AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029307

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029307.t1 MTR_1g112340 100.000 108 0 0 1 108 1 108 3.45e-79 228
MS.gene029307.t1 MTR_2g025480 36.634 101 64 0 4 104 6 106 1.26e-18 74.7
MS.gene029307.t1 MTR_2g025470 35.227 88 57 0 2 89 4 91 2.14e-15 66.6
MS.gene029307.t1 MTR_2g025470 35.227 88 57 0 2 89 4 91 2.61e-15 65.9
MS.gene029307.t1 MTR_7g031440 49.231 65 31 2 44 106 13 77 1.22e-13 62.4
MS.gene029307.t1 MTR_2g025470 35.211 71 46 0 2 72 4 74 5.37e-12 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029307.t1 AT5G20090 82.857 105 18 0 4 108 6 110 2.63e-66 195
MS.gene029307.t1 AT5G20090 82.857 105 18 0 4 108 6 110 2.63e-66 195
MS.gene029307.t1 AT5G20090 82.857 105 18 0 4 108 6 110 2.63e-66 195
MS.gene029307.t1 AT5G20090 85.870 92 13 0 4 95 6 97 7.79e-60 178
MS.gene029307.t1 AT4G14695 36.190 105 63 2 4 108 6 106 5.92e-17 70.5
MS.gene029307.t1 AT4G14695 36.190 105 63 2 4 108 6 106 5.92e-17 70.5
MS.gene029307.t1 AT4G22310 34.884 86 56 0 4 89 6 91 3.69e-16 68.6
MS.gene029307.t1 AT4G05590 34.091 88 58 0 2 89 4 91 9.46e-16 67.4
MS.gene029307.t1 AT4G05590 36.364 66 42 0 2 67 4 69 1.04e-11 56.2
MS.gene029307.t1 AT4G05590 51.163 43 21 0 2 44 4 46 3.11e-11 56.6

Find 23 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGCTGCCTTCAAAGCATTT+TGG 0.198269 1.4:+86320151 MS.gene029307:CDS
TTTGGGGACCTGTTGCTAAC+TGG 0.209422 1.4:+86320205 MS.gene029307:CDS
GTCCTAAAACAACTCACTTT+TGG 0.228614 1.4:+86320187 MS.gene029307:CDS
CCCTTCTGCCCTTGCCCATC+TGG 0.254260 1.4:-86320645 None:intergenic
ATGTTGCCAGAGATCATTTC+TGG 0.312321 1.4:-86320410 None:intergenic
TTGGGGACCTGTTGCTAACT+GGG 0.366196 1.4:+86320206 MS.gene029307:CDS
ACTATTCCAAAATGCTTTGA+AGG 0.425288 1.4:-86320157 None:intergenic
ACAAATCCCCAGTTAGCAAC+AGG 0.476332 1.4:-86320213 None:intergenic
ACCAGATGGGCAAGGGCAGA+AGG 0.477199 1.4:+86320644 MS.gene029307:CDS
AAACCTCCAGAAATGATCTC+TGG 0.493647 1.4:+86320404 MS.gene029307:CDS
TAGGTATCTCTCGGGGAAGA+AGG 0.506852 1.4:+86321193 MS.gene029307:intron
ATGATCTCTGGCAACATGAC+AGG 0.524581 1.4:+86320416 MS.gene029307:CDS
CATTGTTCATGAGATTTGCA+TGG 0.542535 1.4:+86320549 MS.gene029307:CDS
AGCTCTATCAACATACCAGA+TGG 0.550987 1.4:+86320630 MS.gene029307:CDS
GTTCATGAGATTTGCATGGA+TGG 0.554530 1.4:+86320553 MS.gene029307:CDS
TGGGGACCTGTTGCTAACTG+GGG 0.569942 1.4:+86320207 MS.gene029307:CDS
CCAGATGGGCAAGGGCAGAA+GGG 0.596928 1.4:+86320645 MS.gene029307:CDS
TCAACATACCAGATGGGCAA+GGG 0.612119 1.4:+86320637 MS.gene029307:CDS
ATCAACATACCAGATGGGCA+AGG 0.629052 1.4:+86320636 MS.gene029307:CDS
TTGCCAGAGATCATTTCTGG+AGG 0.633949 1.4:-86320407 None:intergenic
ATCTCTGGCAACATGACAGG+AGG 0.639198 1.4:+86320419 MS.gene029307:CDS
GCTCTATCAACATACCAGAT+GGG 0.640411 1.4:+86320631 MS.gene029307:CDS
GCAAGAAGTAGATAGTTACG+TGG 0.764982 1.4:-86320581 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTATTTTATATGGAAA+GGG + chr1.4:86320365-86320384 MS.gene029307:intron 10.0%
!!! TTATTTTATTTTATATGGAA+AGG + chr1.4:86320364-86320383 MS.gene029307:intron 10.0%
!! AATAATAAATAGATGATCAT+AGG - chr1.4:86320257-86320276 None:intergenic 15.0%
!! ATAATAAATAGATGATCATA+GGG - chr1.4:86320256-86320275 None:intergenic 15.0%
!! ATATACTAACATTACATTTA+AGG - chr1.4:86320962-86320981 None:intergenic 15.0%
!! TACTTTATTAGTGTTAAAAA+TGG + chr1.4:86320306-86320325 MS.gene029307:intron 15.0%
!!! ATTTTATTTTATATGGAAAG+GGG + chr1.4:86320366-86320385 MS.gene029307:intron 15.0%
!!! AGTATTTTATTTTGACTGAA+TGG + chr1.4:86321117-86321136 MS.gene029307:intron 20.0%
! ATATGTCGGATTACTAATAA+AGG + chr1.4:86321146-86321165 MS.gene029307:intron 25.0%
! TTGTACATATATTGTTGTCA+TGG + chr1.4:86320922-86320941 MS.gene029307:intron 25.0%
!! ACAATGCATTGATATATGTA+GGG - chr1.4:86321063-86321082 None:intergenic 25.0%
!! ATCTTTGCAATTTCTTTTGT+AGG + chr1.4:86321174-86321193 MS.gene029307:intron 25.0%
!! GCATATTAGTTTAAAACCAA+AGG - chr1.4:86320338-86320357 None:intergenic 25.0%
!! TTAAAAATGGTCTTAACCTT+TGG + chr1.4:86320319-86320338 MS.gene029307:intron 25.0%
ACTATTCCAAAATGCTTTGA+AGG - chr1.4:86320160-86320179 None:intergenic 30.0%
TACATATATTGTTGTCATGG+TGG + chr1.4:86320925-86320944 MS.gene029307:intron 30.0%
TGAAAAGTTGACATTCTTCT+TGG + chr1.4:86320461-86320480 MS.gene029307:intron 30.0%
! AATGCATTGATATATGTAGG+GGG - chr1.4:86321061-86321080 None:intergenic 30.0%
! CAATGCATTGATATATGTAG+GGG - chr1.4:86321062-86321081 None:intergenic 30.0%
! GACAATGCATTGATATATGT+AGG - chr1.4:86321064-86321083 None:intergenic 30.0%
! TTTCTTTTGTAGGTATCTCT+CGG + chr1.4:86321184-86321203 MS.gene029307:intron 30.0%
!! TCCTAAAACAACTCACTTTT+GGG + chr1.4:86320188-86320207 MS.gene029307:CDS 30.0%
!!! ACCTTTTAAGGTGAATAAGT+GGG + chr1.4:86321018-86321037 MS.gene029307:intron 30.0%
AAAGTAGCAGCAAATAGAAC+AGG - chr1.4:86320711-86320730 None:intergenic 35.0%
CATTGTTCATGAGATTTGCA+TGG + chr1.4:86320549-86320568 MS.gene029307:CDS 35.0%
! ATGCATTGATATATGTAGGG+GGG - chr1.4:86321060-86321079 None:intergenic 35.0%
! GTCCTAAAACAACTCACTTT+TGG + chr1.4:86320187-86320206 MS.gene029307:CDS 35.0%
! TATTTTATATGGAAAGGGGC+TGG + chr1.4:86320370-86320389 MS.gene029307:intron 35.0%
! TCAACTTTTCATGAAAGCAG+AGG - chr1.4:86320452-86320471 None:intergenic 35.0%
! TGGCTAGAATTCACCTTTTA+AGG + chr1.4:86321006-86321025 MS.gene029307:intron 35.0%
! TTCTTTTGTAGGTATCTCTC+GGG + chr1.4:86321185-86321204 MS.gene029307:intron 35.0%
!! CCTAAAACAACTCACTTTTG+GGG + chr1.4:86320189-86320208 MS.gene029307:CDS 35.0%
!! CTGAATGGTGCTATATATGT+CGG + chr1.4:86321132-86321151 MS.gene029307:intron 35.0%
!!! CACCTTTTAAGGTGAATAAG+TGG + chr1.4:86321017-86321036 MS.gene029307:intron 35.0%
!!! CCTTTTAAGGTGAATAAGTG+GGG + chr1.4:86321019-86321038 MS.gene029307:intron 35.0%
!!! TTTTTTGTCAAGTAGCCTAG+TGG + chr1.4:86320986-86321005 MS.gene029307:intron 35.0%
AAACCTCCAGAAATGATCTC+TGG + chr1.4:86320404-86320423 MS.gene029307:CDS 40.0%
AAAGGTGAATTCTAGCCACT+AGG - chr1.4:86321004-86321023 None:intergenic 40.0%
AGCTCTATCAACATACCAGA+TGG + chr1.4:86320630-86320649 MS.gene029307:CDS 40.0%
ATGTTGCCAGAGATCATTTC+TGG - chr1.4:86320413-86320432 None:intergenic 40.0%
CCCCACTTATTCACCTTAAA+AGG - chr1.4:86321022-86321041 None:intergenic 40.0%
GCAAGAAGTAGATAGTTACG+TGG - chr1.4:86320584-86320603 None:intergenic 40.0%
GCTCTATCAACATACCAGAT+GGG + chr1.4:86320631-86320650 MS.gene029307:CDS 40.0%
GTTCATGAGATTTGCATGGA+TGG + chr1.4:86320553-86320572 MS.gene029307:CDS 40.0%
TTGACATTCTTCTTGGCGTA+TGG + chr1.4:86320468-86320487 MS.gene029307:intron 40.0%
! TCTTTTGTAGGTATCTCTCG+GGG + chr1.4:86321186-86321205 MS.gene029307:intron 40.0%
!! CCCCAAAAGTGAGTTGTTTT+AGG - chr1.4:86320192-86320211 None:intergenic 40.0%
!!! GCATTTTGGAATAGTCCAGT+TGG + chr1.4:86320165-86320184 MS.gene029307:CDS 40.0%
!!! TGAGTTGTTTTAGGACCAAC+TGG - chr1.4:86320183-86320202 None:intergenic 40.0%
ACAAATCCCCAGTTAGCAAC+AGG - chr1.4:86320216-86320235 None:intergenic 45.0%
ATCAACATACCAGATGGGCA+AGG + chr1.4:86320636-86320655 MS.gene029307:CDS 45.0%
ATGATCTCTGGCAACATGAC+AGG + chr1.4:86320416-86320435 MS.gene029307:CDS 45.0%
CACTAGTACTCTCTCTGTTC+TGG + chr1.4:86320822-86320841 MS.gene029307:intron 45.0%
TCAACATACCAGATGGGCAA+GGG + chr1.4:86320637-86320656 MS.gene029307:CDS 45.0%
TGAGCATAACTCAGTTGGCA+GGG - chr1.4:86321086-86321105 None:intergenic 45.0%
TGCCAACTGAGTTATGCTCA+CGG + chr1.4:86321086-86321105 MS.gene029307:intron 45.0%
! AGGTGAATAAGTGGGGTGTT+CGG + chr1.4:86321026-86321045 MS.gene029307:intron 45.0%
! TACTCTCTCTGTTCTGGATC+TGG + chr1.4:86320828-86320847 MS.gene029307:intron 45.0%
! TTGCCAGAGATCATTTCTGG+AGG - chr1.4:86320410-86320429 None:intergenic 45.0%
!! AACAGAGAGAGTACTAGTGG+TGG - chr1.4:86320821-86320840 None:intergenic 45.0%
!! CAGAACAGAGAGAGTACTAG+TGG - chr1.4:86320824-86320843 None:intergenic 45.0%
!! TGGCTGCCTTCAAAGCATTT+TGG + chr1.4:86320151-86320170 MS.gene029307:CDS 45.0%
!! ATATAAAATAAAATAAAAGT+TGG - chr1.4:86320360-86320379 None:intergenic 5.0%
!!! AACTTTTATTTTATTTTATA+TGG + chr1.4:86320359-86320378 MS.gene029307:intron 5.0%
ATCTCTGGCAACATGACAGG+AGG + chr1.4:86320419-86320438 MS.gene029307:CDS 50.0%
CCAACTGAGTTATGCTCACG+GGG + chr1.4:86321088-86321107 MS.gene029307:intron 50.0%
GCCAACTGAGTTATGCTCAC+GGG + chr1.4:86321087-86321106 MS.gene029307:intron 50.0%
GTGAGCATAACTCAGTTGGC+AGG - chr1.4:86321087-86321106 None:intergenic 50.0%
TAGGTATCTCTCGGGGAAGA+AGG + chr1.4:86321193-86321212 MS.gene029307:intron 50.0%
TCTTCTTGGCGTATGGTCTG+TGG + chr1.4:86320475-86320494 MS.gene029307:intron 50.0%
TGGCAACATGACAGGAGGTT+TGG + chr1.4:86320424-86320443 MS.gene029307:intron 50.0%
TTGGGGACCTGTTGCTAACT+GGG + chr1.4:86320206-86320225 MS.gene029307:CDS 50.0%
TTTGGGGACCTGTTGCTAAC+TGG + chr1.4:86320205-86320224 MS.gene029307:CDS 50.0%
! CTCTGTTCTGGATCTGGTGT+TGG + chr1.4:86320834-86320853 MS.gene029307:intron 50.0%
! GGTGAATAAGTGGGGTGTTC+GGG + chr1.4:86321027-86321046 MS.gene029307:intron 50.0%
! GTGAATAAGTGGGGTGTTCG+GGG + chr1.4:86321028-86321047 MS.gene029307:intron 50.0%
!! TCTGGATCTGGTGTTGGTGT+GGG + chr1.4:86320840-86320859 MS.gene029307:intron 50.0%
!! TTCTGGATCTGGTGTTGGTG+TGG + chr1.4:86320839-86320858 MS.gene029307:intron 50.0%
CCCCGTGAGCATAACTCAGT+TGG - chr1.4:86321091-86321110 None:intergenic 55.0%
TGGGGACCTGTTGCTAACTG+GGG + chr1.4:86320207-86320226 MS.gene029307:CDS 55.0%
ACCAGATGGGCAAGGGCAGA+AGG + chr1.4:86320644-86320663 MS.gene029307:CDS 60.0%
CCAGATGGGCAAGGGCAGAA+GGG + chr1.4:86320645-86320664 MS.gene029307:CDS 60.0%
GGCAAGGGCAGAAGGGTAAG+TGG + chr1.4:86320652-86320671 MS.gene029307:intron 60.0%
CCCTTCTGCCCTTGCCCATC+TGG - chr1.4:86320648-86320667 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 86320150 86321238 86320150 ID=MS.gene029307
chr1.4 mRNA 86320150 86321238 86320150 ID=MS.gene029307.t1;Parent=MS.gene029307
chr1.4 exon 86320150 86320242 86320150 ID=MS.gene029307.t1.exon1;Parent=MS.gene029307.t1
chr1.4 CDS 86320150 86320242 86320150 ID=cds.MS.gene029307.t1;Parent=MS.gene029307.t1
chr1.4 exon 86320386 86320440 86320386 ID=MS.gene029307.t1.exon2;Parent=MS.gene029307.t1
chr1.4 CDS 86320386 86320440 86320386 ID=cds.MS.gene029307.t1;Parent=MS.gene029307.t1
chr1.4 exon 86320531 86320666 86320531 ID=MS.gene029307.t1.exon3;Parent=MS.gene029307.t1
chr1.4 CDS 86320531 86320666 86320531 ID=cds.MS.gene029307.t1;Parent=MS.gene029307.t1
chr1.4 exon 86321196 86321238 86321196 ID=MS.gene029307.t1.exon4;Parent=MS.gene029307.t1
chr1.4 CDS 86321196 86321238 86321196 ID=cds.MS.gene029307.t1;Parent=MS.gene029307.t1
Gene Sequence

>MS.gene029307

ATGGCTGCCTTCAAAGCATTTTGGAATAGTCCAGTTGGTCCTAAAACAACTCACTTTTGGGGACCTGTTGCTAACTGGGGATTTGTCGCAGCTGTGAGTTTCACCCTATGATCATCTATTTATTATTATTATTATTAACAAAGTCGTGCATTTATTTACTTTATTAGTGTTAAAAATGGTCTTAACCTTTGGTTTTAAACTAATATGCCAACTTTTATTTTATTTTATATGGAAAGGGGCTGGCTGACATCAATAAACCTCCAGAAATGATCTCTGGCAACATGACAGGAGGTTTGGCACCTCTGCTTTCATGAAAAGTTGACATTCTTCTTGGCGTATGGTCTGTGGATTAATCATTTTATCTCATTTTTATTGCTGCAGCAATGTGTATATATTCAGCATTGTTCATGAGATTTGCATGGATGGTACAGCCACGTAACTATCTACTTCTTGCATGTCATGCTTCAAATGAGACTGTTCAGCTCTATCAACATACCAGATGGGCAAGGGCAGAAGGGTAAGTGGCTTACATGCAAGCAAAACAAAACATTTTTTCAACCTGTTCTATTTGCTGCTACTTTACGAGACAACAATGTTTCATGTTTTATAAATGCTATTTTAACTTGTAACATGTTTATAATATTAATTGCAATATACTTTTAACTTGACCACCACTAGTACTCTCTCTGTTCTGGATCTGGTGTTGGTGTGGGAAAAGTTTTCTTCAAGTTACAATAAACAACAATACTTTGTGTATTCTCGTTTATTCAAATTGTACATATATTGTTGTCATGGTGGCGTGCACTTGTCCTTAAATGTAATGTTAGTATATATATTTTTTTGTCAAGTAGCCTAGTGGCTAGAATTCACCTTTTAAGGTGAATAAGTGGGGTGTTCGGGGTTCGAACCCCCCTACATATATCAATGCATTGTCCCTGCCAACTGAGTTATGCTCACGGGGACTGTTAGTATTTTATTTTGACTGAATGGTGCTATATATGTCGGATTACTAATAAAGGTTTGTATCTTTGCAATTTCTTTTGTAGGTATCTCTCGGGGAAGAAGGAGAAAGAAGCTTCATCAGAGTGA
Protein sequence

>MS.gene029307.t1

MAAFKAFWNSPVGPKTTHFWGPVANWGFVAAGLADINKPPEMISGNMTGAMCIYSALFMRFAWMVQPRNYLLLACHASNETVQLYQHTRWARAEGYLSGKKEKEASSE