AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene017498

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene017498.t1 MTR_5g098940 99.375 160 1 0 20 179 2 161 2.21e-116 327
MS.gene017498.t1 MTR_5g087820 82.500 160 28 0 20 179 26 185 2.57e-99 285
MS.gene017498.t1 MTR_1g025190 54.286 140 64 0 20 159 2 141 7.11e-52 163
MS.gene017498.t1 MTR_7g100010 43.478 138 78 0 20 157 3 140 1.99e-39 131
MS.gene017498.t1 MTR_8g102180 43.478 138 78 0 20 157 3 140 1.99e-39 131
MS.gene017498.t1 MTR_8g077600 36.810 163 93 2 20 177 2 159 9.50e-31 110
MS.gene017498.t1 MTR_8g077600 34.884 86 51 1 23 103 5 90 3.84e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene017498.t1 AT2G17380 91.875 160 13 0 20 179 2 161 2.50e-110 311
MS.gene017498.t1 AT4G35410 90.625 160 15 0 20 179 2 161 5.71e-108 305
MS.gene017498.t1 AT4G35410 91.753 97 8 0 20 116 2 98 1.73e-64 194
MS.gene017498.t1 AT1G47830 52.857 140 66 0 20 159 2 141 6.26e-51 160
MS.gene017498.t1 AT2G19790 42.754 138 79 0 20 157 3 140 1.37e-38 129
MS.gene017498.t1 AT3G50860 36.943 157 88 2 20 171 2 152 1.36e-29 107
MS.gene017498.t1 AT3G50860 37.410 139 82 1 20 153 2 140 1.74e-29 106

Find 30 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATATAAAGTTGTTTATAAA+AGG 0.214674 5.2:-83338564 MS.gene017498:intron
GAGATTCTTGATCGGTATTT+TGG 0.252220 5.2:-83338360 MS.gene017498:CDS
ACAAGGTGAAAATCACTTTC+AGG 0.289497 5.2:+83339071 None:intergenic
AATTTCATCAAGTATATAAT+AGG 0.297509 5.2:+83337802 None:intergenic
TCTAATTGCTGGCGAGCTTC+AGG 0.306112 5.2:-83337780 MS.gene017498:CDS
CATTGTCTTTCAGGATTCAT+TGG 0.310542 5.2:-83337645 MS.gene017498:intron
ATCGCACAAGCTACTAAATA+AGG 0.320939 5.2:-83337581 None:intergenic
CTTCTTTCCTTCTGAGTGTA+AGG 0.334840 5.2:+83338822 None:intergenic
CTTGATGAAATTCTAATTGC+TGG 0.336106 5.2:-83337791 MS.gene017498:CDS
CAATTTACAGGTCTGTGAAT+TGG 0.339292 5.2:-83338230 MS.gene017498:intron
CTCTACAAAATTACAGAGCT+TGG 0.403422 5.2:+83338594 None:intergenic
GGAAGGTTAGGCTCACAAAA+TGG 0.441892 5.2:-83338851 MS.gene017498:CDS
TGATGATGCTGACAACGAAT+TGG 0.451575 5.2:-83338412 MS.gene017498:CDS
CTTGATATTCAACTTCCATA+AGG 0.468058 5.2:-83338206 MS.gene017498:intron
GATAATATTACTCAAGGAAC+TGG 0.478446 5.2:+83337601 None:intergenic
TTAGTCGTCAAGGGAAGGTT+AGG 0.481414 5.2:-83338863 MS.gene017498:CDS
CACTCAGAAGGAAAGAAGTA+AGG 0.487202 5.2:-83338817 MS.gene017498:intron
TCTACAAAATTACAGAGCTT+GGG 0.509679 5.2:+83338595 None:intergenic
GTGCTTCTCATTAGTCGTCA+AGG 0.528040 5.2:-83338873 MS.gene017498:CDS
TGCTCGGTTGATAGCTGCAC+AGG 0.540072 5.2:-83337738 MS.gene017498:intron
TGTCTTTCAGGATTCATTGG+TGG 0.541167 5.2:-83337642 MS.gene017498:intron
TGCTTCTCATTAGTCGTCAA+GGG 0.558103 5.2:-83338872 MS.gene017498:CDS
AATTACAGAGCTTGGGAGCA+CGG 0.567062 5.2:+83338602 None:intergenic
GAATCACTCCACTGAGCTCA+CGG 0.569834 5.2:+83338629 None:intergenic
TCTCATTAGTCGTCAAGGGA+AGG 0.585870 5.2:-83338868 MS.gene017498:CDS
TTGTGCGATAATATTACTCA+AGG 0.602166 5.2:+83337595 None:intergenic
ATTGGTGGAGACTGCTAAGG+AGG 0.602252 5.2:-83337627 MS.gene017498:CDS
GTATTCACCTTACACTCAGA+AGG 0.607833 5.2:-83338829 MS.gene017498:CDS
TTCATTGGTGGAGACTGCTA+AGG 0.613718 5.2:-83337630 MS.gene017498:CDS
AAGGTAATCCGTGAGCTCAG+TGG 0.653418 5.2:-83338637 MS.gene017498:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTCATCAAGTATATAAT+AGG + chr5.2:83338864-83338883 None:intergenic 15.0%
!! ATATTATATCCTTAAGAAAA+GGG + chr5.2:83338368-83338387 None:intergenic 15.0%
!! GAAATATATTACATTAAACT+TGG + chr5.2:83338676-83338695 None:intergenic 15.0%
!! GATATAAAGTTGTTTATAAA+AGG - chr5.2:83338099-83338118 MS.gene017498:intron 15.0%
!! TATATCCATAATTCAAAATA+AGG - chr5.2:83338502-83338521 MS.gene017498:intron 15.0%
!! TATATTATATCCTTAAGAAA+AGG + chr5.2:83338369-83338388 None:intergenic 15.0%
!! ATAAGAAATCCTATTAACAA+CGG + chr5.2:83337724-83337743 None:intergenic 20.0%
!! ATTATCTGTATGTATTAACA+TGG - chr5.2:83337914-83337933 MS.gene017498:intron 20.0%
!! TATTTCCATAATTCAAAACA+AGG - chr5.2:83338690-83338709 MS.gene017498:intron 20.0%
!!! ATCTCATATTTTTATTGACA+AGG - chr5.2:83338007-83338026 MS.gene017498:intron 20.0%
!!! TCTAAGAACTTTTAAATGAA+TGG - chr5.2:83337679-83337698 MS.gene017498:intron 20.0%
! AAGACAATGTCATACAAATT+TGG + chr5.2:83339007-83339026 None:intergenic 25.0%
! ACCATGAAAGGATTATTAAT+AGG + chr5.2:83338549-83338568 None:intergenic 25.0%
! AGATGTAAATACACATATCA+AGG + chr5.2:83337991-83338010 None:intergenic 25.0%
! ATCGCTTATTCTCTTTATTA+TGG - chr5.2:83337882-83337901 MS.gene017498:intron 25.0%
! ATTCCAAGTACAAAAATACA+AGG + chr5.2:83337612-83337631 None:intergenic 25.0%
! CATGATTAAAAACAAAGAAC+AGG + chr5.2:83338836-83338855 None:intergenic 25.0%
! GATATATATCGCATTAAACT+TGG + chr5.2:83338488-83338507 None:intergenic 25.0%
! GATTATTAATAGGAGTTACA+GGG + chr5.2:83338539-83338558 None:intergenic 25.0%
! TAAGAAATCCTATTAACAAC+GGG + chr5.2:83337723-83337742 None:intergenic 25.0%
! TAATAAAGAGAATAAGCGAT+AGG + chr5.2:83337882-83337901 None:intergenic 25.0%
! TATTAATAATCCTTTCATGG+TGG - chr5.2:83338548-83338567 MS.gene017498:intron 25.0%
! TCCTATTAATAATCCTTTCA+TGG - chr5.2:83338545-83338564 MS.gene017498:intron 25.0%
!! AGAACTTTTAAATGAATGGT+AGG - chr5.2:83337683-83337702 MS.gene017498:intron 25.0%
!! TGAAATGATTCATCATTTTG+TGG - chr5.2:83338281-83338300 MS.gene017498:intron 25.0%
!!! CTGTTCTTTGTTTTTAATCA+TGG - chr5.2:83338834-83338853 MS.gene017498:CDS 25.0%
!!! TCTTTGTTTTTAATCATGGA+AGG - chr5.2:83338838-83338857 MS.gene017498:CDS 25.0%
AAGAAATCCTATTAACAACG+GGG + chr5.2:83337722-83337741 None:intergenic 30.0%
ACTAGACCAATAATAATGAC+AGG + chr5.2:83338799-83338818 None:intergenic 30.0%
ACTAGACTGAATATAATGAC+AGG + chr5.2:83338611-83338630 None:intergenic 30.0%
AGCAGATATTCATTATACCA+TGG + chr5.2:83338197-83338216 None:intergenic 30.0%
CACAAAGTGTATCTACATTT+AGG + chr5.2:83337773-83337792 None:intergenic 30.0%
CTTGATATTCAACTTCCATA+AGG - chr5.2:83338457-83338476 MS.gene017498:intron 30.0%
CTTGATGAAATTCTAATTGC+TGG - chr5.2:83338872-83338891 MS.gene017498:CDS 30.0%
GAATATAATGACAGGTGATA+TGG + chr5.2:83338603-83338622 None:intergenic 30.0%
GATAATATTACTCAAGGAAC+TGG + chr5.2:83339065-83339084 None:intergenic 30.0%
GGATTATTAATAGGAGTTAC+AGG + chr5.2:83338540-83338559 None:intergenic 30.0%
TCTACAAAATTACAGAGCTT+GGG + chr5.2:83338071-83338090 None:intergenic 30.0%
TTAAACTTGGACATACCTTA+TGG + chr5.2:83338475-83338494 None:intergenic 30.0%
TTGTGCGATAATATTACTCA+AGG + chr5.2:83339071-83339090 None:intergenic 30.0%
TTTGTATGACATTGTCTTTC+AGG - chr5.2:83339009-83339028 MS.gene017498:intron 30.0%
! ATCAATGGTCTTTCTCTTTT+GGG - chr5.2:83338949-83338968 MS.gene017498:intron 30.0%
! ATTTTGTGGAGATTCTTGAT+CGG - chr5.2:83338295-83338314 MS.gene017498:intron 30.0%
! TATCAATGGTCTTTCTCTTT+TGG - chr5.2:83338948-83338967 MS.gene017498:intron 30.0%
! TATTAACATGGTGATAGTGA+TGG - chr5.2:83337926-83337945 MS.gene017498:intron 30.0%
!! TCACCTTGTATTTTTGTACT+TGG - chr5.2:83337606-83337625 MS.gene017498:CDS 30.0%
!!! GTAGGCCTTATTTTGAATTA+TGG + chr5.2:83338510-83338529 None:intergenic 30.0%
AAAACAAAGAACAGGTCAGA+AGG + chr5.2:83338828-83338847 None:intergenic 35.0%
AAACAAAGAACAGGTCAGAA+GGG + chr5.2:83338639-83338658 None:intergenic 35.0%
AATAATAATGACAGGCGATG+TGG + chr5.2:83338791-83338810 None:intergenic 35.0%
ACAAGGTGAAAATCACTTTC+AGG + chr5.2:83337595-83337614 None:intergenic 35.0%
ACATCGCCTGTCATTATTAT+TGG - chr5.2:83338790-83338809 MS.gene017498:intron 35.0%
AGGATGTTTATCATGCAATG+TGG + chr5.2:83337971-83337990 None:intergenic 35.0%
ATGGTCACTTGTCAATTTAC+AGG - chr5.2:83338421-83338440 MS.gene017498:CDS 35.0%
CAATTTACAGGTCTGTGAAT+TGG - chr5.2:83338433-83338452 MS.gene017498:CDS 35.0%
CATGATCACAAACAAAGAAC+AGG + chr5.2:83338648-83338667 None:intergenic 35.0%
CATTGTCTTTCAGGATTCAT+TGG - chr5.2:83339018-83339037 MS.gene017498:intron 35.0%
CTCTACAAAATTACAGAGCT+TGG + chr5.2:83338072-83338091 None:intergenic 35.0%
GCTTGATGTTTAATTGACCA+TGG - chr5.2:83338177-83338196 MS.gene017498:intron 35.0%
GGTGATATGGTCAATAATCA+AGG + chr5.2:83338590-83338609 None:intergenic 35.0%
GTGTCACACTAACTTGATAA+TGG - chr5.2:83338402-83338421 MS.gene017498:CDS 35.0%
! AGCTCTGTAATTTTGTAGAG+TGG - chr5.2:83338072-83338091 MS.gene017498:intron 35.0%
! CTGTTCTTTGTTTGTGATCA+TGG - chr5.2:83338646-83338665 MS.gene017498:intron 35.0%
! GAGATTCTTGATCGGTATTT+TGG - chr5.2:83338303-83338322 MS.gene017498:intron 35.0%
! TCTTTGTTTGTGATCATGGA+AGG - chr5.2:83338650-83338669 MS.gene017498:intron 35.0%
! TGTAATTTTGTAGAGTGGAG+AGG - chr5.2:83338077-83338096 MS.gene017498:intron 35.0%
! TTGAAGAGTCCCTTTTCTTA+AGG - chr5.2:83338356-83338375 MS.gene017498:CDS 35.0%
!! CAGCTTTATAGTCTTTTGCA+AGG - chr5.2:83338140-83338159 MS.gene017498:intron 35.0%
!!! GTAGGCCTTGTTTTGAATTA+TGG + chr5.2:83338698-83338717 None:intergenic 35.0%
CAAACAAAGAACAGGTCAGA+AGG + chr5.2:83338640-83338659 None:intergenic 40.0%
CACTCAGAAGGAAAGAAGTA+AGG - chr5.2:83337846-83337865 MS.gene017498:intron 40.0%
CGAGCAAAAAAACTGTTGCT+CGG - chr5.2:83338909-83338928 MS.gene017498:intron 40.0%
CTTCTTTCCTTCTGAGTGTA+AGG + chr5.2:83337844-83337863 None:intergenic 40.0%
GGAGTTACAGGGAAATAAGT+AGG + chr5.2:83338528-83338547 None:intergenic 40.0%
GGAGTTACAGGGAATTAAGT+AGG + chr5.2:83338716-83338735 None:intergenic 40.0%
GTATTCACCTTACACTCAGA+AGG - chr5.2:83337834-83337853 MS.gene017498:intron 40.0%
TAATCAAGGCTCATTCAGTG+TGG + chr5.2:83338576-83338595 None:intergenic 40.0%
TAATTGAGGCTCATTCAGTG+TGG + chr5.2:83338764-83338783 None:intergenic 40.0%
TGCTTCTCATTAGTCGTCAA+GGG - chr5.2:83337791-83337810 MS.gene017498:CDS 40.0%
TGTCTTTCAGGATTCATTGG+TGG - chr5.2:83339021-83339040 MS.gene017498:intron 40.0%
TTGCAAGGCAATCTTCTGTT+TGG - chr5.2:83338155-83338174 MS.gene017498:intron 40.0%
! TGATGATGCTGACAACGAAT+TGG - chr5.2:83338251-83338270 MS.gene017498:intron 40.0%
AATTACAGAGCTTGGGAGCA+CGG + chr5.2:83338064-83338083 None:intergenic 45.0%
GATAGCTGCACAGGTATCAA+TGG - chr5.2:83338934-83338953 MS.gene017498:intron 45.0%
GGAAGGTTAGGCTCACAAAA+TGG - chr5.2:83337812-83337831 MS.gene017498:intron 45.0%
GGCGATGTGGTCAATAATTG+AGG + chr5.2:83338778-83338797 None:intergenic 45.0%
GTGCTTCTCATTAGTCGTCA+AGG - chr5.2:83337790-83337809 MS.gene017498:CDS 45.0%
TCTCATTAGTCGTCAAGGGA+AGG - chr5.2:83337795-83337814 MS.gene017498:CDS 45.0%
TTAGTCGTCAAGGGAAGGTT+AGG - chr5.2:83337800-83337819 MS.gene017498:CDS 45.0%
TTCATTGGTGGAGACTGCTA+AGG - chr5.2:83339033-83339052 MS.gene017498:intron 45.0%
AAGGTAATCCGTGAGCTCAG+TGG - chr5.2:83338026-83338045 MS.gene017498:intron 50.0%
ATTGGTGGAGACTGCTAAGG+AGG - chr5.2:83339036-83339055 MS.gene017498:intron 50.0%
CAGTGTGGATCCACCATGAA+AGG + chr5.2:83338561-83338580 None:intergenic 50.0%
CCTATTAACAACGGGGAGAG+AGG + chr5.2:83337715-83337734 None:intergenic 50.0%
CCTCTCTCCCCGTTGTTAAT+AGG - chr5.2:83337712-83337731 MS.gene017498:intron 50.0%
GAATCACTCCACTGAGCTCA+CGG + chr5.2:83338037-83338056 None:intergenic 50.0%
TCTAATTGCTGGCGAGCTTC+AGG - chr5.2:83338883-83338902 MS.gene017498:CDS 50.0%
!! TGCTCGGTTGATAGCTGCAC+AGG - chr5.2:83338925-83338944 MS.gene017498:intron 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 83337583 83339102 83337583 ID=MS.gene017498
chr5.2 mRNA 83337583 83339102 83337583 ID=MS.gene017498.t1;Parent=MS.gene017498
chr5.2 exon 83339046 83339102 83339046 ID=MS.gene017498.t1.exon1;Parent=MS.gene017498.t1
chr5.2 CDS 83339046 83339102 83339046 ID=cds.MS.gene017498.t1;Parent=MS.gene017498.t1
chr5.2 exon 83338818 83338904 83338818 ID=MS.gene017498.t1.exon2;Parent=MS.gene017498.t1
chr5.2 CDS 83338818 83338904 83338818 ID=cds.MS.gene017498.t1;Parent=MS.gene017498.t1
chr5.2 exon 83338565 83338656 83338565 ID=MS.gene017498.t1.exon3;Parent=MS.gene017498.t1
chr5.2 CDS 83338565 83338656 83338565 ID=cds.MS.gene017498.t1;Parent=MS.gene017498.t1
chr5.2 exon 83338356 83338464 83338356 ID=MS.gene017498.t1.exon4;Parent=MS.gene017498.t1
chr5.2 CDS 83338356 83338464 83338356 ID=cds.MS.gene017498.t1;Parent=MS.gene017498.t1
chr5.2 exon 83338207 83338242 83338207 ID=MS.gene017498.t1.exon5;Parent=MS.gene017498.t1
chr5.2 CDS 83338207 83338242 83338207 ID=cds.MS.gene017498.t1;Parent=MS.gene017498.t1
chr5.2 exon 83337739 83337825 83337739 ID=MS.gene017498.t1.exon6;Parent=MS.gene017498.t1
chr5.2 CDS 83337739 83337825 83337739 ID=cds.MS.gene017498.t1;Parent=MS.gene017498.t1
chr5.2 exon 83337583 83337654 83337583 ID=MS.gene017498.t1.exon7;Parent=MS.gene017498.t1
chr5.2 CDS 83337583 83337654 83337583 ID=cds.MS.gene017498.t1;Parent=MS.gene017498.t1
Gene Sequence

>MS.gene017498

ATGAAGTTACCTGAAAGTGATTTTCACCTTGTATTTTTGTACTTGGAATTCATATATGTATGAATGCTTATTTATTATATGATTGAATTCTGAAAGTCTAAGAACTTTTAAATGAATGGTAGGATTGTGCCTCTCTCCCCGTTGTTAATAGGATTTCTTATTTCAACTTGCATGCTTTATTCTTCTTCCTAAATGTAGATACACTTTGTGCTTCTCATTAGTCGTCAAGGGAAGGTTAGGCTCACAAAATGGTATTCACCTTACACTCAGAAGGAAAGAAGTAAGGTAACTAACAACCTATCGCTTATTCTCTTTATTATGGAAATATGTTATTATCTGTATGTATTAACATGGTGATAGTGATGGTCATTGCATGCTGAGCACACCACATTGCATGATAAACATCCTTGATATGTGTATTTACATCTCATATTTTTATTGACAAGGTAATCCGTGAGCTCAGTGGAGTGATTCTTAGCCGTGCTCCCAAGCTCTGTAATTTTGTAGAGTGGAGAGGATATAAAGTTGTTTATAAAAGGTATTTTGACTAGAGTAGACAGCTTTATAGTCTTTTGCAAGGCAATCTTCTGTTTGGCTTGATGTTTAATTGACCATGGTATAATGAATATCTGCTGCAGATATGCTAGTCTATATTTCTGTATGTGTATTGATGATGCTGACAACGAATTGGAAGTACTTGAAATGATTCATCATTTTGTGGAGATTCTTGATCGGTATTTTGGCAGTGTAAGTTCTATCAAAAGTTTTGACTTTTGAAGAGTCCCTTTTCTTAAGGATATAATATAAGAAGCATTTCTCGTGTCACACTAACTTGATAATGGTCACTTGTCAATTTACAGGTCTGTGAATTGGACTTGATATTCAACTTCCATAAGGTATGTCCAAGTTTAATGCGATATATATCCATAATTCAAAATAAGGCCTACTTATTTCCCTGTAACTCCTATTAATAATCCTTTCATGGTGGATCCACACTGAATGAGCCTTGATTATTGACCATATCACCTGTCATTATATTCAGTCTAGTAATCTCCCTTCTGACCTGTTCTTTGTTTGTGATCATGGAAGGCCAAGTTTAATGTAATATATTTCCATAATTCAAAACAAGGCCTACTTAATTCCCTGTAACTCCTATTAATAATCCTTTCATGGTGGATCCACACTGAATGAGCCTCAATTATTGACCACATCGCCTGTCATTATTATTGGTCTAGTAATCTCCCTTCTGACCTGTTCTTTGTTTTTAATCATGGAAGGCCTATTATATACTTGATGAAATTCTAATTGCTGGCGAGCTTCAGGAGTCGAGCAAAAAAACTGTTGCTCGGTTGATAGCTGCACAGGTATCAATGGTCTTTCTCTTTTGGGTATGTTTTGATTCTTCAATCAGTTTTTCTAATCCAAATTTGTATGACATTGTCTTTCAGGATTCATTGGTGGAGACTGCTAAGGAGGAAGCCAGTTCCTTGAGTAATATTATCGCACAAGCTACTAAATAA
Protein sequence

>MS.gene017498.t1

MKLPESDFHLVFLYLEFIYIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILSRAPKLCNFVEWRGYKVVYKRYASLYFCMCIDDADNELEVLEMIHHFVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSLVETAKEEASSLSNIIAQATK