AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044352


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044352.t1 MTR_3g082970 97.788 226 5 0 1 226 1 226 1.53e-166 458
MS.gene044352.t1 MTR_2g025740 71.875 224 49 2 2 225 23 232 4.18e-110 315
MS.gene044352.t1 MTR_4g133060 70.335 209 62 0 17 225 13 221 4.17e-105 303
MS.gene044352.t1 MTR_4g133060 73.196 194 52 0 32 225 2 195 3.59e-102 294
MS.gene044352.t1 MTR_4g133060 65.366 205 67 1 17 217 13 217 1.12e-90 266
MS.gene044352.t1 MTR_8g097200 67.052 173 57 0 53 225 59 231 8.05e-86 254
MS.gene044352.t1 MTR_3g084940 63.636 176 63 1 52 226 52 227 1.99e-78 235
MS.gene044352.t1 MTR_7g097270 51.337 187 88 3 38 223 33 217 5.89e-63 196
MS.gene044352.t1 MTR_7g097270 49.600 125 60 3 38 161 33 155 4.06e-33 118
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044352.t1 AT3G07880 77.114 201 45 1 25 225 38 237 3.48e-113 324
MS.gene044352.t1 AT1G62450 64.319 213 73 2 15 225 11 222 1.56e-91 268
MS.gene044352.t1 AT1G12070 59.912 227 84 2 1 225 1 222 1.64e-88 261

Find 56 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTGAGCAATAACATTGTTTC+TGG 0.193009 3.3:-69653940 MS.gene044352:CDS
CATAGGACCTAGCTGTATTT+TGG 0.248019 3.3:+69654675 None:intergenic
CCAGAGGGTGTGACTTCTTC+TGG 0.286287 3.3:+69653708 None:intergenic
AAATGGAAGGAGCAGCTTCT+TGG 0.366946 3.3:-69654465 MS.gene044352:CDS
TGTTTGGAAGACTGCTGTTA+AGG 0.371169 3.3:-69653899 MS.gene044352:CDS
GAGGAGGAAGAAGATGAATA+TGG 0.374764 3.3:-69654700 MS.gene044352:CDS
GTTTGGAAGACTGCTGTTAA+GGG 0.387643 3.3:-69653898 MS.gene044352:intron
AATGGAAGGAGCAGCTTCTT+GGG 0.389589 3.3:-69654464 MS.gene044352:CDS
TAAAATACACCAATACTGTT+TGG 0.391465 3.3:-69653915 MS.gene044352:CDS
TATAGGACGATGAGAGTCTA+AGG 0.397474 3.3:-69654488 MS.gene044352:intron
GTTCTTCCCATTCCTGAAGA+TGG 0.408171 3.3:-69654030 MS.gene044352:CDS
CCAGAAGAAGTCACACCCTC+TGG 0.416770 3.3:-69653708 MS.gene044352:CDS
AGGCTTGTAAAATTCACTTC+AGG 0.420910 3.3:+69654084 None:intergenic
GATAATGAAAACAAAGAAAC+AGG 0.423638 3.3:-69654808 MS.gene044352:CDS
TCTGGCATCTCATGTGTGTA+AGG 0.427995 3.3:+69653726 None:intergenic
GTGTGTAAGGCTCTGGTTGA+GGG 0.432758 3.3:+69653739 None:intergenic
ATCTCATGTGTGTAAGGCTC+TGG 0.437007 3.3:+69653732 None:intergenic
ACGATGAGAGTCTAAGGAAA+TGG 0.439473 3.3:-69654482 MS.gene044352:CDS
TGAGCAATAACATTGTTTCT+GGG 0.463614 3.3:-69653939 MS.gene044352:CDS
CAAAATACAGCTAGGTCCTA+TGG 0.489028 3.3:-69654674 MS.gene044352:CDS
AGAACACCTTGAGAAAGATA+AGG 0.492651 3.3:-69654641 MS.gene044352:intron
AGAAGATTCACTCGTATGCC+TGG 0.493330 3.3:+69654735 None:intergenic
TGTGTGTAAGGCTCTGGTTG+AGG 0.496739 3.3:+69653738 None:intergenic
TTGTGGTTTACTCTTAAAGA+AGG 0.514851 3.3:-69653994 MS.gene044352:CDS
CACCCTCTGGGATATTTGCT+AGG 0.518348 3.3:-69653695 MS.gene044352:CDS
TCCTGAAGATGGAAAACCAC+AGG 0.525613 3.3:-69654019 MS.gene044352:CDS
TGATGACAATAAATGTTACT+TGG 0.527867 3.3:-69653413 MS.gene044352:CDS
AGCCTTTCTATAATCTCTCC+TGG 0.528718 3.3:-69654066 MS.gene044352:CDS
ATGGAAAACCACAGGGATTG+TGG 0.531586 3.3:-69654011 MS.gene044352:CDS
ACCCTCTGGGATATTTGCTA+GGG 0.538296 3.3:-69653694 MS.gene044352:CDS
TCACTCGTATGCCTGGTAAG+AGG 0.546518 3.3:+69654742 None:intergenic
ACAAAACCTTATCTTTCTCA+AGG 0.549448 3.3:+69654635 None:intergenic
AACATCATGAGCCTCTTACC+AGG 0.549984 3.3:-69654753 MS.gene044352:CDS
ACAGGACAAACTAGTGAGGC+TGG 0.550189 3.3:-69654790 MS.gene044352:CDS
AAGCTGAATTTCAGACGGTA+AGG 0.552089 3.3:+69653967 None:intergenic
ACAATATTCTGCAAGATCAA+AGG 0.554037 3.3:-69653670 MS.gene044352:intron
GATAGCTCAAAAGAGATGCT+TGG 0.554702 3.3:-69653771 MS.gene044352:CDS
GTCGATGTCAACAACATTGG+AGG 0.554851 3.3:-69654438 MS.gene044352:intron
AGCAGTCTTCCAAACAGTAT+TGG 0.558230 3.3:+69653906 None:intergenic
CAGAAGAAGTCACACCCTCT+GGG 0.582116 3.3:-69653707 MS.gene044352:CDS
TACCAGGAGAGATTATAGAA+AGG 0.583890 3.3:+69654064 None:intergenic
TATGGAGCCAAAATACAGCT+AGG 0.601518 3.3:-69654682 MS.gene044352:CDS
TGTTCTTTAATAGTGACCAT+AGG 0.603238 3.3:+69654658 None:intergenic
AGTGTCGATGTCAACAACAT+TGG 0.603658 3.3:-69654441 MS.gene044352:CDS
CCCCTAGCAAATATCCCAGA+GGG 0.617735 3.3:+69653693 None:intergenic
TGAGAGTCTAAGGAAATGGA+AGG 0.619544 3.3:-69654478 MS.gene044352:CDS
TTCTGTCTATGCAACTGAGG+AGG 0.624555 3.3:-69654716 MS.gene044352:CDS
AGAACAATGTCATCTCTACC+AGG 0.626041 3.3:+69654048 None:intergenic
CAACAAAGCTGAATTTCAGA+CGG 0.649490 3.3:+69653962 None:intergenic
CCTGAAGATGGAAAACCACA+GGG 0.658329 3.3:-69654018 MS.gene044352:CDS
CCCTCTGGGATATTTGCTAG+GGG 0.670702 3.3:-69653693 MS.gene044352:CDS
AGAGTAAACCACAATCCCTG+TGG 0.676637 3.3:+69654003 None:intergenic
GGACAAACTAGTGAGGCTGG+TGG 0.680791 3.3:-69654787 MS.gene044352:CDS
ATCTTCTGTCTATGCAACTG+AGG 0.702591 3.3:-69654719 MS.gene044352:CDS
AGAAACAGGACAAACTAGTG+AGG 0.703043 3.3:-69654794 MS.gene044352:CDS
TCCCCTAGCAAATATCCCAG+AGG 0.719574 3.3:+69653692 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATTGTATAATTTTTTTGT+TGG - chr3.3:69654715-69654734 MS.gene044352:CDS 10.0%
!! GTAATTTAAGTAATTTACTT+AGG + chr3.3:69653625-69653644 None:intergenic 15.0%
!! GTTACCAATAAATAATTATG+AGG + chr3.3:69654626-69654645 None:intergenic 20.0%
!! TGTTCCTCATAATTATTTAT+TGG - chr3.3:69654619-69654638 MS.gene044352:intron 20.0%
!! TTGTTACACTTAATATGTAA+CGG + chr3.3:69654650-69654669 None:intergenic 20.0%
!!! TAAAACAAATGTTATTTCAG+TGG - chr3.3:69654396-69654415 MS.gene044352:intron 20.0%
!!! TCAACTATACTTTTGATATT+AGG - chr3.3:69654802-69654821 MS.gene044352:CDS 20.0%
!!! TGAACAATTTTCTTTTACAA+AGG + chr3.3:69653833-69653852 None:intergenic 20.0%
!!! TGTTCATTGTTTATGTTTTT+GGG - chr3.3:69653665-69653684 MS.gene044352:intron 20.0%
!!! TTGTTCATTGTTTATGTTTT+TGG - chr3.3:69653664-69653683 MS.gene044352:intron 20.0%
! GATAATGAAAACAAAGAAAC+AGG - chr3.3:69653381-69653400 MS.gene044352:CDS 25.0%
! GTGTTACAAAATTGGAAATT+TGG + chr3.3:69654351-69654370 None:intergenic 25.0%
! TAAAATACACCAATACTGTT+TGG - chr3.3:69654274-69654293 MS.gene044352:intron 25.0%
! TGATGACAATAAATGTTACT+TGG - chr3.3:69654776-69654795 MS.gene044352:CDS 25.0%
!! CTATACTTTTGATATTAGGA+AGG - chr3.3:69654806-69654825 MS.gene044352:CDS 25.0%
!! TTTTGATATTAGGAAGGATT+GGG - chr3.3:69654812-69654831 MS.gene044352:CDS 25.0%
!!! AGATAAGGTTTTGTTTCTTT+TGG - chr3.3:69653563-69653582 MS.gene044352:intron 25.0%
ACAAAACCTTATCTTTCTCA+AGG + chr3.3:69653557-69653576 None:intergenic 30.0%
ACAATATTCTGCAAGATCAA+AGG - chr3.3:69654519-69654538 MS.gene044352:intron 30.0%
AGGGATAAGTGTTACAAAAT+TGG + chr3.3:69654359-69654378 None:intergenic 30.0%
TGTTCTTTAATAGTGACCAT+AGG + chr3.3:69653534-69653553 None:intergenic 30.0%
TTGTGGTTTACTCTTAAAGA+AGG - chr3.3:69654195-69654214 MS.gene044352:intron 30.0%
! CATTGGAGGTATATAAATCA+CGG - chr3.3:69653765-69653784 MS.gene044352:CDS 30.0%
! CTTTTGATATTAGGAAGGAT+TGG - chr3.3:69654811-69654830 MS.gene044352:CDS 30.0%
! TATTTTTCTTGTGCAGTTTC+TGG - chr3.3:69654752-69654771 MS.gene044352:CDS 30.0%
! TGAGCAATAACATTGTTTCT+GGG - chr3.3:69654250-69654269 MS.gene044352:intron 30.0%
AGAACACCTTGAGAAAGATA+AGG - chr3.3:69653548-69653567 MS.gene044352:intron 35.0%
AGGCTTGTAAAATTCACTTC+AGG + chr3.3:69654108-69654127 None:intergenic 35.0%
CAACAAAGCTGAATTTCAGA+CGG + chr3.3:69654230-69654249 None:intergenic 35.0%
GTGAGCAATAACATTGTTTC+TGG - chr3.3:69654249-69654268 MS.gene044352:intron 35.0%
TACCAGGAGAGATTATAGAA+AGG + chr3.3:69654128-69654147 None:intergenic 35.0%
TGGGTTGTACGAATGAATAT+AGG - chr3.3:69653684-69653703 MS.gene044352:CDS 35.0%
AAGCTGAATTTCAGACGGTA+AGG + chr3.3:69654225-69654244 None:intergenic 40.0%
ACGATGAGAGTCTAAGGAAA+TGG - chr3.3:69653707-69653726 MS.gene044352:CDS 40.0%
AGAAACAGGACAAACTAGTG+AGG - chr3.3:69653395-69653414 MS.gene044352:CDS 40.0%
AGAACAATGTCATCTCTACC+AGG + chr3.3:69654144-69654163 None:intergenic 40.0%
AGCAGTCTTCCAAACAGTAT+TGG + chr3.3:69654286-69654305 None:intergenic 40.0%
AGCCTTTCTATAATCTCTCC+TGG - chr3.3:69654123-69654142 MS.gene044352:intron 40.0%
ATCTTCTGTCTATGCAACTG+AGG - chr3.3:69653470-69653489 MS.gene044352:intron 40.0%
CAAAATACAGCTAGGTCCTA+TGG - chr3.3:69653515-69653534 MS.gene044352:intron 40.0%
GAGGAGGAAGAAGATGAATA+TGG - chr3.3:69653489-69653508 MS.gene044352:intron 40.0%
GATAGCTCAAAAGAGATGCT+TGG - chr3.3:69654418-69654437 MS.gene044352:intron 40.0%
GTTTGGAAGACTGCTGTTAA+GGG - chr3.3:69654291-69654310 MS.gene044352:intron 40.0%
TATAGGACGATGAGAGTCTA+AGG - chr3.3:69653701-69653720 MS.gene044352:CDS 40.0%
TATGGAGCCAAAATACAGCT+AGG - chr3.3:69653507-69653526 MS.gene044352:intron 40.0%
TGAGAGTCTAAGGAAATGGA+AGG - chr3.3:69653711-69653730 MS.gene044352:CDS 40.0%
TGTTTGGAAGACTGCTGTTA+AGG - chr3.3:69654290-69654309 MS.gene044352:intron 40.0%
! CATAGGACCTAGCTGTATTT+TGG + chr3.3:69653517-69653536 None:intergenic 40.0%
! GGTTTTCCATCTTCAGGAAT+GGG + chr3.3:69654168-69654187 None:intergenic 40.0%
! TGGTTTTCCATCTTCAGGAA+TGG + chr3.3:69654169-69654188 None:intergenic 40.0%
!! AGTGTCGATGTCAACAACAT+TGG - chr3.3:69653748-69653767 MS.gene044352:CDS 40.0%
AAATGGAAGGAGCAGCTTCT+TGG - chr3.3:69653724-69653743 MS.gene044352:CDS 45.0%
AACATCATGAGCCTCTTACC+AGG - chr3.3:69653436-69653455 MS.gene044352:intron 45.0%
AATGGAAGGAGCAGCTTCTT+GGG - chr3.3:69653725-69653744 MS.gene044352:CDS 45.0%
AGAAGATTCACTCGTATGCC+TGG + chr3.3:69653457-69653476 None:intergenic 45.0%
AGAGTAAACCACAATCCCTG+TGG + chr3.3:69654189-69654208 None:intergenic 45.0%
ATCTCATGTGTGTAAGGCTC+TGG + chr3.3:69654460-69654479 None:intergenic 45.0%
ATGGAAAACCACAGGGATTG+TGG - chr3.3:69654178-69654197 MS.gene044352:intron 45.0%
CCTGAAGATGGAAAACCACA+GGG - chr3.3:69654171-69654190 MS.gene044352:intron 45.0%
GTCGATGTCAACAACATTGG+AGG - chr3.3:69653751-69653770 MS.gene044352:CDS 45.0%
GTTCTTCCCATTCCTGAAGA+TGG - chr3.3:69654159-69654178 MS.gene044352:intron 45.0%
TCCTGAAGATGGAAAACCAC+AGG - chr3.3:69654170-69654189 MS.gene044352:intron 45.0%
TCTGGCATCTCATGTGTGTA+AGG + chr3.3:69654466-69654485 None:intergenic 45.0%
TTCTGTCTATGCAACTGAGG+AGG - chr3.3:69653473-69653492 MS.gene044352:intron 45.0%
!! ACAAGTGTGTCGATTGTTGC+AGG - chr3.3:69653986-69654005 MS.gene044352:CDS 45.0%
!! ACCCTCTGGGATATTTGCTA+GGG - chr3.3:69654495-69654514 MS.gene044352:intron 45.0%
!! CAAGTGTGTCGATTGTTGCA+GGG - chr3.3:69653987-69654006 MS.gene044352:CDS 45.0%
!! TAATACAATTAAAATTAAAA+GGG + chr3.3:69654378-69654397 None:intergenic 5.0%
!! TTAATACAATTAAAATTAAA+AGG + chr3.3:69654379-69654398 None:intergenic 5.0%
ACAGGACAAACTAGTGAGGC+TGG - chr3.3:69653399-69653418 MS.gene044352:CDS 50.0%
CAGAAGAAGTCACACCCTCT+GGG - chr3.3:69654482-69654501 MS.gene044352:CDS 50.0%
CCCCTAGCAAATATCCCAGA+GGG + chr3.3:69654499-69654518 None:intergenic 50.0%
TCACTCGTATGCCTGGTAAG+AGG + chr3.3:69653450-69653469 None:intergenic 50.0%
TCCCCTAGCAAATATCCCAG+AGG + chr3.3:69654500-69654519 None:intergenic 50.0%
! CCCTGTGGTTTTCCATCTTC+AGG + chr3.3:69654174-69654193 None:intergenic 50.0%
! GTGTGTAAGGCTCTGGTTGA+GGG + chr3.3:69654453-69654472 None:intergenic 50.0%
! TGTGTGTAAGGCTCTGGTTG+AGG + chr3.3:69654454-69654473 None:intergenic 50.0%
!! CACCCTCTGGGATATTTGCT+AGG - chr3.3:69654494-69654513 MS.gene044352:intron 50.0%
!! CCCTCTGGGATATTTGCTAG+GGG - chr3.3:69654496-69654515 MS.gene044352:intron 50.0%
CCAGAAGAAGTCACACCCTC+TGG - chr3.3:69654481-69654500 MS.gene044352:CDS 55.0%
GGACAAACTAGTGAGGCTGG+TGG - chr3.3:69653402-69653421 MS.gene044352:CDS 55.0%
! CCAGAGGGTGTGACTTCTTC+TGG + chr3.3:69654484-69654503 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 69653372 69654839 69653372 ID=MS.gene044352
chr3.3 mRNA 69653372 69654839 69653372 ID=MS.gene044352.t1;Parent=MS.gene044352
chr3.3 exon 69654642 69654839 69654642 ID=MS.gene044352.t1.exon1;Parent=MS.gene044352.t1
chr3.3 CDS 69654642 69654839 69654642 ID=cds.MS.gene044352.t1;Parent=MS.gene044352.t1
chr3.3 exon 69654439 69654505 69654439 ID=MS.gene044352.t1.exon2;Parent=MS.gene044352.t1
chr3.3 CDS 69654439 69654505 69654439 ID=cds.MS.gene044352.t1;Parent=MS.gene044352.t1
chr3.3 exon 69653899 69654117 69653899 ID=MS.gene044352.t1.exon3;Parent=MS.gene044352.t1
chr3.3 CDS 69653899 69654117 69653899 ID=cds.MS.gene044352.t1;Parent=MS.gene044352.t1
chr3.3 exon 69653671 69653795 69653671 ID=MS.gene044352.t1.exon4;Parent=MS.gene044352.t1
chr3.3 CDS 69653671 69653795 69653671 ID=cds.MS.gene044352.t1;Parent=MS.gene044352.t1
chr3.3 exon 69653372 69653443 69653372 ID=MS.gene044352.t1.exon5;Parent=MS.gene044352.t1
chr3.3 CDS 69653372 69653443 69653372 ID=cds.MS.gene044352.t1;Parent=MS.gene044352.t1
Gene Sequence

>MS.gene044352

ATGGGGTCTGATAATGAAAACAAAGAAACAGGACAAACTAGTGAGGCTGGTGGAGAAAAAGAAGAACATCATGAGCCTCTTACCAGGCATACGAGTGAATCTTCTGTCTATGCAACTGAGGAGGAAGAAGATGAATATGGAGCCAAAATACAGCTAGGTCCTATGGTCACTATTAAAGAACACCTTGAGAAAGATAAGGTTTTGTTTCTTTTGGAACTACACATTTGTCTTGTTAATATAATGTTTAATTCCTAAGTAAATTACTTAAATTACATTTTTCATGCTTTATTTTTTGTTCATTGTTTATGTTTTTGGGTTGTACGAATGAATATAGGACGATGAGAGTCTAAGGAAATGGAAGGAGCAGCTTCTTGGGAGTGTCGATGTCAACAACATTGGAGGTATATAAATCACGGTTGTCTCTTTTATAACACTATCATGTCTGATTACAATTGTCACCTTTGTAAAAGAAAATTGTTCAAAATCAACGTCACTTTCAATCTTTATTGTAATATTAATTATTCTTTTTATAATTATATATTATAATTAATATTGTGTACATTACTCTCAAGTGAATATCAACTATTTACGTTTTTTTAATTTGTGTGAAATAAACAAGTGTGTCGATTGTTGCAGGGCGAATCGAGTATGTGTTTATGCATGATTGATGAATATGTTCATTTTGAGAATTTACTTATTTTTTTCAATTTATTTGTTTGTAGAAATTCTTGAACCTGAAGTGAATTTTACAAGCCTTTCTATAATCTCTCCTGGTAGAGATGACATTGTTCTTCCCATTCCTGAAGATGGAAAACCACAGGGATTGTGGTTTACTCTTAAAGAAGGTAGTCCTTACCGTCTGAAATTCAGCTTTGTTGTGAGCAATAACATTGTTTCTGGGTTAAAATACACCAATACTGTTTGGAAGACTGCTGTTAAGGGTATGTTGAATTTAATTCATATAGTCTAATGTTTTCCAAATTTCCAATTTTGTAACACTTATCCCTTTTAATTTTAATTGTATTAAAACAAATGTTATTTCAGTGGATAGCTCAAAAGAGATGCTTGGAACTTTCAGCCCTCAACCAGAGCCTTACACACATGAGATGCCAGAAGAAGTCACACCCTCTGGGATATTTGCTAGGGGACAATATTCTGCAAGATCAAAGGTAATTTAGATTGCAATTAACTGCACTGATTTTGATTGAACAATTATAACATATATGCACTTTCATAATTAGATGAAATGTTCCTCATAATTATTTATTGGTAACTCCGTTACATATTAAGTGTAACAATTTCTCTCAAAAAAAAAATTAAGTGTAACAATTATTACATTTAAAATATTGTATAATTTTTTTGTTGGAAGATAATGATACATATTTTTCTTGTGCAGTTTCTGGATGATGACAATAAATGTTACTTGGAGATCAACTATACTTTTGATATTAGGAAGGATTGGGCTTGA

Protein sequence

>MS.gene044352.t1

MGSDNENKETGQTSEAGGEKEEHHEPLTRHTSESSVYATEEEEDEYGAKIQLGPMVTIKEHLEKDKDDESLRKWKEQLLGSVDVNNIGEILEPEVNFTSLSIISPGRDDIVLPIPEDGKPQGLWFTLKEGSPYRLKFSFVVSNNIVSGLKYTNTVWKTAVKVDSSKEMLGTFSPQPEPYTHEMPEEVTPSGIFARGQYSARSKFLDDDNKCYLEINYTFDIRKDWA