AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene50126


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50126.t1 MTR_5g080880 81.250 256 43 3 1 253 1 254 4.38e-137 389
MS.gene50126.t1 MTR_5g080870 68.504 254 46 5 1 254 1 220 1.10e-111 325
MS.gene50126.t1 MTR_7g063520 42.231 251 123 6 8 253 20 253 2.44e-57 183
MS.gene50126.t1 MTR_4g006560 32.075 159 100 3 97 253 83 235 1.47e-22 93.2
MS.gene50126.t1 MTR_1g013120 30.041 243 143 9 24 253 4 232 2.77e-21 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene50126.t1 AT5G05990 37.500 264 142 6 5 253 3 258 6.38e-53 172
MS.gene50126.t1 AT3G55605 40.959 271 128 9 1 253 1 257 1.77e-50 166
MS.gene50126.t1 AT2G39795 42.564 195 103 3 63 253 60 249 3.14e-48 160
MS.gene50126.t1 AT5G02050 36.803 269 151 6 1 253 1 266 1.35e-42 146
MS.gene50126.t1 AT2G39790 29.741 232 145 4 31 254 19 240 8.05e-27 104
MS.gene50126.t1 AT1G15870 29.193 161 103 4 96 253 88 240 1.81e-20 87.4
MS.gene50126.t1 AT1G80720 30.120 166 104 5 92 253 31 188 6.03e-16 74.3
MS.gene50126.t1 AT1G80720 30.120 166 104 5 92 253 83 240 1.01e-15 74.7
MS.gene50126.t1 AT4G31930 29.630 162 99 5 97 252 80 232 5.24e-13 67.0

Find 44 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATTATCAACTATCTTAAA+TGG 0.175868 5.4:-63305027 None:intergenic
AGTGTTATTGTCTGATTTCC+TGG 0.252098 5.4:-63305048 None:intergenic
ATCAGACAATAACACTTAAA+AGG 0.289378 5.4:+63305055 MS.gene50126:CDS
TTATCAAGGTGAAGAAATTC+AGG 0.325526 5.4:+63305080 MS.gene50126:CDS
CCAAGTCAAGCACTTTCCTT+AGG 0.334931 5.4:+63304540 MS.gene50126:CDS
TGCAAGAAATTTACTGTGCT+TGG 0.359052 5.4:-63305776 None:intergenic
CAGCGAATAACCATCTCATC+TGG 0.375769 5.4:-63305267 None:intergenic
TTAGAAACCTTGACTGAAAG+TGG 0.404401 5.4:-63305204 None:intergenic
CTCTTATTTCTAAGTACTTG+TGG 0.408675 5.4:-63305745 None:intergenic
TGCAAGAGTACATGATCAAC+AGG 0.410602 5.4:+63305795 MS.gene50126:CDS
TTCAGTCAAGGTTTCTAAGA+AGG 0.418352 5.4:+63305209 MS.gene50126:CDS
CACAAGTACTTAGAAATAAG+AGG 0.434165 5.4:+63305746 MS.gene50126:CDS
GATTATCAACTATCTTAAAT+GGG 0.456111 5.4:-63305026 None:intergenic
TAATCATCAAAAGGATGATA+AGG 0.475586 5.4:+63305146 MS.gene50126:CDS
GAGAAAAGTCTCATCGGAGT+TGG 0.476774 5.4:-63304699 None:intergenic
CAGGAAAAGTAGAGACTACT+TGG 0.480599 5.4:+63305814 MS.gene50126:CDS
CAAGTCAAGCACTTTCCTTA+GGG 0.487750 5.4:+63304541 MS.gene50126:CDS
ATCGAAAATCACTTGTGCTC+AGG 0.490320 5.4:+63304733 MS.gene50126:CDS
GTCAAGGTTTCTAAGAAGGA+TGG 0.493043 5.4:+63305213 MS.gene50126:CDS
AGAAAAGTCTCATCGGAGTT+GGG 0.497268 5.4:-63304698 None:intergenic
CTCGTAGCGGTTGACGGCAG+CGG 0.497835 5.4:-63304624 None:intergenic
TTTAAGATAGTTGATAATCC+AGG 0.504200 5.4:+63305030 MS.gene50126:CDS
TGAACCCTCGTAGCGGTTGA+CGG 0.507166 5.4:-63304630 None:intergenic
AGAACATGATAATCATCAAA+AGG 0.514345 5.4:+63305137 MS.gene50126:CDS
ATCTTAAATGGGAAATTGCT+CGG 0.515748 5.4:-63305015 None:intergenic
GAAAGCACGGCGCGATGACC+CGG 0.519271 5.4:-63304602 None:intergenic
ACACTTAAAAGGACTTATCA+AGG 0.527097 5.4:+63305066 MS.gene50126:CDS
AAGCATTCCACTTTCAGTCA+AGG 0.530679 5.4:+63305197 MS.gene50126:CDS
AACACATTTGAATTTCAAAG+AGG 0.535659 5.4:-63305238 None:intergenic
GTTTACAGCGCGGAACTCAT+CGG 0.541419 5.4:-63304759 None:intergenic
CGCTGCCGTCAACCGCTACG+AGG 0.550566 5.4:+63304625 MS.gene50126:CDS
GTTGACGGCAGCGGAAAGCA+CGG 0.551406 5.4:-63304615 None:intergenic
TGATTATCATGTTCTTCACC+AGG 0.551810 5.4:-63305129 None:intergenic
CCTAAGGAAAGTGCTTGACT+TGG 0.566876 5.4:-63304540 None:intergenic
TCAAGGTTTCTAAGAAGGAT+GGG 0.576019 5.4:+63305214 MS.gene50126:CDS
AATCTTGCAACAAGCAGCTG+CGG 0.606350 5.4:-63305320 None:intergenic
AGCGAATAACCATCTCATCT+GGG 0.609542 5.4:-63305266 None:intergenic
TAAACGGAGAAAAGTCTCAT+CGG 0.611707 5.4:-63304705 None:intergenic
GCTGCCGTCAACCGCTACGA+GGG 0.613894 5.4:+63304626 MS.gene50126:CDS
TGTTGCTTACCCAGATGAGA+TGG 0.638083 5.4:+63305257 MS.gene50126:CDS
TCAGAAGAAAAGTGAAACGT+AGG 0.644962 5.4:-63304659 None:intergenic
AAAGTAGAGACTACTTGGTG+TGG 0.647167 5.4:+63305819 MS.gene50126:CDS
AAGTGCTTGACTTGGAACGA+AGG 0.662607 5.4:-63304532 None:intergenic
GAACAAATGAACCCTCGTAG+CGG 0.717050 5.4:-63304637 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATGTTGAAAATTTGATTT+TGG + chr5.4:63304971-63304990 MS.gene50126:intron 15.0%
!!! TGAGATTATGATTTTTAATT+TGG + chr5.4:63305104-63305123 MS.gene50126:CDS 15.0%
!! AATTGAAAGTAATACAAACA+GGG - chr5.4:63305644-63305663 None:intergenic 20.0%
!! ATGGTATGAAAATTTGAATT+TGG + chr5.4:63304916-63304935 MS.gene50126:intron 20.0%
!! GATTATCAACTATCTTAAAT+GGG - chr5.4:63305029-63305048 None:intergenic 20.0%
!! TAATTGAAAGTAATACAAAC+AGG - chr5.4:63305645-63305664 None:intergenic 20.0%
!!! AATTTGATTTTGGTTGATAT+AGG + chr5.4:63304981-63305000 MS.gene50126:intron 20.0%
!!! ATTTGATTTTGGTTGATATA+GGG + chr5.4:63304982-63305001 MS.gene50126:intron 20.0%
!!! TGATTTTCGATTCAATTAAA+CGG - chr5.4:63304724-63304743 None:intergenic 20.0%
! AACACATTTGAATTTCAAAG+AGG - chr5.4:63305241-63305260 None:intergenic 25.0%
! ACATCAGTGATGTTAAATAA+AGG + chr5.4:63305416-63305435 MS.gene50126:intron 25.0%
! AGAACATGATAATCATCAAA+AGG + chr5.4:63305137-63305156 MS.gene50126:CDS 25.0%
! AGAATAAAATAATCAGAACG+AGG - chr5.4:63305357-63305376 None:intergenic 25.0%
! ATCAGACAATAACACTTAAA+AGG + chr5.4:63305055-63305074 MS.gene50126:CDS 25.0%
! ATCATGAGTCTAGTAAATTA+AGG - chr5.4:63304793-63304812 None:intergenic 25.0%
! ATGTTAAATAAAGGCTATAG+CGG + chr5.4:63305425-63305444 MS.gene50126:intron 25.0%
! GGATTATCAACTATCTTAAA+TGG - chr5.4:63305030-63305049 None:intergenic 25.0%
! TAATCATCAAAAGGATGATA+AGG + chr5.4:63305146-63305165 MS.gene50126:CDS 25.0%
! TTTAATCATACCAGCTTATA+AGG - chr5.4:63304880-63304899 None:intergenic 25.0%
!! ATTTTCATACCATTACGAAA+TGG - chr5.4:63304909-63304928 None:intergenic 25.0%
!! TTTTCATACCATTACGAAAT+GGG - chr5.4:63304908-63304927 None:intergenic 25.0%
!!! ATGATTTTTAATTTGGTTCC+TGG + chr5.4:63305111-63305130 MS.gene50126:CDS 25.0%
!!! TTTAAGATAGTTGATAATCC+AGG + chr5.4:63305030-63305049 MS.gene50126:CDS 25.0%
AAAAAAGACCCATTTCGTAA+TGG + chr5.4:63304897-63304916 MS.gene50126:intron 30.0%
ACACTTAAAAGGACTTATCA+AGG + chr5.4:63305066-63305085 MS.gene50126:CDS 30.0%
ATCTTAAATGGGAAATTGCT+CGG - chr5.4:63305018-63305037 None:intergenic 30.0%
ATTGATCAGAAAAACTCAAC+CGG + chr5.4:63304583-63304602 MS.gene50126:CDS 30.0%
CACAAGTACTTAGAAATAAG+AGG + chr5.4:63305746-63305765 MS.gene50126:CDS 30.0%
TGAACTTATACCTTATAAGC+TGG + chr5.4:63304867-63304886 MS.gene50126:intron 30.0%
TTATCAAGGTGAAGAAATTC+AGG + chr5.4:63305080-63305099 MS.gene50126:CDS 30.0%
! GTGCATTCAATATTTGAAAC+CGG + chr5.4:63305389-63305408 MS.gene50126:intron 30.0%
! TGCATTCAATATTTGAAACC+GGG + chr5.4:63305390-63305409 MS.gene50126:intron 30.0%
!! CTCTTATTTCTAAGTACTTG+TGG - chr5.4:63305748-63305767 None:intergenic 30.0%
CCAATCTCAATTTCAAATCG+CGG - chr5.4:63305524-63305543 None:intergenic 35.0%
TAAACGGAGAAAAGTCTCAT+CGG - chr5.4:63304708-63304727 None:intergenic 35.0%
TCAGAAGAAAAGTGAAACGT+AGG - chr5.4:63304662-63304681 None:intergenic 35.0%
TCCAAATCCCTGGAAAAAAA+TGG - chr5.4:63305704-63305723 None:intergenic 35.0%
TGATTATCATGTTCTTCACC+AGG - chr5.4:63305132-63305151 None:intergenic 35.0%
TGCAAGAAATTTACTGTGCT+TGG - chr5.4:63305779-63305798 None:intergenic 35.0%
TTAGAAACCTTGACTGAAAG+TGG - chr5.4:63305207-63305226 None:intergenic 35.0%
TTGATCAGAAAAACTCAACC+GGG + chr5.4:63304584-63304603 MS.gene50126:CDS 35.0%
TTGCAGTTCAGAATCAGATT+GGG + chr5.4:63305597-63305616 MS.gene50126:intron 35.0%
! AGTGTTATTGTCTGATTTCC+TGG - chr5.4:63305051-63305070 None:intergenic 35.0%
! CGCGATTTGAAATTGAGATT+GGG + chr5.4:63305522-63305541 MS.gene50126:intron 35.0%
! GATTTGAAATTGAGATTGGG+TGG + chr5.4:63305525-63305544 MS.gene50126:intron 35.0%
! GCATTCAATATTTGAAACCG+GGG + chr5.4:63305391-63305410 MS.gene50126:intron 35.0%
! TCAAGGTTTCTAAGAAGGAT+GGG + chr5.4:63305214-63305233 MS.gene50126:CDS 35.0%
! TCAGAATCAGATTGGGATTT+TGG + chr5.4:63305604-63305623 MS.gene50126:intron 35.0%
! TTCAGTCAAGGTTTCTAAGA+AGG + chr5.4:63305209-63305228 MS.gene50126:CDS 35.0%
!! TTTTGGTTGATATAGGGTGA+GGG + chr5.4:63304988-63305007 MS.gene50126:intron 35.0%
!!! AGATTCTGCCATTTTTTTCC+AGG + chr5.4:63305693-63305712 MS.gene50126:intron 35.0%
!!! ATTTTGGTTGATATAGGGTG+AGG + chr5.4:63304987-63305006 MS.gene50126:intron 35.0%
!!! GATTCTGCCATTTTTTTCCA+GGG + chr5.4:63305694-63305713 MS.gene50126:intron 35.0%
AAGCATTCCACTTTCAGTCA+AGG + chr5.4:63305197-63305216 MS.gene50126:CDS 40.0%
AGAAAAGTCTCATCGGAGTT+GGG - chr5.4:63304701-63304720 None:intergenic 40.0%
AGCGAATAACCATCTCATCT+GGG - chr5.4:63305269-63305288 None:intergenic 40.0%
ATCGAAAATCACTTGTGCTC+AGG + chr5.4:63304733-63304752 MS.gene50126:CDS 40.0%
CAAGTCAAGCACTTTCCTTA+GGG + chr5.4:63304541-63304560 MS.gene50126:CDS 40.0%
CAGGAAAAGTAGAGACTACT+TGG + chr5.4:63305814-63305833 MS.gene50126:CDS 40.0%
CCACTATAGCTGCTATGATA+TGG - chr5.4:63305453-63305472 None:intergenic 40.0%
CCATATCATAGCAGCTATAG+TGG + chr5.4:63305450-63305469 MS.gene50126:intron 40.0%
GTTGCAGTTCAGAATCAGAT+TGG + chr5.4:63305596-63305615 MS.gene50126:intron 40.0%
TAACATCACTGATGTAACCC+CGG - chr5.4:63305411-63305430 None:intergenic 40.0%
! AAAGTAGAGACTACTTGGTG+TGG + chr5.4:63305819-63305838 MS.gene50126:CDS 40.0%
! CCGCGATTTGAAATTGAGAT+TGG + chr5.4:63305521-63305540 MS.gene50126:intron 40.0%
! GTCAAGGTTTCTAAGAAGGA+TGG + chr5.4:63305213-63305232 MS.gene50126:CDS 40.0%
! TGCAAGAGTACATGATCAAC+AGG + chr5.4:63305795-63305814 MS.gene50126:CDS 40.0%
! TTTTTCCAGGGATTTGGATG+AGG + chr5.4:63305706-63305725 MS.gene50126:intron 40.0%
!!! GCCATTTTTTTCCAGGGATT+TGG + chr5.4:63305700-63305719 MS.gene50126:intron 40.0%
AATCTTGCAACAAGCAGCTG+CGG - chr5.4:63305323-63305342 None:intergenic 45.0%
CAGCGAATAACCATCTCATC+TGG - chr5.4:63305270-63305289 None:intergenic 45.0%
CCAAGTCAAGCACTTTCCTT+AGG + chr5.4:63304540-63304559 MS.gene50126:CDS 45.0%
GAACAAATGAACCCTCGTAG+CGG - chr5.4:63304640-63304659 None:intergenic 45.0%
GAGAAAAGTCTCATCGGAGT+TGG - chr5.4:63304702-63304721 None:intergenic 45.0%
GCTATAGCACCTTTGCATAG+CGG + chr5.4:63305476-63305495 MS.gene50126:intron 45.0%
GTTCAAACTCCGCTATGCAA+AGG - chr5.4:63305488-63305507 None:intergenic 45.0%
TCGCAGAAGAAAAAGCCCTA+AGG - chr5.4:63304559-63304578 None:intergenic 45.0%
TCTCTACAACCAAGCAGTAC+AGG - chr5.4:63305560-63305579 None:intergenic 45.0%
TGTTGCTAACCTGTACTGCT+TGG + chr5.4:63305548-63305567 MS.gene50126:intron 45.0%
! TGTTGCTTACCCAGATGAGA+TGG + chr5.4:63305257-63305276 MS.gene50126:CDS 45.0%
!! AAGTGCTTGACTTGGAACGA+AGG - chr5.4:63304535-63304554 None:intergenic 45.0%
!! CCTAAGGAAAGTGCTTGACT+TGG - chr5.4:63304543-63304562 None:intergenic 45.0%
GGAAGACGAAGTTTACAGCG+CGG - chr5.4:63304772-63304791 None:intergenic 50.0%
GTTTACAGCGCGGAACTCAT+CGG - chr5.4:63304762-63304781 None:intergenic 50.0%
CAACGCCTCATCCAAATCCC+TGG - chr5.4:63305714-63305733 None:intergenic 55.0%
TGAACCCTCGTAGCGGTTGA+CGG - chr5.4:63304633-63304652 None:intergenic 55.0%
GTTGACGGCAGCGGAAAGCA+CGG - chr5.4:63304618-63304637 None:intergenic 60.0%
CTCGTAGCGGTTGACGGCAG+CGG - chr5.4:63304627-63304646 None:intergenic 65.0%
GCTGCCGTCAACCGCTACGA+GGG + chr5.4:63304626-63304645 MS.gene50126:CDS 65.0%
! GAAAGCACGGCGCGATGACC+CGG - chr5.4:63304605-63304624 None:intergenic 65.0%
CGCTGCCGTCAACCGCTACG+AGG + chr5.4:63304625-63304644 MS.gene50126:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 63304515 63305874 63304515 ID=MS.gene50126
chr5.4 mRNA 63304515 63305874 63304515 ID=MS.gene50126.t1;Parent=MS.gene50126
chr5.4 exon 63304515 63304775 63304515 ID=MS.gene50126.t1.exon1;Parent=MS.gene50126.t1
chr5.4 CDS 63304515 63304775 63304515 ID=cds.MS.gene50126.t1;Parent=MS.gene50126.t1
chr5.4 exon 63305003 63305346 63305003 ID=MS.gene50126.t1.exon2;Parent=MS.gene50126.t1
chr5.4 CDS 63305003 63305346 63305003 ID=cds.MS.gene50126.t1;Parent=MS.gene50126.t1
chr5.4 exon 63305715 63305874 63305715 ID=MS.gene50126.t1.exon3;Parent=MS.gene50126.t1
chr5.4 CDS 63305715 63305874 63305715 ID=cds.MS.gene50126.t1;Parent=MS.gene50126.t1
Gene Sequence

>MS.gene50126

ATGGCGTTCAATTCAATCCTTCGTTCCAAGTCAAGCACTTTCCTTAGGGCTTTTTCTTCTGCGACTCAATTGATCAGAAAAACTCAACCGGGTCATCGCGCCGTGCTTTCCGCTGCCGTCAACCGCTACGAGGGTTCATTTGTTCCTACGTTTCACTTTTCTTCTGAAGCTGTCAAAAACGAACCCAACTCCGATGAGACTTTTCTCCGTTTAATTGAATCGAAAATCACTTGTGCTCAGGAAACCGATGAGTTCCGCGCTGTAAACTTCGTCTTCCTTAATTTACTAGACTCATGATTGTAGTAATAGAAACAATGTTTTTCTTTTTAATTTCATTAGCTAGACACAATTTTGAACTTATACCTTATAAGCTGGTATGATTAAAAAAGACCCATTTCGTAATGGTATGAAAATTTGAATTTGGTTGTTAATTATGATAATTATTATTATGTTGTGAAATGTTGAAAATTTGATTTTGGTTGATATAGGGTGAGGGAGTTCCGAGCAATTTCCCATTTAAGATAGTTGATAATCCAGGAAATCAGACAATAACACTTAAAAGGACTTATCAAGGTGAAGAAATTCAGGTTGAGATTATGATTTTTAATTTGGTTCCTGGTGAAGAACATGATAATCATCAAAAGGATGATAAGGATGATGAGAGTGAGAGAGCAACTCAATCAAGCATTCCACTTTCAGTCAAGGTTTCTAAGAAGGATGGGACCTCTTTGAAATTCAAATGTGTTGCTTACCCAGATGAGATGGTTATTCGCTGCTTGTTTATTAAGAATCGTGATGAACAGATCCGCAGCTGCTTGTTGCAAGATTTTCAGTATGTACCTCGTTCTGATTATTTTATTCTGTTTATAAATATGTGCATTCAATATTTGAAACCGGGGTTACATCAGTGATGTTAAATAAAGGCTATAGCGGTACCATATCATAGCAGCTATAGTGGTGCGCTATAGCACCTTTGCATAGCGGAGTTTGAACAAATAACTATTTTCCGCGATTTGAAATTGAGATTGGGTGGTGTTGCTAACCTGTACTGCTTGGTTGTAGAGACATGAAAAATATTGATGTTGCAGTTCAGAATCAGATTGGGATTTTGGAGCTTTTTGTAAAACCCTGTTTGTATTACTTTCAATTAATGTTGTAGCTTATACATTGTTTGATTGAGATTCTGCCATTTTTTTCCAGGGATTTGGATGAGGCGTTGCAAAAGTCATTCCACAAGTACTTAGAAATAAGAGGAATCAAACCAAGCACAGTAAATTTCTTGCAAGAGTACATGATCAACAGGAAAAGTAGAGACTACTTGGTGTGGTTGAATAAGCTCAAGAATTTCATTAAAGCATGA

Protein sequence

>MS.gene50126.t1

MAFNSILRSKSSTFLRAFSSATQLIRKTQPGHRAVLSAAVNRYEGSFVPTFHFSSEAVKNEPNSDETFLRLIESKITCAQETDEFRAGEGVPSNFPFKIVDNPGNQTITLKRTYQGEEIQVEIMIFNLVPGEEHDNHQKDDKDDESERATQSSIPLSVKVSKKDGTSLKFKCVAYPDEMVIRCLFIKNRDEQIRSCLLQDFQDLDEALQKSFHKYLEIRGIKPSTVNFLQEYMINRKSRDYLVWLNKLKNFIKA