
!! TCTTCAATTCTTATTATTAC+TGG - chr5.2:67730185-67730204 MS.gene78488:intron 20.0%
!!! TGAATTATTCTGTTTCTATA+TGG - chr5.2:67730104-67730123 MS.gene78488:intron 20.0%
!!! TTTTTTTTTTTTGAACAAGG+AGG + chr5.2:67729886-67729905 None:intergenic 20.0%
! ATGAAATTATTCATCCAAAC+AGG + chr5.2:67730497-67730516 None:intergenic 25.0%
! TATAAGAAAACAGTTTGACT+TGG + chr5.2:67730681-67730700 None:intergenic 25.0%
! TGAAATTATTCATCCAAACA+GGG + chr5.2:67730496-67730515 None:intergenic 25.0%
! TTTCTGTAAACAAATACATG+TGG - chr5.2:67731034-67731053 MS.gene78488:intron 25.0%
!! AATATAATGTGAGACTGTTT+TGG + chr5.2:67730797-67730816 None:intergenic 25.0%
!! ATAAGAAAACAGTTTGACTT+GGG + chr5.2:67730680-67730699 None:intergenic 25.0%
AGAACCTAGACATTTGAAAA+AGG + chr5.2:67730413-67730432 None:intergenic 30.0%
ATAGAACAGAAAAGACATGT+AGG + chr5.2:67731225-67731244 None:intergenic 30.0%
ATGTACAGAAAAGCAATTGT+AGG + chr5.2:67730902-67730921 None:intergenic 30.0%
CAGTCTCACATTATATTTGA+TGG - chr5.2:67730800-67730819 MS.gene78488:intron 30.0%
CATCGAGGAATCAAAATATA+AGG + chr5.2:67729926-67729945 None:intergenic 30.0%
CTTATGGAAAAAGCTGAAAA+CGG - chr5.2:67730736-67730755 MS.gene78488:intron 30.0%
GAACCTAGACATTTGAAAAA+GGG + chr5.2:67730412-67730431 None:intergenic 30.0%
GCTAATCAAACCTGATAAAA+CGG + chr5.2:67730060-67730079 None:intergenic 30.0%
GCTGAATATCTCATAAATGT+GGG - chr5.2:67729844-67729863 MS.gene78488:CDS 30.0%
TAATTGTTCAGACCTTTGAT+TGG - chr5.2:67730383-67730402 MS.gene78488:intron 30.0%
TAGAACAGAAAAGACATGTA+GGG + chr5.2:67731224-67731243 None:intergenic 30.0%
! AAGTTATTCTAGAGAGCTTA+TGG - chr5.2:67730720-67730739 MS.gene78488:intron 30.0%
! TACATGTCTTTTCTGTTCTA+TGG - chr5.2:67731224-67731243 MS.gene78488:intron 30.0%
!! TTATCAGGTTTGATTAGCTT+CGG - chr5.2:67730062-67730081 MS.gene78488:intron 30.0%
!!! CACAAACAACTTGTTACTTT+TGG - chr5.2:67730848-67730867 MS.gene78488:intron 30.0%
!!! TTTCCCTTTTTCAAATGTCT+AGG - chr5.2:67730406-67730425 MS.gene78488:intron 30.0%
!!! TTTTTTTGAACAAGGAGGAA+AGG + chr5.2:67729881-67729900 None:intergenic 30.0%
AGAACAGAAAAGACATGTAG+GGG + chr5.2:67731223-67731242 None:intergenic 35.0%
ATAGATGCACTTACTTTGTC+TGG + chr5.2:67731120-67731139 None:intergenic 35.0%
ATGAAGTTCCATGTTGTTCT+TGG - chr5.2:67731007-67731026 MS.gene78488:intron 35.0%
GAAAAAGGGAAACCAATCAA+AGG + chr5.2:67730398-67730417 None:intergenic 35.0%
GAAAGAAACCAAGAACAACA+TGG + chr5.2:67731018-67731037 None:intergenic 35.0%
GGCTGAATATCTCATAAATG+TGG - chr5.2:67729843-67729862 MS.gene78488:CDS 35.0%
GGTTCAATGGTAAATGTAAC+TGG + chr5.2:67730945-67730964 None:intergenic 35.0%
GTGCTTTATAACTGTTTCCA+GGG - chr5.2:67731185-67731204 MS.gene78488:intron 35.0%
TAGAGCTATAATCGTAGGAA+TGG - chr5.2:67729960-67729979 MS.gene78488:intron 35.0%
TATGCAGTGAATCAAGTTCA+TGG - chr5.2:67729989-67730008 MS.gene78488:intron 35.0%
! GTCTTTTCTGTTCTATGGAA+TGG - chr5.2:67731229-67731248 MS.gene78488:intron 35.0%
! TATTACTTTGTTTGCGTTCC+TGG - chr5.2:67730974-67730993 MS.gene78488:intron 35.0%
AACCTGATAAAACGGTTGAG+TGG + chr5.2:67730052-67730071 None:intergenic 40.0%
AACCTGCAGAATAGATCATC+AGG - chr5.2:67730217-67730236 MS.gene78488:intron 40.0%
AACTTCATACCACAGAAACC+AGG + chr5.2:67730995-67731014 None:intergenic 40.0%
CAAGTTAAGAAGTTGTCTCG+TGG - chr5.2:67730024-67730043 MS.gene78488:intron 40.0%
CAGTGAATCAAGTTCATGGA+TGG - chr5.2:67729993-67730012 MS.gene78488:intron 40.0%
GAACTTGATTCACTGCATAC+TGG + chr5.2:67729988-67730007 None:intergenic 40.0%
GGCTATAGAGCTATAATCGT+AGG - chr5.2:67729955-67729974 MS.gene78488:intron 40.0%
GGTGCTTTATAACTGTTTCC+AGG - chr5.2:67731184-67731203 MS.gene78488:intron 40.0%
TCATCCCTATTAAGCAACTG+CGG - chr5.2:67731267-67731286 MS.gene78488:intron 40.0%
TGTATTCCTCTCAAGGTCTT+AGG + chr5.2:67730648-67730667 None:intergenic 40.0%
! CTTACTTTGTCTGGTTTGTC+AGG + chr5.2:67731111-67731130 None:intergenic 40.0%
! TACCACTCAACCGTTTTATC+AGG - chr5.2:67730047-67730066 MS.gene78488:intron 40.0%
! TTATAGCTCTATAGCCTGCA+CGG + chr5.2:67729951-67729970 None:intergenic 40.0%
! TTCTATGGAATGGATTCAGC+TGG - chr5.2:67731239-67731258 MS.gene78488:intron 40.0%
ATCGAACCTAAGACCTTGAG+AGG - chr5.2:67730639-67730658 MS.gene78488:intron 45.0%
CATCCCTATTAAGCAACTGC+GGG - chr5.2:67731268-67731287 MS.gene78488:intron 45.0%
CTCTGCAACTGCAAAAGAGA+AGG + chr5.2:67731073-67731092 None:intergenic 45.0%
CTGGATTACTAAGCCCTGTT+TGG - chr5.2:67730480-67730499 MS.gene78488:intron 45.0%
CTTGAGAGGAATACAGTCCA+AGG - chr5.2:67730653-67730672 MS.gene78488:intron 45.0%
CTTGGACTGTATTCCTCTCA+AGG + chr5.2:67730655-67730674 None:intergenic 45.0%
TACTGAACCAGATCTACTGG+TGG - chr5.2:67730445-67730464 MS.gene78488:intron 45.0%
TCTCCCGCAGTTGCTTAATA+GGG + chr5.2:67731274-67731293 None:intergenic 45.0%
TGCCTGATGATCTATTCTGC+AGG + chr5.2:67730222-67730241 None:intergenic 45.0%
TTCTCCCGCAGTTGCTTAAT+AGG + chr5.2:67731275-67731294 None:intergenic 45.0%
! ATTCTCCCTGGTGCCAATTT+CGG + chr5.2:67730621-67730640 None:intergenic 45.0%
! CTTCTCTTTTGCAGTTGCAG+AGG - chr5.2:67731071-67731090 MS.gene78488:CDS 45.0%
!! AACAGTTTGACTTGGGACCT+TGG + chr5.2:67730673-67730692 None:intergenic 45.0%
AGGGGTGATCAAATCTTCCC+TGG + chr5.2:67731205-67731224 None:intergenic 50.0%
CACCAAGTGACGAAGATGGA+GGG - chr5.2:67731330-67731349 MS.gene78488:intron 50.0%
CCAAACTAGCCCACCGAAAT+TGG - chr5.2:67730605-67730624 MS.gene78488:intron 50.0%
CCAGATCTACTGGTGGCATA+TGG - chr5.2:67730452-67730471 MS.gene78488:intron 50.0%
CCATATGCCACCAGTAGATC+TGG + chr5.2:67730455-67730474 None:intergenic 50.0%
CTCCATCTTCGTCACTTGGT+GGG + chr5.2:67731331-67731350 None:intergenic 50.0%
CTGGTGGCATATGGTAAAGC+TGG - chr5.2:67730461-67730480 MS.gene78488:intron 50.0%
GCGTACTGAACCAGATCTAC+TGG - chr5.2:67730442-67730461 MS.gene78488:intron 50.0%
GTCTTAGGTTCGATTCTCCC+TGG + chr5.2:67730633-67730652 None:intergenic 50.0%
GTTTGCGTTCCTGGTTTCTG+TGG - chr5.2:67730983-67731002 MS.gene78488:intron 50.0%
TTCCCTCCATCTTCGTCACT+TGG + chr5.2:67731335-67731354 None:intergenic 50.0%
! TCGTCACTTGGTGGGTCAAA+GGG + chr5.2:67731323-67731342 None:intergenic 50.0%
! TTCGTCACTTGGTGGGTCAA+AGG + chr5.2:67731324-67731343 None:intergenic 50.0%
!! CCAATTTCGGTGGGCTAGTT+TGG + chr5.2:67730608-67730627 None:intergenic 50.0%
!! GTGGGTCAAAGGGTATTTCG+TGG + chr5.2:67731313-67731332 None:intergenic 50.0%
!! TCAAAGGGTATTTCGTGGCG+CGG + chr5.2:67731308-67731327 None:intergenic 50.0%
ATAGCCTGCACGGTACATCG+AGG + chr5.2:67729941-67729960 None:intergenic 55.0%
CCACCAAGTGACGAAGATGG+AGG - chr5.2:67731329-67731348 MS.gene78488:intron 55.0%
CCTCCATCTTCGTCACTTGG+TGG + chr5.2:67731332-67731351 None:intergenic 55.0%
GACCCACCAAGTGACGAAGA+TGG - chr5.2:67731326-67731345 MS.gene78488:intron 55.0%
GATTCCTCGATGTACCGTGC+AGG - chr5.2:67729934-67729953 MS.gene78488:intron 55.0%
! TCCCTGGTGCCAATTTCGGT+GGG + chr5.2:67730617-67730636 None:intergenic 55.0%
AGCCCACCGAAATTGGCACC+AGG - chr5.2:67730612-67730631 MS.gene78488:intron 60.0%
GCCCACCGAAATTGGCACCA+GGG - chr5.2:67730613-67730632 MS.gene78488:intron 60.0%
! CTCCCTGGTGCCAATTTCGG+TGG + chr5.2:67730618-67730637 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 67729766 67731361 67729766 ID=MS.gene78488
chr5.2 mRNA 67729766 67731361 67729766 ID=MS.gene78488.t1;Parent=MS.gene78488
chr5.2 exon 67731355 67731361 67731355 ID=MS.gene78488.t1.exon1;Parent=MS.gene78488.t1
chr5.2 CDS 67731355 67731361 67731355 ID=cds.MS.gene78488.t1;Parent=MS.gene78488.t1
chr5.2 exon 67731059 67731171 67731059 ID=MS.gene78488.t1.exon2;Parent=MS.gene78488.t1
chr5.2 CDS 67731059 67731171 67731059 ID=cds.MS.gene78488.t1;Parent=MS.gene78488.t1
chr5.2 exon 67730654 67730699 67730654 ID=MS.gene78488.t1.exon3;Parent=MS.gene78488.t1
chr5.2 CDS 67730654 67730699 67730654 ID=cds.MS.gene78488.t1;Parent=MS.gene78488.t1
chr5.2 exon 67730002 67730042 67730002 ID=MS.gene78488.t1.exon4;Parent=MS.gene78488.t1
chr5.2 CDS 67730002 67730042 67730002 ID=cds.MS.gene78488.t1;Parent=MS.gene78488.t1
chr5.2 exon 67729766 67729921 67729766 ID=MS.gene78488.t1.exon5;Parent=MS.gene78488.t1
chr5.2 CDS 67729766 67729921 67729766 ID=cds.MS.gene78488.t1;Parent=MS.gene78488.t1
Gene Sequence

>MS.gene78488

ATGTTTGGTAAGTAATTTAAATATCTCCTATCAATACAACAAATTATTATTAAATTTAATTAGCAACATATTGATAAGGCTGAATATCTCATAAATGTGGGAAAAATGTTTTCCTTTCCTCCTTGTTCAAAAAAAAAAAAAAAAAAAATCTTTTCATCCTTATATTTTGATTCCTCGATGTACCGTGCAGGCTATAGAGCTATAATCGTAGGAATGGATCCAGTATGCAGTGAATCAAGTTCATGGATGGAAAATGCACAAGTTAAGAAGTTGTCTCGTGGTACCACTCAACCGTTTTATCAGGTTTGATTAGCTTCGGAACATAAATTTCATTTCTGTGAATTATTCTGTTTCTATATGGTCATATTTAATTATTACCGAATAATTTTAACTCTATAAGCATTTGATTCTTCTTGTACTCTTCAATTCTTATTATTACTGGTAGTACTTCAACCTGCAGAATAGATCATCAGGCAATACAATGCTTCATTTGAATGAAACATTATTTTCAATCTTGTATGCAAAATGAATATGAATTGTAAATGTATTTATGGTTTTCGATATGTTGCCTTATATGTTTTTGTTATTGTATTAATAACTGGAATGACTTTGATTAATAATTGTTCAGACCTTTGATTGGTTTCCCTTTTTCAAATGTCTAGGTTCTTGTTGACGTGCGTACTGAACCAGATCTACTGGTGGCATATGGTAAAGCTGGATTACTAAGCCCTGTTTGGATGAATAATTTCATTAAGTGTGTATAATATAAGTGCTTATGTATAAAGCTGTTTTTATAACAAAAGATAGAATAAAGTCAAACTGTTTTTTTTTTTAAGAAGCCAAACTAGCCCACCGAAATTGGCACCAGGGAGAATCGAACCTAAGACCTTGAGAGGAATACAGTCCAAGGTCCCAAGTCAAACTGTTTTCTTATAAACAATAAGCTGTTTTCATAAGTTATTCTAGAGAGCTTATGGAAAAAGCTGAAAACGGATTATGAAGTGTCATAAGTTATTTTCATAAGCTCTCCAAAACAGTCTCACATTATATTTGATGGCACTATTCATATAATCTTTCTCGTGCACAAACAACTTGTTACTTTTGGTCACAAAAAAAAAAGAACTTGTTACTTACCTACAATTGCTTTTCTGTACATTTCTTTCTACATTTCACTTACCAGTTACATTTACCATTGAACCAATTAATATTATTACTTTGTTTGCGTTCCTGGTTTCTGTGGTATGAAGTTCCATGTTGTTCTTGGTTTCTTTCTGTAAACAAATACATGTGGATTGAATTTTTCTCCTTCTCTTTTGCAGTTGCAGAGGAGAATCTTTTAGTACCTGACAAACCAGACAAAGTAAGTGCATCTATATTTGAAAAGAAATGCATTATGATGTTATTTATGTTCTTTAATTGGTGCTTTATAACTGTTTCCAGGGAAGATTTGATCACCCCTACATGTCTTTTCTGTTCTATGGAATGGATTCAGCTGGAGATTTCATCCCTATTAAGCAACTGCGGGAGAAGTACAATAAACCGCGCCACGAAATACCCTTTGACCCACCAAGTGACGAAGATGGAGGGAAAGCTTAA
Protein sequence

>MS.gene78488.t1

MFGYRAIIVGMDPVCSESSSWMENAQVKKLSRGTTQPFYQVLVDVRTEPDLLVAYVAEENLLVPDKPDKGRFDHPYMSFLFYGMDSAGDFIPIKQLREKYNKPRHEIPFDPPSDEDGGKA