AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene38248


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38248.t1 MTR_5g096700 94.848 330 15 1 1 328 1 330 0.0 649
MS.gene38248.t1 MTR_5g096700 94.465 271 15 0 58 328 1 271 0.0 530
MS.gene38248.t1 MTR_3g061090 64.134 329 115 3 1 327 1 328 1.03e-152 432
MS.gene38248.t1 MTR_3g061090 65.759 257 85 3 73 327 1 256 1.38e-117 340
MS.gene38248.t1 MTR_1g029850 44.615 325 175 3 7 327 5 328 4.70e-99 295
MS.gene38248.t1 MTR_3g088560 46.273 322 168 4 5 323 2 321 8.03e-98 292
MS.gene38248.t1 MTR_5g096790 45.619 331 153 10 6 323 6 322 2.50e-88 268
MS.gene38248.t1 MTR_3g088560 46.444 239 124 3 88 323 14 251 4.59e-67 211
MS.gene38248.t1 MTR_3g088560 46.414 237 123 3 90 323 31 266 2.75e-66 209
MS.gene38248.t1 MTR_3g088560 46.970 198 101 3 129 323 3 199 5.39e-54 176
MS.gene38248.t1 MTR_3g072160 33.537 164 105 3 133 292 33 196 1.88e-13 69.3
MS.gene38248.t1 MTR_3g072160 33.537 164 105 3 133 292 70 233 1.89e-13 69.7
MS.gene38248.t1 MTR_7g094490 28.000 150 96 3 153 291 197 345 2.75e-12 67.4
MS.gene38248.t1 MTR_7g094900 29.231 130 90 2 163 292 545 672 4.33e-12 67.4
MS.gene38248.t1 MTR_5g005940 29.078 141 97 3 163 302 536 674 4.92e-12 67.0
MS.gene38248.t1 MTR_7g094910 29.231 130 90 2 163 292 526 653 5.04e-12 67.0
MS.gene38248.t1 MTR_1g072650 27.815 151 97 3 153 292 201 350 9.55e-12 65.9
MS.gene38248.t1 MTR_3g088660 28.289 152 103 3 174 323 94 241 9.67e-12 64.7
MS.gene38248.t1 MTR_5g087500 29.487 156 90 4 153 292 191 342 3.36e-11 63.9
MS.gene38248.t1 MTR_5g087500 29.487 156 90 4 153 292 191 342 3.36e-11 64.3
MS.gene38248.t1 MTR_5g087500 30.065 153 87 4 153 289 191 339 3.96e-11 63.5
MS.gene38248.t1 MTR_3g069000 25.000 160 108 2 142 290 37 195 5.01e-11 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene38248.t1 AT1G55760 57.622 328 137 2 1 327 1 327 4.80e-139 397
MS.gene38248.t1 AT1G21780 47.516 322 166 3 7 327 5 324 1.96e-109 322
MS.gene38248.t1 AT1G21780 47.516 322 166 3 7 327 5 324 1.96e-109 322
MS.gene38248.t1 AT1G01640 29.787 188 128 4 142 327 3 188 1.66e-15 74.7
MS.gene38248.t1 AT3G56230 29.870 154 105 3 142 292 90 243 2.59e-14 72.4
MS.gene38248.t1 AT2G39760 28.947 152 96 2 151 291 182 332 8.45e-14 71.6
MS.gene38248.t1 AT2G39760 28.947 152 96 2 151 291 182 332 1.13e-13 71.2
MS.gene38248.t1 AT2G39760 28.947 152 96 2 151 291 182 332 1.13e-13 71.2
MS.gene38248.t1 AT1G01640 29.586 169 115 4 161 327 1 167 1.88e-13 68.2
MS.gene38248.t1 AT2G39760 28.947 152 96 2 151 291 182 332 2.29e-13 70.9
MS.gene38248.t1 AT1G05690 26.415 159 108 4 149 301 40 195 1.71e-11 65.1
MS.gene38248.t1 AT5G63160 28.824 170 114 4 161 325 23 190 3.31e-11 63.5
MS.gene38248.t1 AT5G63160 28.824 170 114 4 161 325 23 190 3.64e-11 63.9
MS.gene38248.t1 AT3G06190 27.632 152 98 3 151 291 190 340 6.17e-11 63.2
MS.gene38248.t1 AT2G30600 28.671 143 97 3 138 275 326 468 8.48e-11 63.5
MS.gene38248.t1 AT2G30600 28.671 143 97 3 138 275 326 468 8.48e-11 63.5
MS.gene38248.t1 AT2G30600 28.671 143 97 3 138 275 326 468 8.48e-11 63.5
MS.gene38248.t1 AT2G30600 28.671 143 97 3 138 275 326 468 8.48e-11 63.5

Find 44 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCAATATCTTGTGAAATT+TGG 0.204904 5.3:+78105177 MS.gene38248:CDS
ATTGATACAAAGTTGCAATT+TGG 0.261172 5.3:-78105131 None:intergenic
GTGGGGAAGCTTGCTCTATT+TGG 0.265550 5.3:+78104704 MS.gene38248:CDS
CCATTGAACTAGACGATTCA+TGG 0.288711 5.3:-78103933 None:intergenic
CAATTGCATCTTTCATAGTT+AGG 0.300214 5.3:+78104186 MS.gene38248:CDS
GCTTGCTCTATTTGGCCTAA+TGG 0.324580 5.3:+78104712 MS.gene38248:CDS
AGAATTTCTTATACATAGAT+TGG 0.343658 5.3:+78105005 MS.gene38248:CDS
ACTTGTCAGCTGCATGTAAT+AGG 0.350791 5.3:-78105029 None:intergenic
TCAAAGAAATTCTTGATGCT+TGG 0.368629 5.3:+78105274 MS.gene38248:CDS
ATGTCAATTATAAACTTTCC+AGG 0.368972 5.3:-78104442 None:intergenic
ATAGCTTTCTGTGGGAGATT+GGG 0.369080 5.3:+78104410 MS.gene38248:CDS
GATAGCTTTCTGTGGGAGAT+TGG 0.372741 5.3:+78104409 MS.gene38248:CDS
AGCAAAATCTTGACTCAATC+AGG 0.374788 5.3:+78104230 MS.gene38248:CDS
GTTAGGATTCTTAGTTATGC+TGG 0.386999 5.3:+78104203 MS.gene38248:CDS
AGGGTTGTGTGTGATTGTTT+TGG 0.394454 5.3:-78104162 None:intergenic
GCCATAAAGAAAATTTATAA+AGG 0.401897 5.3:-78104968 None:intergenic
TCAAAATAGCCATGTGGAAC+TGG 0.403978 5.3:+78104002 MS.gene38248:CDS
TTCTCTTATCATTCGACCTA+GGG 0.404879 5.3:-78104773 None:intergenic
ATTATAAACTTTCCAGGTAG+TGG 0.426082 5.3:-78104436 None:intergenic
CTAACTATGAAAGATGCAAT+TGG 0.440177 5.3:-78104185 None:intergenic
CCATGAATCGTCTAGTTCAA+TGG 0.453483 5.3:+78103933 MS.gene38248:CDS
TCATTCGACCTAGGGATTCA+AGG 0.458286 5.3:-78104765 None:intergenic
CTCTGCTGCATGAATCCATT+AGG 0.476375 5.3:-78104727 None:intergenic
GAGATTGGGGTTCCACTACC+TGG 0.484202 5.3:+78104424 MS.gene38248:CDS
GGCAAAATATATGATATTCA+AGG 0.488841 5.3:+78105198 MS.gene38248:CDS
CTTCTCTTATCATTCGACCT+AGG 0.496175 5.3:-78104774 None:intergenic
TAGCTTTCTGTGGGAGATTG+GGG 0.530521 5.3:+78104411 MS.gene38248:CDS
CATTCGACCTAGGGATTCAA+GGG 0.532711 5.3:-78104764 None:intergenic
ATGAGCTCTTATGCTTCCCT+CGG 0.548636 5.3:-78104830 None:intergenic
CAATAACGATAGCTTTCTGT+GGG 0.562302 5.3:+78104402 MS.gene38248:CDS
ACTATGAAAGATGCAATTGG+AGG 0.571379 5.3:-78104182 None:intergenic
GCAGCGGCCCTTGAATCCCT+AGG 0.588324 5.3:+78104757 MS.gene38248:CDS
AACAATCAACGTCAATTCCG+AGG 0.588705 5.3:+78104813 MS.gene38248:CDS
GCAATAACGATAGCTTTCTG+TGG 0.597072 5.3:+78104401 MS.gene38248:CDS
TTTGAAAACTACATGTCCAA+AGG 0.597428 5.3:+78104477 MS.gene38248:CDS
CTATGAAAGATGCAATTGGA+GGG 0.614089 5.3:-78104181 None:intergenic
GATATGAAGGCATTTATCAG+TGG 0.615660 5.3:+78104097 MS.gene38248:intron
ACAATCAACGTCAATTCCGA+GGG 0.626764 5.3:+78104814 MS.gene38248:CDS
TTGACTTTACCAGTTCCACA+TGG 0.646739 5.3:-78104011 None:intergenic
GAAAACATGCTGCGAAACAC+AGG 0.659506 5.3:-78104877 None:intergenic
TTATCAGTGGAAAAGAACTG+TGG 0.666641 5.3:+78104110 MS.gene38248:CDS
AAAAGATTGAATTGACATGT+CGG 0.667795 5.3:-78104941 None:intergenic
GCAGCAGAGACAAAATGCAG+CGG 0.684257 5.3:+78104741 MS.gene38248:CDS
ATCCATTCAAAATAGCCATG+TGG 0.702367 5.3:+78103996 MS.gene38248:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATAATATATCCAAATTA+AGG + chr5.3:78104508-78104527 MS.gene38248:intron 10.0%
!! CAAACAAAATAAAAAGTAAA+TGG - chr5.3:78104573-78104592 None:intergenic 15.0%
!! TATTATTCAATACCTTAATT+TGG - chr5.3:78104523-78104542 None:intergenic 15.0%
!!! ACCTTTATAAATTTTCTTTA+TGG + chr5.3:78104967-78104986 MS.gene38248:CDS 15.0%
!!! ATCAAGGAAAATTTTAAATT+AGG - chr5.3:78104673-78104692 None:intergenic 15.0%
!!! CATTTACTTTTTATTTTGTT+TGG + chr5.3:78104571-78104590 MS.gene38248:intron 15.0%
!! AGAATTTCTTATACATAGAT+TGG + chr5.3:78105005-78105024 MS.gene38248:CDS 20.0%
!! ATTATATACTTACATACCTT+TGG - chr5.3:78104496-78104515 None:intergenic 20.0%
!! GCCATAAAGAAAATTTATAA+AGG - chr5.3:78104971-78104990 None:intergenic 20.0%
!!! ATAATCATAGTATTGATATG+AGG + chr5.3:78104624-78104643 MS.gene38248:intron 20.0%
!!! TAATCATAGTATTGATATGA+GGG + chr5.3:78104625-78104644 MS.gene38248:intron 20.0%
! AAAAGATTGAATTGACATGT+CGG - chr5.3:78104944-78104963 None:intergenic 25.0%
! ATGCAATATCTTGTGAAATT+TGG + chr5.3:78105177-78105196 MS.gene38248:CDS 25.0%
! ATGTCAATTATAAACTTTCC+AGG - chr5.3:78104445-78104464 None:intergenic 25.0%
! ATTGATACAAAGTTGCAATT+TGG - chr5.3:78105134-78105153 None:intergenic 25.0%
! GGCAAAATATATGATATTCA+AGG + chr5.3:78105198-78105217 MS.gene38248:CDS 25.0%
!!! ATTTTCCTTGATTTGAATGA+AGG + chr5.3:78104681-78104700 MS.gene38248:intron 25.0%
!!! GTTTTGTTCTTATGATATGA+AGG + chr5.3:78104084-78104103 MS.gene38248:intron 25.0%
!!! TGATATTTTTGAGTTAAGAG+AGG + chr5.3:78105053-78105072 MS.gene38248:CDS 25.0%
!!! TTTTCCTTGATTTGAATGAA+GGG + chr5.3:78104682-78104701 MS.gene38248:intron 25.0%
ATTATAAACTTTCCAGGTAG+TGG - chr5.3:78104439-78104458 None:intergenic 30.0%
CAATTGCATCTTTCATAGTT+AGG + chr5.3:78104186-78104205 MS.gene38248:CDS 30.0%
CTAACTATGAAAGATGCAAT+TGG - chr5.3:78104188-78104207 None:intergenic 30.0%
TCAAAGAAATTCTTGATGCT+TGG + chr5.3:78105274-78105293 MS.gene38248:CDS 30.0%
TTTGAAAACTACATGTCCAA+AGG + chr5.3:78104477-78104496 MS.gene38248:CDS 30.0%
! CATGTTTTCACATAATGTCA+AGG + chr5.3:78104891-78104910 MS.gene38248:CDS 30.0%
!!! CTTTTATTTCTACATCAGTG+TGG - chr5.3:78104369-78104388 None:intergenic 30.0%
!!! TGTTTGGTGTTGATTTTTGA+AGG + chr5.3:78104587-78104606 MS.gene38248:intron 30.0%
ACTATGAAAGATGCAATTGG+AGG - chr5.3:78104185-78104204 None:intergenic 35.0%
AGCAAAATCTTGACTCAATC+AGG + chr5.3:78104230-78104249 MS.gene38248:CDS 35.0%
ATCCATTCAAAATAGCCATG+TGG + chr5.3:78103996-78104015 MS.gene38248:CDS 35.0%
CAATAACGATAGCTTTCTGT+GGG + chr5.3:78104402-78104421 MS.gene38248:CDS 35.0%
CTATGAAAGATGCAATTGGA+GGG - chr5.3:78104184-78104203 None:intergenic 35.0%
GTTAGGATTCTTAGTTATGC+TGG + chr5.3:78104203-78104222 MS.gene38248:CDS 35.0%
TTATCAGTGGAAAAGAACTG+TGG + chr5.3:78104110-78104129 MS.gene38248:CDS 35.0%
TTCTCTTATCATTCGACCTA+GGG - chr5.3:78104776-78104795 None:intergenic 35.0%
!! GATATGAAGGCATTTATCAG+TGG + chr5.3:78104097-78104116 MS.gene38248:intron 35.0%
!! TTCCACATGGCTATTTTGAA+TGG - chr5.3:78104001-78104020 None:intergenic 35.0%
!!! GTGATTGTTTTGGACATTTC+TGG - chr5.3:78104155-78104174 None:intergenic 35.0%
AACAATCAACGTCAATTCCG+AGG + chr5.3:78104813-78104832 MS.gene38248:CDS 40.0%
ACAATCAACGTCAATTCCGA+GGG + chr5.3:78104814-78104833 MS.gene38248:CDS 40.0%
ACTTGTCAGCTGCATGTAAT+AGG - chr5.3:78105032-78105051 None:intergenic 40.0%
ATAGCTTTCTGTGGGAGATT+GGG + chr5.3:78104410-78104429 MS.gene38248:CDS 40.0%
CCATTGAACTAGACGATTCA+TGG - chr5.3:78103936-78103955 None:intergenic 40.0%
CTTCTCTTATCATTCGACCT+AGG - chr5.3:78104777-78104796 None:intergenic 40.0%
GCAATAACGATAGCTTTCTG+TGG + chr5.3:78104401-78104420 MS.gene38248:CDS 40.0%
TCAAAATAGCCATGTGGAAC+TGG + chr5.3:78104002-78104021 MS.gene38248:CDS 40.0%
TTGACTTTACCAGTTCCACA+TGG - chr5.3:78104014-78104033 None:intergenic 40.0%
! AGGGTTGTGTGTGATTGTTT+TGG - chr5.3:78104165-78104184 None:intergenic 40.0%
! CCATGAATCGTCTAGTTCAA+TGG + chr5.3:78103933-78103952 MS.gene38248:CDS 40.0%
! CCTTGATTTGAATGAAGGGT+GGG + chr5.3:78104686-78104705 MS.gene38248:intron 40.0%
! CTTGATTTGAATGAAGGGTG+GGG + chr5.3:78104687-78104706 MS.gene38248:intron 40.0%
! TCCTTGATTTGAATGAAGGG+TGG + chr5.3:78104685-78104704 MS.gene38248:intron 40.0%
ATGAGCTCTTATGCTTCCCT+CGG - chr5.3:78104833-78104852 None:intergenic 45.0%
CATTCGACCTAGGGATTCAA+GGG - chr5.3:78104767-78104786 None:intergenic 45.0%
CCCACCCTTCATTCAAATCA+AGG - chr5.3:78104689-78104708 None:intergenic 45.0%
CTCTGCTGCATGAATCCATT+AGG - chr5.3:78104730-78104749 None:intergenic 45.0%
GAAAACATGCTGCGAAACAC+AGG - chr5.3:78104880-78104899 None:intergenic 45.0%
GATAGCTTTCTGTGGGAGAT+TGG + chr5.3:78104409-78104428 MS.gene38248:CDS 45.0%
GCTTGCTCTATTTGGCCTAA+TGG + chr5.3:78104712-78104731 MS.gene38248:CDS 45.0%
TAGCTTTCTGTGGGAGATTG+GGG + chr5.3:78104411-78104430 MS.gene38248:CDS 45.0%
TCATTCGACCTAGGGATTCA+AGG - chr5.3:78104768-78104787 None:intergenic 45.0%
GCAGCAGAGACAAAATGCAG+CGG + chr5.3:78104741-78104760 MS.gene38248:CDS 50.0%
! GTGGGGAAGCTTGCTCTATT+TGG + chr5.3:78104704-78104723 MS.gene38248:CDS 50.0%
GAGATTGGGGTTCCACTACC+TGG + chr5.3:78104424-78104443 MS.gene38248:CDS 55.0%
GCAGCGGCCCTTGAATCCCT+AGG + chr5.3:78104757-78104776 MS.gene38248:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 78103905 78105305 78103905 ID=MS.gene38248
chr5.3 mRNA 78103905 78105305 78103905 ID=MS.gene38248.t1;Parent=MS.gene38248
chr5.3 exon 78103905 78104023 78103905 ID=MS.gene38248.t1.exon1;Parent=MS.gene38248.t1
chr5.3 CDS 78103905 78104023 78103905 ID=cds.MS.gene38248.t1;Parent=MS.gene38248.t1
chr5.3 exon 78104106 78104251 78104106 ID=MS.gene38248.t1.exon2;Parent=MS.gene38248.t1
chr5.3 CDS 78104106 78104251 78104106 ID=cds.MS.gene38248.t1;Parent=MS.gene38248.t1
chr5.3 exon 78104380 78104498 78104380 ID=MS.gene38248.t1.exon3;Parent=MS.gene38248.t1
chr5.3 CDS 78104380 78104498 78104380 ID=cds.MS.gene38248.t1;Parent=MS.gene38248.t1
chr5.3 exon 78104703 78105305 78104703 ID=MS.gene38248.t1.exon4;Parent=MS.gene38248.t1
chr5.3 CDS 78104703 78105305 78104703 ID=cds.MS.gene38248.t1;Parent=MS.gene38248.t1
Gene Sequence

>MS.gene38248

ATGAATGATTATGCATACAAAGTTGAAACCATGAATCGTCTAGTTCAATGGAAAATTCACAATTTATCAACATGCACTTATATCAAAGCTGATCCATTCAAAATAGCCATGTGGAACTGGTAAAGTCAAGTTTACAATTTTAATATTTTTTAGTATTATATTCGTTTACATATTGCTAAGTTTTGTTCTTATGATATGAAGGCATTTATCAGTGGAAAAGAACTGTGGTTTACGTATTGAATTATATCCAGAAATGTCCAAAACAATCACACACAACCCTCCAATTGCATCTTTCATAGTTAGGATTCTTAGTTATGCTGGAAATAGCAAAATCTTGACTCAATCAGGTGATTCAAGTTCTATGTTTAAAAAAATATATAATTTAGTTAACACAAATAGTATTTGATTTAACAAGTTAGCTATAGTATTAATATGTGTGTTGATTTTGATCTTTATCTTTTCCACACTGATGTAGAAATAAAAGATAAACTTCTTAGCAATAACGATAGCTTTCTGTGGGAGATTGGGGTTCCACTACCTGGAAAGTTTATAATTGACATTGAGTTTCTTGATTTGAAAACTACATGTCCAAAGGTATGTAAGTATATAATATATCCAAATTAAGGTATTGAATAATATATGTAAACATTGATACAATTTTTTTTCCATTTACTTTTTATTTTGTTTGGTGTTGATTTTTGAAGGACTAGTCATGAAGCATAATCATAGTATTGATATGAGGGTTATTGACTTACAATTTGTTCACCTAATTTAAAATTTTCCTTGATTTGAATGAAGGGTGGGGAAGCTTGCTCTATTTGGCCTAATGGATTCATGCAGCAGAGACAAAATGCAGCGGCCCTTGAATCCCTAGGTCGAATGATAAGAGAAGATATCTATACAGACATAACAATCAACGTCAATTCCGAGGGAAGCATAAGAGCTCATCGAGCTGTTCTTGCTTCACAATCACCTGTGTTTCGCAGCATGTTTTCACATAATGTCAAGGAGACTGATTTGTCTACGATAAACATCACCGACATGTCAATTCAATCTTTTCAGACCTTTATAAATTTTCTTTATGGCAATGTCAATGATGAAGAATTTCTTATACATAGATTGGACCTATTACATGCAGCTGACAAGTATGATATTTTTGAGTTAAGAGAGGCATGTGAAAAGAGTCTTCAAGAAGATATTGATCTAAAAAATGTACTTGAGAGACTCCAAATTGCAACTTTGTATCAATTAACAACGTTGAAGTTTAGTTGTATGCAATATCTTGTGAAATTTGGCAAAATATATGATATTCAAGGTGATTTAAGTTCATTCTTGCAAACTGCTGATAGAGATTTGATATGTGAAGTCTTCAAAGAAATTCTTGATGCTTGGAAAAAGTGA

Protein sequence

>MS.gene38248.t1

MNDYAYKVETMNRLVQWKIHNLSTCTYIKADPFKIAMWNWHLSVEKNCGLRIELYPEMSKTITHNPPIASFIVRILSYAGNSKILTQSEIKDKLLSNNDSFLWEIGVPLPGKFIIDIEFLDLKTTCPKGGEACSIWPNGFMQQRQNAAALESLGRMIREDIYTDITINVNSEGSIRAHRAVLASQSPVFRSMFSHNVKETDLSTINITDMSIQSFQTFINFLYGNVNDEEFLIHRLDLLHAADKYDIFELREACEKSLQEDIDLKNVLERLQIATLYQLTTLKFSCMQYLVKFGKIYDIQGDLSSFLQTADRDLICEVFKEILDAWKK