AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29238


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29238.t1 MTR_1g038650 95.319 235 8 1 1 232 1 235 2.81e-164 453
MS.gene29238.t1 MTR_1g114380 61.633 245 57 5 16 230 18 255 5.37e-84 251
MS.gene29238.t1 MTR_2g006150 75.000 84 18 1 20 100 115 198 1.71e-36 133
MS.gene29238.t1 MTR_5g039600 78.205 78 12 1 28 100 58 135 1.80e-36 132
MS.gene29238.t1 MTR_2g006150 75.000 84 18 1 20 100 115 198 1.95e-36 134
MS.gene29238.t1 MTR_7g028160 54.400 125 53 1 1 121 15 139 3.27e-36 129
MS.gene29238.t1 MTR_4g108370 70.930 86 21 1 19 100 80 165 9.63e-36 131
MS.gene29238.t1 MTR_1g063870 78.082 73 13 1 25 94 39 111 6.24e-35 124
MS.gene29238.t1 MTR_1g101810 65.934 91 30 1 5 94 36 126 1.23e-32 121
MS.gene29238.t1 MTR_1g101810 65.934 91 30 1 5 94 66 156 2.78e-32 120
MS.gene29238.t1 MTR_8g033070 72.603 73 20 0 28 100 76 148 2.28e-31 117
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29238.t1 AT5G23280 56.574 251 62 6 10 232 19 250 1.27e-74 226
MS.gene29238.t1 AT5G08330 57.143 238 64 8 16 230 13 235 2.36e-63 197
MS.gene29238.t1 AT1G72010 81.944 72 13 0 29 100 60 131 5.33e-37 133
MS.gene29238.t1 AT1G69690 68.889 90 23 1 16 100 31 120 5.59e-37 132
MS.gene29238.t1 AT3G47620 67.708 96 25 2 11 100 90 185 1.53e-36 134
MS.gene29238.t1 AT1G35560 83.333 72 12 0 29 100 52 123 8.18e-35 127
MS.gene29238.t1 AT3G27010 63.000 100 28 2 3 93 40 139 1.44e-33 123
MS.gene29238.t1 AT3G27010 63.000 100 28 2 3 93 40 139 1.44e-33 123
MS.gene29238.t1 AT5G51910 67.059 85 28 0 28 112 53 137 4.44e-32 119
MS.gene29238.t1 AT5G51910 67.059 85 28 0 28 112 53 137 4.44e-32 119
MS.gene29238.t1 AT2G45680 76.471 68 16 0 27 94 70 137 1.23e-31 119
MS.gene29238.t1 AT1G58100 51.389 144 47 3 32 172 60 183 2.76e-29 113
MS.gene29238.t1 AT5G41030 67.164 67 22 0 28 94 64 130 4.12e-28 107
MS.gene29238.t1 AT2G37000 75.000 60 15 0 32 91 43 102 4.13e-27 103
MS.gene29238.t1 AT3G45150 52.055 73 35 0 33 105 18 90 7.26e-20 83.6

Find 61 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACACGTGCGGCGCAGATTA+TGG 0.191163 1.1:+23198751 None:intergenic
CTACTGCTCCGCCGGGGTTT+TGG 0.252668 1.1:-23198508 MS.gene29238:CDS
CAACCTTCTCCGTTTATTCT+TGG 0.258658 1.1:-23198578 MS.gene29238:CDS
AATTTGTTGGCTTCATTGTC+TGG 0.298075 1.1:-23198263 MS.gene29238:CDS
GAAGCTTCGGCGGCGAGGTT+AGG 0.304875 1.1:-23198308 MS.gene29238:CDS
TCAACAGCAACAAGGCTCTA+TGG 0.307887 1.1:-23198333 MS.gene29238:CDS
GTTGATGCTGCTGGTGGTGC+TGG 0.308604 1.1:+23198351 None:intergenic
GACCAAGCTCACGTGTTAAC+TGG 0.329708 1.1:+23198726 None:intergenic
GCTGCTGGTGGTGCTGGTGC+TGG 0.334270 1.1:+23198357 None:intergenic
TCCTGGTCATCTGAATTTGT+TGG 0.361921 1.1:-23198276 MS.gene29238:CDS
ACACGTGCGGCGCAGATTAT+GGG 0.390746 1.1:+23198752 None:intergenic
CTTGTTGCTGTTGATGCTGC+TGG 0.395955 1.1:+23198342 None:intergenic
TGCTGCACCTACTGCTCCGC+CGG 0.410157 1.1:-23198516 MS.gene29238:CDS
GAAAGAAGCAGGTGTAGTTC+CGG 0.413992 1.1:+23198631 None:intergenic
TGATGATGGTGATGCTGTTT+CGG 0.418538 1.1:-23198540 MS.gene29238:CDS
TCTGGTGGGAATGGAAATTC+TGG 0.419287 1.1:-23198245 MS.gene29238:CDS
AAGCTTCGGCGGCGAGGTTA+GGG 0.419803 1.1:-23198307 MS.gene29238:CDS
AACGGAGAAGGTTGAAGAAA+AGG 0.424552 1.1:+23198587 None:intergenic
TGCTGCTGCTCAACCGCCGC+CGG 0.429682 1.1:-23198453 MS.gene29238:CDS
GCTGCTCAACCGCCGCCGGA+AGG 0.449544 1.1:-23198449 MS.gene29238:CDS
CTCCAAAGCTGAGCAAAATC+CGG 0.465288 1.1:+23198482 None:intergenic
AAACGTTTACCAAGAATAAA+CGG 0.469719 1.1:+23198569 None:intergenic
ATCATCGCCGCCACCGGTAC+CGG 0.476622 1.1:-23198650 MS.gene29238:CDS
CAACAGCAACAAGGCTCTAT+GGG 0.478969 1.1:-23198332 MS.gene29238:CDS
TGTAGTTCCGGTACCGGTGG+CGG 0.480445 1.1:+23198643 None:intergenic
GCTGCACCTACTGCTCCGCC+GGG 0.481411 1.1:-23198515 MS.gene29238:CDS
GCTTCATTGTCTGGTGGGAA+TGG 0.484637 1.1:-23198254 MS.gene29238:CDS
AGGTTAGGGAATTATCTTCC+TGG 0.487752 1.1:-23198293 MS.gene29238:CDS
AGCAGGTGTAGTTCCGGTAC+CGG 0.496500 1.1:+23198637 None:intergenic
AGAAGTGGGTTCTACTAGAT+CGG 0.502592 1.1:+23198856 None:intergenic
AGGCTCTATGGGTGAAGCTT+CGG 0.504366 1.1:-23198321 MS.gene29238:CDS
GAAAGAGAAGAGAAAGAAGC+AGG 0.509335 1.1:+23198620 None:intergenic
TGATCGACGGTTCAGCTTGA+CGG 0.511819 1.1:+23198669 None:intergenic
TTCCAGTTAACACGTGAGCT+TGG 0.518020 1.1:-23198728 MS.gene29238:CDS
TTCCGTCTACTTTACTGTGA+CGG 0.524053 1.1:+23198795 None:intergenic
AAATCCGGCCGCCAAAACCC+CGG 0.528380 1.1:+23198497 None:intergenic
TGTTGGCTTCATTGTCTGGT+GGG 0.531348 1.1:-23198259 MS.gene29238:CDS
CCGTCGATCATCGCCGCCAC+CGG 0.537613 1.1:-23198656 MS.gene29238:CDS
CACAGTAAAGTAGACGGAAG+AGG 0.537838 1.1:-23198791 MS.gene29238:CDS
CAAAACCCCGGCGGAGCAGT+AGG 0.540114 1.1:+23198509 None:intergenic
TTGTTGGCTTCATTGTCTGG+TGG 0.543932 1.1:-23198260 MS.gene29238:CDS
GGGAATGGAAATTCTGGTCG+TGG 0.548380 1.1:-23198239 MS.gene29238:CDS
TTCTACTAGATCGGTTGTTG+TGG 0.553500 1.1:+23198865 None:intergenic
GCCAACAAATTCAGATGACC+AGG 0.560326 1.1:+23198275 None:intergenic
CCGGTGGCGGCGATGATCGA+CGG 0.572268 1.1:+23198656 None:intergenic
TGATAGTTGTTGTTTCCTTG+TGG 0.582444 1.1:+23198888 None:intergenic
GTTGCTGTTGATGCTGCTGG+TGG 0.588478 1.1:+23198345 None:intergenic
CTCTATGGGTGAAGCTTCGG+CGG 0.604764 1.1:-23198318 MS.gene29238:CDS
TTACCAAGAATAAACGGAGA+AGG 0.605589 1.1:+23198575 None:intergenic
AGGTGTAGTTCCGGTACCGG+TGG 0.608264 1.1:+23198640 None:intergenic
CCATTCGATAGTTTGACCGT+CGG 0.631339 1.1:+23198697 None:intergenic
CAGCAGCATCAACAGCAACA+AGG 0.632046 1.1:-23198341 MS.gene29238:CDS
ACCTCAAATGTCTAACCACA+AGG 0.638869 1.1:-23198903 None:intergenic
GACCGTCACAGTAAAGTAGA+CGG 0.641647 1.1:-23198797 MS.gene29238:CDS
CCGACGGTCAAACTATCGAA+TGG 0.646959 1.1:-23198697 MS.gene29238:CDS
TGGGTGAAGCTTCGGCGGCG+AGG 0.659727 1.1:-23198313 MS.gene29238:CDS
AAACGTTTACGTGATGATGA+TGG 0.660458 1.1:-23198554 MS.gene29238:CDS
GAGCTTGGTCATAAATCCGA+CGG 0.680249 1.1:-23198713 MS.gene29238:CDS
CTGCACCTACTGCTCCGCCG+GGG 0.682389 1.1:-23198514 MS.gene29238:CDS
TCCGGCCGCCAAAACCCCGG+CGG 0.699527 1.1:+23198500 None:intergenic
TGTTAACTGGAAAACACGTG+CGG 0.728936 1.1:+23198739 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAACGTTTACCAAGAATAAA+CGG + chr1.1:23198550-23198569 None:intergenic 25.0%
TGAGAAACAGAAAAACCTTC+CGG + chr1.1:23198685-23198704 None:intergenic 35.0%
TTACCAAGAATAAACGGAGA+AGG + chr1.1:23198544-23198563 None:intergenic 35.0%
! AAACGTTTACGTGATGATGA+TGG - chr1.1:23198562-23198581 MS.gene29238:CDS 35.0%
!! AATTTGTTGGCTTCATTGTC+TGG - chr1.1:23198853-23198872 MS.gene29238:CDS 35.0%
!! TGATAGTTGTTGTTTCCTTG+TGG + chr1.1:23198231-23198250 None:intergenic 35.0%
!!! GTTAGAGTGTTTTGAGAAGT+GGG + chr1.1:23198277-23198296 None:intergenic 35.0%
!!! TGTTAGAGTGTTTTGAGAAG+TGG + chr1.1:23198278-23198297 None:intergenic 35.0%
AACGGAGAAGGTTGAAGAAA+AGG + chr1.1:23198532-23198551 None:intergenic 40.0%
AGGTTAGGGAATTATCTTCC+TGG - chr1.1:23198823-23198842 MS.gene29238:CDS 40.0%
CAACCTTCTCCGTTTATTCT+TGG - chr1.1:23198538-23198557 MS.gene29238:CDS 40.0%
GAAAGAGAAGAGAAAGAAGC+AGG + chr1.1:23198499-23198518 None:intergenic 40.0%
TCCTGGTCATCTGAATTTGT+TGG - chr1.1:23198840-23198859 MS.gene29238:CDS 40.0%
TGTTAACTGGAAAACACGTG+CGG + chr1.1:23198380-23198399 None:intergenic 40.0%
TTCCGTCTACTTTACTGTGA+CGG + chr1.1:23198324-23198343 None:intergenic 40.0%
TTCTACTAGATCGGTTGTTG+TGG + chr1.1:23198254-23198273 None:intergenic 40.0%
! AGAAGTGGGTTCTACTAGAT+CGG + chr1.1:23198263-23198282 None:intergenic 40.0%
! TTACTGTGACGGTCTTTTGA+CGG + chr1.1:23198313-23198332 None:intergenic 40.0%
!! TGATGATGGTGATGCTGTTT+CGG - chr1.1:23198576-23198595 MS.gene29238:CDS 40.0%
CAACAGCAACAAGGCTCTAT+GGG - chr1.1:23198784-23198803 MS.gene29238:CDS 45.0%
CACAGTAAAGTAGACGGAAG+AGG - chr1.1:23198325-23198344 MS.gene29238:CDS 45.0%
CCATTCGATAGTTTGACCGT+CGG + chr1.1:23198422-23198441 None:intergenic 45.0%
CTCCAAAGCTGAGCAAAATC+CGG + chr1.1:23198637-23198656 None:intergenic 45.0%
GAAACAGAAAAACCTTCCGG+CGG + chr1.1:23198682-23198701 None:intergenic 45.0%
GAAAGAAGCAGGTGTAGTTC+CGG + chr1.1:23198488-23198507 None:intergenic 45.0%
GACCGTCACAGTAAAGTAGA+CGG - chr1.1:23198319-23198338 MS.gene29238:CDS 45.0%
GAGCTTGGTCATAAATCCGA+CGG - chr1.1:23198403-23198422 MS.gene29238:CDS 45.0%
GCCAACAAATTCAGATGACC+AGG + chr1.1:23198844-23198863 None:intergenic 45.0%
TCAACAGCAACAAGGCTCTA+TGG - chr1.1:23198783-23198802 MS.gene29238:CDS 45.0%
TCTGGTGGGAATGGAAATTC+TGG - chr1.1:23198871-23198890 MS.gene29238:CDS 45.0%
TTCCAGTTAACACGTGAGCT+TGG - chr1.1:23198388-23198407 MS.gene29238:CDS 45.0%
!! TGTTGGCTTCATTGTCTGGT+GGG - chr1.1:23198857-23198876 MS.gene29238:CDS 45.0%
!! TTGTTGGCTTCATTGTCTGG+TGG - chr1.1:23198856-23198875 MS.gene29238:CDS 45.0%
AGGCTCTATGGGTGAAGCTT+CGG - chr1.1:23198795-23198814 MS.gene29238:CDS 50.0%
CAGCAGCATCAACAGCAACA+AGG - chr1.1:23198775-23198794 MS.gene29238:CDS 50.0%
CCGACGGTCAAACTATCGAA+TGG - chr1.1:23198419-23198438 MS.gene29238:CDS 50.0%
GACCAAGCTCACGTGTTAAC+TGG + chr1.1:23198393-23198412 None:intergenic 50.0%
GCTTCATTGTCTGGTGGGAA+TGG - chr1.1:23198862-23198881 MS.gene29238:CDS 50.0%
GGGAATGGAAATTCTGGTCG+TGG - chr1.1:23198877-23198896 MS.gene29238:CDS 50.0%
TGATCGACGGTTCAGCTTGA+CGG + chr1.1:23198450-23198469 None:intergenic 50.0%
! CTTGTTGCTGTTGATGCTGC+TGG + chr1.1:23198777-23198796 None:intergenic 50.0%
AACACGTGCGGCGCAGATTA+TGG + chr1.1:23198368-23198387 None:intergenic 55.0%
ACACGTGCGGCGCAGATTAT+GGG + chr1.1:23198367-23198386 None:intergenic 55.0%
ACAGAAAAACCTTCCGGCGG+CGG + chr1.1:23198679-23198698 None:intergenic 55.0%
AGCAGGTGTAGTTCCGGTAC+CGG + chr1.1:23198482-23198501 None:intergenic 55.0%
CTCTATGGGTGAAGCTTCGG+CGG - chr1.1:23198798-23198817 MS.gene29238:CDS 55.0%
! CTGTGACGGTCTTTTGACGG+TGG + chr1.1:23198310-23198329 None:intergenic 55.0%
! GGCCGGATTTTGCTCAGCTT+TGG - chr1.1:23198632-23198651 MS.gene29238:CDS 55.0%
! GTTGCTGTTGATGCTGCTGG+TGG + chr1.1:23198774-23198793 None:intergenic 55.0%
AAATCCGGCCGCCAAAACCC+CGG + chr1.1:23198622-23198641 None:intergenic 60.0%
AAGCTTCGGCGGCGAGGTTA+GGG - chr1.1:23198809-23198828 MS.gene29238:CDS 60.0%
! AGGTGTAGTTCCGGTACCGG+TGG + chr1.1:23198479-23198498 None:intergenic 60.0%
! GTTGATGCTGCTGGTGGTGC+TGG + chr1.1:23198768-23198787 None:intergenic 60.0%
!! TGTAGTTCCGGTACCGGTGG+CGG + chr1.1:23198476-23198495 None:intergenic 60.0%
ATCATCGCCGCCACCGGTAC+CGG - chr1.1:23198466-23198485 MS.gene29238:CDS 65.0%
CAAAACCCCGGCGGAGCAGT+AGG + chr1.1:23198610-23198629 None:intergenic 65.0%
GAAGCTTCGGCGGCGAGGTT+AGG - chr1.1:23198808-23198827 MS.gene29238:CDS 65.0%
TGCTGCACCTACTGCTCCGC+CGG - chr1.1:23198600-23198619 MS.gene29238:CDS 65.0%
! CTACTGCTCCGCCGGGGTTT+TGG - chr1.1:23198608-23198627 MS.gene29238:CDS 65.0%
CCGTCGATCATCGCCGCCAC+CGG - chr1.1:23198460-23198479 MS.gene29238:CDS 70.0%
CTGCACCTACTGCTCCGCCG+GGG - chr1.1:23198602-23198621 MS.gene29238:CDS 70.0%
GCTGCACCTACTGCTCCGCC+GGG - chr1.1:23198601-23198620 MS.gene29238:CDS 70.0%
TGCTGCTGCTCAACCGCCGC+CGG - chr1.1:23198663-23198682 MS.gene29238:CDS 70.0%
TGGGTGAAGCTTCGGCGGCG+AGG - chr1.1:23198803-23198822 MS.gene29238:CDS 70.0%
! CCGGTGGCGGCGATGATCGA+CGG + chr1.1:23198463-23198482 None:intergenic 70.0%
!! CTGCTCCGCCGGGGTTTTGG+CGG - chr1.1:23198611-23198630 MS.gene29238:CDS 70.0%
!! GCTGCTGGTGGTGCTGGTGC+TGG + chr1.1:23198762-23198781 None:intergenic 70.0%
GCTGCTCAACCGCCGCCGGA+AGG - chr1.1:23198667-23198686 MS.gene29238:CDS 75.0%
TCCGGCCGCCAAAACCCCGG+CGG + chr1.1:23198619-23198638 None:intergenic 75.0%
!! TCCGCCGGGGTTTTGGCGGC+CGG - chr1.1:23198615-23198634 MS.gene29238:CDS 75.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 23198220 23198918 23198220 ID=MS.gene29238
chr1.1 mRNA 23198220 23198918 23198220 ID=MS.gene29238.t1;Parent=MS.gene29238
chr1.1 exon 23198220 23198918 23198220 ID=MS.gene29238.t1.exon1;Parent=MS.gene29238.t1
chr1.1 CDS 23198220 23198918 23198220 ID=cds.MS.gene29238.t1;Parent=MS.gene29238.t1
Gene Sequence

>MS.gene29238

ATGTCTAACCACAAGGAAACAACAACTATCACCACAACAACCGATCTAGTAGAACCCACTTCTCAAAACACTCTAACAGTAAAAAAACCACCGTCAAAAGACCGTCACAGTAAAGTAGACGGAAGAGGAAGACGCATAAGAATGCCCATAATCTGCGCCGCACGTGTTTTCCAGTTAACACGTGAGCTTGGTCATAAATCCGACGGTCAAACTATCGAATGGCTTCTCCGTCAAGCTGAACCGTCGATCATCGCCGCCACCGGTACCGGAACTACACCTGCTTCTTTCTCTTCTCTTTCTGAGCATAAACCTTTTCTTCAACCTTCTCCGTTTATTCTTGGTAAACGTTTACGTGATGATGATGGTGATGCTGTTTCGGTTGCTGCACCTACTGCTCCGCCGGGGTTTTGGCGGCCGGATTTTGCTCAGCTTTGGAGCTTTGCTGCTGCTGCTCAACCGCCGCCGGAAGGTTTTTCTGTTTCTCAGCATAATTCATTGTTTCATCATCAACAACAGCAACAGCAGCAGCAGCAACAACACCAGCACCAGCACCACCAGCAGCATCAACAGCAACAAGGCTCTATGGGTGAAGCTTCGGCGGCGAGGTTAGGGAATTATCTTCCTGGTCATCTGAATTTGTTGGCTTCATTGTCTGGTGGGAATGGAAATTCTGGTCGTGGAGATGACGAAGATCGTTGA

Protein sequence

>MS.gene29238.t1

MSNHKETTTITTTTDLVEPTSQNTLTVKKPPSKDRHSKVDGRGRRIRMPIICAARVFQLTRELGHKSDGQTIEWLLRQAEPSIIAATGTGTTPASFSSLSEHKPFLQPSPFILGKRLRDDDGDAVSVAAPTAPPGFWRPDFAQLWSFAAAAQPPPEGFSVSQHNSLFHHQQQQQQQQQQHQHQHHQQHQQQQGSMGEASAARLGNYLPGHLNLLASLSGGNGNSGRGDDEDR