AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene79320

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79320.t1 MTR_6g465420 73.485 132 28 3 1 130 88 214 2.58e-63 194
MS.gene79320.t1 MTR_6g465530 88.189 127 15 0 1 127 67 193 5.56e-62 188
MS.gene79320.t1 MTR_6g465460 69.118 136 32 4 1 133 88 216 6.02e-59 183
MS.gene79320.t1 MTR_6g465450 73.529 136 28 3 1 133 88 218 3.14e-57 178
MS.gene79320.t1 MTR_6g465430 69.853 136 32 4 1 133 88 217 3.09e-54 171
MS.gene79320.t1 MTR_6g465510 81.752 137 15 2 1 127 67 203 2.58e-52 164
MS.gene79320.t1 MTR_6g466000 61.765 136 39 4 1 127 91 222 1.42e-48 155
MS.gene79320.t1 MTR_6g465690 61.702 141 40 3 1 133 97 231 1.80e-47 154
MS.gene79320.t1 MTR_6g466130 65.625 128 39 2 1 127 100 223 1.13e-41 138
MS.gene79320.t1 MTR_6g465850 65.041 123 38 2 6 127 156 274 2.83e-37 128
MS.gene79320.t1 MTR_1g101600 53.488 129 50 2 1 127 75 195 3.05e-29 105
MS.gene79320.t1 MTR_6g466020 46.875 128 41 3 1 127 77 178 3.64e-24 92.0
MS.gene79320.t1 MTR_6g465990 53.571 112 39 4 25 127 81 188 1.09e-23 90.9
MS.gene79320.t1 MTR_4g102660 43.443 122 61 3 1 117 81 199 4.46e-17 74.3
MS.gene79320.t1 MTR_5g010930 36.691 139 62 4 1 122 89 218 1.17e-16 73.6
MS.gene79320.t1 MTR_5g010910 64.706 51 18 0 1 51 89 139 4.12e-16 72.0
MS.gene79320.t1 MTR_5g010940 64.706 51 18 0 1 51 94 144 5.52e-16 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79320.t1 AT4G25470 44.118 136 61 4 1 128 85 213 3.89e-24 92.8
MS.gene79320.t1 AT5G51990 43.750 128 60 4 1 119 88 212 9.43e-22 86.7
MS.gene79320.t1 AT1G63030 73.585 53 14 0 1 53 64 116 1.88e-21 85.1
MS.gene79320.t1 AT1G63030 73.585 53 14 0 1 53 64 116 1.88e-21 85.1
MS.gene79320.t1 AT4G25490 47.407 135 52 5 1 122 82 210 2.69e-21 85.5
MS.gene79320.t1 AT1G12610 41.353 133 70 2 1 125 64 196 2.58e-20 82.8
MS.gene79320.t1 AT4G25480 50.926 108 42 2 1 103 85 186 5.02e-20 82.0

Find 28 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGTTGCAGCGATGGCATTA+AGG 0.265866 6.3:+56247315 MS.gene79320:CDS
GCCAGAGTTGTGGAGGAATA+TGG 0.338237 6.3:+56247580 MS.gene79320:CDS
CGTTGCAGCGATGGCATTAA+GGG 0.377499 6.3:+56247316 MS.gene79320:CDS
TCGCTGCAACGTCGTGTGCT+CGG 0.389912 6.3:-56247304 None:intergenic
CGCTGCAACGTCGTGTGCTC+GGG 0.398592 6.3:-56247303 None:intergenic
AATGTCCCCTACACATAGTT+TGG 0.427502 6.3:+56247607 MS.gene79320:CDS
CTGAAACAAAAGACATTCAA+AGG 0.491926 6.3:+56247399 MS.gene79320:CDS
GTAGTCGTTAAAGTCTTGTC+TGG 0.505167 6.3:-56247452 None:intergenic
GCCATATTCCTCCACAACTC+TGG 0.506491 6.3:-56247581 None:intergenic
CATGCACCAAACTATGTGTA+GGG 0.511168 6.3:-56247613 None:intergenic
GGCAGCTGCAGAAGCCGCTG+AGG 0.513356 6.3:+56247421 MS.gene79320:CDS
TGTGGAAGTCGAAGAAGAAG+AGG 0.518171 6.3:+56247544 MS.gene79320:CDS
AGCACACGACGTTGCAGCGA+TGG 0.528674 6.3:+56247307 MS.gene79320:CDS
TACTGACATTGACACGGTTG+TGG 0.536605 6.3:+56247472 MS.gene79320:CDS
TGTACAATTTCAAGAGGAAG+AGG 0.538906 6.3:+56247652 MS.gene79320:CDS
TGTCGTTGCAGTCGAAGAAG+AGG 0.540894 6.3:+56247499 MS.gene79320:CDS
CGAGTCTGCAAAATTGAGAC+AGG 0.547018 6.3:-56247348 None:intergenic
TGAAACAAAAGACATTCAAA+GGG 0.555993 6.3:+56247400 MS.gene79320:CDS
GTTTCAGAAGAGGCAGGAGT+AGG 0.561690 6.3:-56247383 None:intergenic
TCATGCACCAAACTATGTGT+AGG 0.576797 6.3:-56247614 None:intergenic
AACGACTACTGACATTGACA+CGG 0.611733 6.3:+56247466 MS.gene79320:CDS
TGTTGAATATGCCAGAGTTG+TGG 0.615027 6.3:+56247570 MS.gene79320:CDS
GTTGCAGCGATGGCATTAAG+GGG 0.638430 6.3:+56247317 MS.gene79320:CDS
TTCTTCGACTGCAACGACAA+CGG 0.675808 6.3:-56247495 None:intergenic
GTCTGGTCTGAAAGCCTCAG+CGG 0.676858 6.3:-56247435 None:intergenic
ATGCACCAAACTATGTGTAG+GGG 0.684106 6.3:-56247612 None:intergenic
TGAATATGCCAGAGTTGTGG+AGG 0.686416 6.3:+56247573 MS.gene79320:CDS
CAAAATTGAGACAGGCGTAG+CGG 0.688544 6.3:-56247340 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAAGAATAATAAAACTT+TGG + chr6.3:56248188-56248207 MS.gene79320:intron 10.0%
!! TATGAATATAATTACTAATT+GGG + chr6.3:56248133-56248152 MS.gene79320:intron 10.0%
!! TTATGAATATAATTACTAAT+TGG + chr6.3:56248132-56248151 MS.gene79320:intron 10.0%
!!! ATCACTTTTTTTTTTTTTTG+TGG + chr6.3:56248044-56248063 MS.gene79320:intron 15.0%
!! TATATTGATATACAACAAGT+TGG + chr6.3:56247978-56247997 MS.gene79320:intron 20.0%
!! TATGTATTAATATTGACCTT+TGG + chr6.3:56248229-56248248 MS.gene79320:intron 20.0%
!! TATTCATCAACAAAAAAAGA+AGG + chr6.3:56248252-56248271 MS.gene79320:intron 20.0%
!! TCAAAATCCGTATAAATATA+CGG - chr6.3:56247828-56247847 None:intergenic 20.0%
!!! TGTTTTTTTAGATTGTAGAA+TGG + chr6.3:56247719-56247738 MS.gene79320:intron 20.0%
! AGCTAATTGCAATATATTGA+GGG + chr6.3:56248315-56248334 MS.gene79320:intron 25.0%
! TAGCTAATTGCAATATATTG+AGG + chr6.3:56248314-56248333 MS.gene79320:intron 25.0%
! TGAAACAAAAGACATTCAAA+GGG + chr6.3:56247400-56247419 MS.gene79320:CDS 25.0%
!! ACAAGTACCGTATATTTATA+CGG + chr6.3:56247818-56247837 MS.gene79320:intron 25.0%
!! CTCTATACTACAATTTTTGT+TGG + chr6.3:56247747-56247766 MS.gene79320:intron 25.0%
!! TATACTACAATTTTTGTTGG+TGG + chr6.3:56247750-56247769 MS.gene79320:intron 25.0%
!! TTTTGATGTACAATTTCAAG+AGG + chr6.3:56247646-56247665 MS.gene79320:CDS 25.0%
!!! ATGTTTTGTTTACACAGTTT+AGG + chr6.3:56247793-56247812 MS.gene79320:intron 25.0%
!!! TTTTTGTTGATGAATACCAA+AGG - chr6.3:56248248-56248267 None:intergenic 25.0%
CTGAAACAAAAGACATTCAA+AGG + chr6.3:56247399-56247418 MS.gene79320:CDS 30.0%
TGCACAATATATGTAAGATC+CGG - chr6.3:56248086-56248105 None:intergenic 30.0%
! CAACAAGTTGGAATTTCAAA+AGG + chr6.3:56247990-56248009 MS.gene79320:intron 30.0%
!! AATGTCTTTTGTTTCAGAAG+AGG - chr6.3:56247396-56247415 None:intergenic 30.0%
!! ACTTCTAAAGTTGAAGTGTT+TGG + chr6.3:56247687-56247706 MS.gene79320:intron 30.0%
!!! TACAATTTTTGTTGGTGGTA+TGG + chr6.3:56247755-56247774 MS.gene79320:intron 30.0%
!!! TTTTTTCTCTTCTCTTTTGC+AGG + chr6.3:56248368-56248387 MS.gene79320:intron 30.0%
TGTACAATTTCAAGAGGAAG+AGG + chr6.3:56247652-56247671 MS.gene79320:CDS 35.0%
TTGATTGCAATTTCGACTGT+TGG + chr6.3:56248278-56248297 MS.gene79320:intron 35.0%
!! AGTGCTGAATATGTTTTGTG+TGG + chr6.3:56247526-56247545 MS.gene79320:CDS 35.0%
AACGACTACTGACATTGACA+CGG + chr6.3:56247466-56247485 MS.gene79320:CDS 40.0%
AATGTCCCCTACACATAGTT+TGG + chr6.3:56247607-56247626 MS.gene79320:CDS 40.0%
ATGCACCAAACTATGTGTAG+GGG - chr6.3:56247615-56247634 None:intergenic 40.0%
CATGCACCAAACTATGTGTA+GGG - chr6.3:56247616-56247635 None:intergenic 40.0%
TCATGCACCAAACTATGTGT+AGG - chr6.3:56247617-56247636 None:intergenic 40.0%
TGGTGATCGAAGTTTAACTC+CGG + chr6.3:56248064-56248083 MS.gene79320:intron 40.0%
TGTTGAATATGCCAGAGTTG+TGG + chr6.3:56247570-56247589 MS.gene79320:CDS 40.0%
! CTGTCTCAATTTTGCAGACT+CGG + chr6.3:56247349-56247368 MS.gene79320:CDS 40.0%
! GTAGTCGTTAAAGTCTTGTC+TGG - chr6.3:56247455-56247474 None:intergenic 40.0%
!! AAGTCCACACTCGTTGATTT+AGG + chr6.3:56247905-56247924 MS.gene79320:intron 40.0%
!! AGTCCACACTCGTTGATTTA+GGG + chr6.3:56247906-56247925 MS.gene79320:intron 40.0%
!! TCTTTTGTTTCAGAAGAGGC+AGG - chr6.3:56247392-56247411 None:intergenic 40.0%
!! TGATTTAGGGTGTTGAGATG+TGG + chr6.3:56247919-56247938 MS.gene79320:intron 40.0%
ACACCCTAAATCAACGAGTG+TGG - chr6.3:56247912-56247931 None:intergenic 45.0%
CAAAATTGAGACAGGCGTAG+CGG - chr6.3:56247343-56247362 None:intergenic 45.0%
CAATTTCGACTGTTGGCGTT+TGG + chr6.3:56248285-56248304 MS.gene79320:intron 45.0%
CGAGTCTGCAAAATTGAGAC+AGG - chr6.3:56247351-56247370 None:intergenic 45.0%
TACTGACATTGACACGGTTG+TGG + chr6.3:56247472-56247491 MS.gene79320:CDS 45.0%
TCAACGAGTGTGGACTTCTT+CGG - chr6.3:56247902-56247921 None:intergenic 45.0%
TGAATATGCCAGAGTTGTGG+AGG + chr6.3:56247573-56247592 MS.gene79320:CDS 45.0%
TGTGGAAGTCGAAGAAGAAG+AGG + chr6.3:56247544-56247563 MS.gene79320:CDS 45.0%
TTCTTCGACTGCAACGACAA+CGG - chr6.3:56247498-56247517 None:intergenic 45.0%
!! AAGAGGAAGAGGTATCGCTA+TGG + chr6.3:56247663-56247682 MS.gene79320:intron 45.0%
!!! TCAATTTTGCAGACTCGGTG+TGG + chr6.3:56247354-56247373 MS.gene79320:CDS 45.0%
ACGTTGCAGCGATGGCATTA+AGG + chr6.3:56247315-56247334 MS.gene79320:CDS 50.0%
CGTTGCAGCGATGGCATTAA+GGG + chr6.3:56247316-56247335 MS.gene79320:CDS 50.0%
GCCAGAGTTGTGGAGGAATA+TGG + chr6.3:56247580-56247599 MS.gene79320:CDS 50.0%
GCCATATTCCTCCACAACTC+TGG - chr6.3:56247584-56247603 None:intergenic 50.0%
GTTGCAGCGATGGCATTAAG+GGG + chr6.3:56247317-56247336 MS.gene79320:CDS 50.0%
GTTTCAGAAGAGGCAGGAGT+AGG - chr6.3:56247386-56247405 None:intergenic 50.0%
TGTCGTTGCAGTCGAAGAAG+AGG + chr6.3:56247499-56247518 MS.gene79320:CDS 50.0%
!!! ATTTTGCAGACTCGGTGTGG+AGG + chr6.3:56247357-56247376 MS.gene79320:CDS 50.0%
GTCTGGTCTGAAAGCCTCAG+CGG - chr6.3:56247438-56247457 None:intergenic 55.0%
AGCACACGACGTTGCAGCGA+TGG + chr6.3:56247307-56247326 MS.gene79320:CDS 60.0%
TCGCTGCAACGTCGTGTGCT+CGG - chr6.3:56247307-56247326 None:intergenic 60.0%
CGCTGCAACGTCGTGTGCTC+GGG - chr6.3:56247306-56247325 None:intergenic 65.0%
GGCAGCTGCAGAAGCCGCTG+AGG + chr6.3:56247421-56247440 MS.gene79320:CDS 70.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 56247296 56248416 56247296 ID=MS.gene79320
chr6.3 mRNA 56247296 56248416 56247296 ID=MS.gene79320.t1;Parent=MS.gene79320
chr6.3 exon 56247296 56247673 56247296 ID=MS.gene79320.t1.exon1;Parent=MS.gene79320.t1
chr6.3 CDS 56247296 56247673 56247296 ID=cds.MS.gene79320.t1;Parent=MS.gene79320.t1
chr6.3 exon 56248390 56248416 56248390 ID=MS.gene79320.t1.exon2;Parent=MS.gene79320.t1
chr6.3 CDS 56248390 56248416 56248390 ID=cds.MS.gene79320.t1;Parent=MS.gene79320.t1
Gene Sequence

>MS.gene79320

ATGGCTGCCCGAGCACACGACGTTGCAGCGATGGCATTAAGGGGCCGCTACGCCTGTCTCAATTTTGCAGACTCGGTGTGGAGGCTTCCTACTCCTGCCTCTTCTGAAACAAAAGACATTCAAAGGGCAGCTGCAGAAGCCGCTGAGGCTTTCAGACCAGACAAGACTTTAACGACTACTGACATTGACACGGTTGTGGCCGTTGTCGTTGCAGTCGAAGAAGAGGAAGAAGTGCTGAATATGTTTTGTGTGGAAGTCGAAGAAGAAGAGGAAGTGTTGAATATGCCAGAGTTGTGGAGGAATATGGCACTAATGTCCCCTACACATAGTTTGGTGCATGAGTATGAAGATTTTGATGTACAATTTCAAGAGGAAGAGGTATCGCTATGGAACTTCTAAAGTTGAAGTGTTTGGCTTACTTTTTGTTTTTTTAGATTGTAGAATGGAAAATCTCTATACTACAATTTTTGTTGGTGGTATGGATTTTACGTAGAGAAATGTTTTGTTTACACAGTTTAGGACACAAGTACCGTATATTTATACGGATTTTGAGTTTTAAATTGTTTTTTTCTCTATCTTCAAGTGTTTGTTCTCTCTTTGACACCGAAGAAGTCCACACTCGTTGATTTAGGGTGTTGAGATGTGGTGTCAAAAATTGTGTGTTTAAATTACACAGCTGCAATATATTGATATACAACAAGTTGGAATTTCAAAAGGATTTTTAATTTGTAGCTTATCTGTGAATGTAATCACTTTTTTTTTTTTTTGTGGTGATCGAAGTTTAACTCCGGATCTTACATATATTGTGCATTGTCTCTATCAACTGAGCTAAGCTATTATGAATATAATTACTAATTGGGCATAAAGTGCATCTTATCACTTTTATTTATATATAAAAGAATAATAAAACTTTGGAATGTCAAAATATCTGTCTATGTATTAATATTGACCTTTGGTATTCATCAACAAAAAAAGAAGGCATTTGATTGCAATTTCGACTGTTGGCGTTTGGCTTAATTAGCTAATTGCAATATATTGAGGGATATAATTAAAATCAGTGTCTCACTTCTTATTTTTTCTCTTCTCTTTTGCAGGTATTAAAAAAAAATCAGTTACAATGA
Protein sequence

>MS.gene79320.t1

MAARAHDVAAMALRGRYACLNFADSVWRLPTPASSETKDIQRAAAEAAEAFRPDKTLTTTDIDTVVAVVVAVEEEEEVLNMFCVEVEEEEEVLNMPELWRNMALMSPTHSLVHEYEDFDVQFQEEEVLKKNQLQ