AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene67539

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67539.t1 MTR_5g023600 93.939 198 12 0 1 198 1 198 2.58e-126 357
MS.gene67539.t1 MTR_5g023390 92.424 198 15 0 1 198 1 198 2.29e-125 355
MS.gene67539.t1 MTR_5g023370 90.909 198 18 0 1 198 1 198 5.56e-122 347
MS.gene67539.t1 MTR_5g023350 91.414 198 17 0 1 198 1 198 6.55e-122 346
MS.gene67539.t1 MTR_5g023340 89.899 198 20 0 1 198 1 198 4.59e-120 342
MS.gene67539.t1 MTR_5g023530 88.945 199 21 1 1 198 1 199 5.30e-120 342
MS.gene67539.t1 MTR_5g023320 88.442 199 22 1 1 198 1 199 9.90e-119 338
MS.gene67539.t1 MTR_5g023470 87.940 199 23 1 1 198 1 199 2.03e-118 337
MS.gene67539.t1 MTR_5g023580 86.364 198 27 0 1 198 1 198 9.70e-116 333
MS.gene67539.t1 MTR_5g023550 87.245 196 25 0 3 198 2 197 5.97e-115 328
MS.gene67539.t1 MTR_5g023520 85.641 195 28 0 3 197 2 196 8.32e-113 323
MS.gene67539.t1 MTR_8g074450 71.503 193 55 0 6 198 5 197 4.30e-96 281
MS.gene67539.t1 MTR_8g074510 67.358 193 61 1 6 198 5 195 1.09e-90 267
MS.gene67539.t1 MTR_8g074420 66.327 196 66 0 3 198 2 197 2.27e-86 256
MS.gene67539.t1 MTR_5g023460 86.869 99 13 0 100 198 11 109 1.03e-56 177
MS.gene67539.t1 MTR_5g023410 86.869 99 13 0 3 101 2 100 1.55e-50 162
MS.gene67539.t1 MTR_8g074380 39.109 202 115 2 1 194 7 208 4.52e-41 142
MS.gene67539.t1 MTR_8g074530 42.268 194 108 3 3 194 17 208 1.35e-40 140
MS.gene67539.t1 MTR_5g023290 39.086 197 115 2 3 194 9 205 2.14e-38 134
MS.gene67539.t1 MTR_5g023650 38.579 197 115 2 4 194 10 206 1.70e-36 129
MS.gene67539.t1 MTR_4g070590 35.385 195 121 3 7 197 14 207 4.93e-29 109
MS.gene67539.t1 MTR_3g116950 35.500 200 123 5 2 198 8 204 7.55e-27 103
MS.gene67539.t1 MTR_4g070570 31.034 203 130 5 2 198 11 209 7.69e-27 103
MS.gene67539.t1 MTR_4g070530 33.333 192 121 2 7 194 13 201 2.77e-26 102
MS.gene67539.t1 MTR_4g070540 35.714 154 92 2 7 156 13 163 4.83e-23 94.0
MS.gene67539.t1 MTR_3g116920 31.841 201 131 4 2 198 8 206 3.13e-21 89.0
MS.gene67539.t1 MTR_3g115150 31.333 150 92 4 6 151 27 169 3.03e-17 78.6
MS.gene67539.t1 MTR_1g037820 29.861 144 100 1 52 194 9 152 5.14e-17 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene67539.t1 AT4G35690 39.796 196 111 3 7 196 9 203 8.97e-45 150
MS.gene67539.t1 AT4G35710 40.698 172 95 3 7 173 9 178 5.76e-36 127
MS.gene67539.t1 AT2G17680 40.196 204 102 6 7 196 9 206 6.01e-36 127
MS.gene67539.t1 AT2G17080 36.923 195 111 3 3 197 2 184 2.78e-33 120
MS.gene67539.t1 AT2G17070 36.410 195 112 3 3 197 2 184 1.33e-31 115
MS.gene67539.t1 AT4G35210 32.821 195 109 4 3 197 2 174 6.14e-29 108
MS.gene67539.t1 AT4G35200 33.846 195 110 4 3 197 2 177 6.84e-29 108
MS.gene67539.t1 AT4G35680 36.000 200 114 4 3 194 13 206 1.41e-23 95.5
MS.gene67539.t1 AT4G35720 30.366 191 131 1 6 194 14 204 5.65e-22 91.7
MS.gene67539.t1 AT4G35660 34.000 200 125 5 1 194 9 207 6.22e-21 88.2
MS.gene67539.t1 AT1G76240 26.531 196 127 5 5 190 28 216 8.39e-16 74.3
MS.gene67539.t1 AT1G76220 31.000 200 107 7 2 191 5 183 3.55e-13 66.6
MS.gene67539.t1 AT1G76210 29.365 126 87 2 68 193 26 149 3.59e-12 63.5
MS.gene67539.t1 AT3G51410 33.582 134 75 3 8 141 39 158 8.21e-11 60.1

Find 31 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCTCCCTTTCTCCTTCTA+AGG 0.157858 5.4:+15099514 None:intergenic
AAACATATGGAAACTAAATT+TGG 0.157953 5.4:-15099408 MS.gene67539:CDS
CCACAAATTTCTCACCTTGA+TGG 0.264918 5.4:+15099637 None:intergenic
CACTTCACTCTTCCCTTAGA+AGG 0.345532 5.4:-15099527 MS.gene67539:CDS
GAAATTTGTGGAAGAGTTGT+TGG 0.365610 5.4:-15099625 MS.gene67539:CDS
GATCACATCTTTAAAACATA+TGG 0.374642 5.4:-15099421 MS.gene67539:CDS
TTGTTCTATTCTTGTGGAGT+TGG 0.376848 5.4:+15099803 None:intergenic
GTTTGAGCGAACATGGTAAT+TGG 0.377515 5.4:+15099848 None:intergenic
TGTTCTATTCTTGTGGAGTT+GGG 0.378838 5.4:+15099804 None:intergenic
GGATGGTTCAGTGAAAGTTT+TGG 0.423908 5.4:-15099604 MS.gene67539:CDS
TAGCTCTTGTTCTATTCTTG+TGG 0.426456 5.4:+15099797 None:intergenic
CTCTTCCCTTAGAAGGAGAA+AGG 0.440449 5.4:-15099520 MS.gene67539:CDS
CCATCAAGGTGAGAAATTTG+TGG 0.460090 5.4:-15099637 MS.gene67539:CDS
ACAAATCTTCAAGCAAGTAA+AGG 0.525919 5.4:+15099715 None:intergenic
ATCTCCCTTTCTCCTTCTAA+GGG 0.536266 5.4:+15099515 None:intergenic
TGGATATCTGTGGCATCACA+AGG 0.539961 5.4:-15099584 MS.gene67539:CDS
GAAAGCTGTTTGAGCGAACA+TGG 0.544237 5.4:+15099841 None:intergenic
TTCAAGCAAGTAAAGGCCAT+TGG 0.545983 5.4:+15099722 None:intergenic
AAGCTTGTTTCTCACCATCA+AGG 0.549955 5.4:-15099651 MS.gene67539:CDS
AGCTATGCAAAATGAAGACA+TGG 0.554384 5.4:-15099779 MS.gene67539:CDS
TCTTCCCTTAGAAGGAGAAA+GGG 0.559612 5.4:-15099519 MS.gene67539:CDS
TTTGTGGAAGAGTTGTTGGA+TGG 0.615570 5.4:-15099621 MS.gene67539:CDS
ACATCTGATTCAATTACCAA+TGG 0.619749 5.4:-15099738 MS.gene67539:CDS
TTGATCTTGATTCGAAAGTG+AGG 0.621821 5.4:+15099380 None:intergenic
AGTGATTACAGTTCTTAGAG+AGG 0.623623 5.4:-15099346 MS.gene67539:CDS
ATTGGTAATTGAATCAGATG+TGG 0.626315 5.4:+15099740 None:intergenic
ATCAGATGTGGATGTTGATG+TGG 0.645441 5.4:+15099752 None:intergenic
GGATATCTGTGGCATCACAA+GGG 0.651501 5.4:-15099583 MS.gene67539:CDS
GAACTGTAATCACTGCAACA+AGG 0.656672 5.4:+15099355 None:intergenic
GCTATGCAAAATGAAGACAT+GGG 0.719093 5.4:-15099778 MS.gene67539:CDS
GAGTTGGGATGAGATTGAGA+AGG 0.749032 5.4:+15099819 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACATATGGAAACTAAATT+TGG - chr5.4:15099734-15099753 MS.gene67539:CDS 20.0%
!!! GATCACATCTTTAAAACATA+TGG - chr5.4:15099721-15099740 MS.gene67539:CDS 25.0%
ACAAATCTTCAAGCAAGTAA+AGG + chr5.4:15099430-15099449 None:intergenic 30.0%
ACATCTGATTCAATTACCAA+TGG - chr5.4:15099404-15099423 MS.gene67539:CDS 30.0%
! ATTGGTAATTGAATCAGATG+TGG + chr5.4:15099405-15099424 None:intergenic 30.0%
! TCAATCTGTTTTGTCTTTCT+TGG - chr5.4:15099844-15099863 MS.gene67539:CDS 30.0%
AGCTATGCAAAATGAAGACA+TGG - chr5.4:15099363-15099382 MS.gene67539:CDS 35.0%
AGTGATTACAGTTCTTAGAG+AGG - chr5.4:15099796-15099815 MS.gene67539:CDS 35.0%
GAAATTTGTGGAAGAGTTGT+TGG - chr5.4:15099517-15099536 MS.gene67539:CDS 35.0%
GCTATGCAAAATGAAGACAT+GGG - chr5.4:15099364-15099383 MS.gene67539:CDS 35.0%
TAGCTCTTGTTCTATTCTTG+TGG + chr5.4:15099348-15099367 None:intergenic 35.0%
TGTTCTATTCTTGTGGAGTT+GGG + chr5.4:15099341-15099360 None:intergenic 35.0%
TTGTTCTATTCTTGTGGAGT+TGG + chr5.4:15099342-15099361 None:intergenic 35.0%
! TCTGTTTTGTCTTTCTTGGT+TGG - chr5.4:15099848-15099867 MS.gene67539:CDS 35.0%
! TTGATCTTGATTCGAAAGTG+AGG + chr5.4:15099765-15099784 None:intergenic 35.0%
!!! GTGAAAGTTTTGGATATCTG+TGG - chr5.4:15099548-15099567 MS.gene67539:CDS 35.0%
AATCTCCCTTTCTCCTTCTA+AGG + chr5.4:15099631-15099650 None:intergenic 40.0%
ATCAGATGTGGATGTTGATG+TGG + chr5.4:15099393-15099412 None:intergenic 40.0%
ATCTCCCTTTCTCCTTCTAA+GGG + chr5.4:15099630-15099649 None:intergenic 40.0%
CCACAAATTTCTCACCTTGA+TGG + chr5.4:15099508-15099527 None:intergenic 40.0%
CCATCAAGGTGAGAAATTTG+TGG - chr5.4:15099505-15099524 MS.gene67539:CDS 40.0%
GAACTGTAATCACTGCAACA+AGG + chr5.4:15099790-15099809 None:intergenic 40.0%
GTTTGAGCGAACATGGTAAT+TGG + chr5.4:15099297-15099316 None:intergenic 40.0%
TCTTCCCTTAGAAGGAGAAA+GGG - chr5.4:15099623-15099642 MS.gene67539:CDS 40.0%
TTCAAGCAAGTAAAGGCCAT+TGG + chr5.4:15099423-15099442 None:intergenic 40.0%
TTTGTGGAAGAGTTGTTGGA+TGG - chr5.4:15099521-15099540 MS.gene67539:CDS 40.0%
! AAGCTTGTTTCTCACCATCA+AGG - chr5.4:15099491-15099510 MS.gene67539:CDS 40.0%
! GGATGGTTCAGTGAAAGTTT+TGG - chr5.4:15099538-15099557 MS.gene67539:CDS 40.0%
CACTTCACTCTTCCCTTAGA+AGG - chr5.4:15099615-15099634 MS.gene67539:CDS 45.0%
CTCTTCCCTTAGAAGGAGAA+AGG - chr5.4:15099622-15099641 MS.gene67539:CDS 45.0%
GAAAGCTGTTTGAGCGAACA+TGG + chr5.4:15099304-15099323 None:intergenic 45.0%
GAGTTGGGATGAGATTGAGA+AGG + chr5.4:15099326-15099345 None:intergenic 45.0%
GGATATCTGTGGCATCACAA+GGG - chr5.4:15099559-15099578 MS.gene67539:CDS 45.0%
TGGATATCTGTGGCATCACA+AGG - chr5.4:15099558-15099577 MS.gene67539:CDS 45.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 15099284 15099880 15099284 ID=MS.gene67539
chr5.4 mRNA 15099284 15099880 15099284 ID=MS.gene67539.t1;Parent=MS.gene67539
chr5.4 exon 15099284 15099880 15099284 ID=MS.gene67539.t1.exon1;Parent=MS.gene67539.t1
chr5.4 CDS 15099284 15099880 15099284 ID=cds.MS.gene67539.t1;Parent=MS.gene67539.t1
Gene Sequence

>MS.gene67539

ATGGCAAGCACCAATTACCATGTTCGCTCAAACAGCTTTCCTTCTCAATCTCATCCCAACTCCACAAGAATAGAACAAGAGCTATGCAAAATGAAGACATGGGTAGCCACATCAACATCCACATCTGATTCAATTACCAATGGCCTTTACTTGCTTGAAGATTTGTATATATCTTTAGAAAATCTTCTAAATATGACATCAACACAGAAGCTTGTTTCTCACCATCAAGGTGAGAAATTTGTGGAAGAGTTGTTGGATGGTTCAGTGAAAGTTTTGGATATCTGTGGCATCACAAGGGACACTATGTTACAAATTAAAGAAAATGTTCAGTCACTTCACTCTTCCCTTAGAAGGAGAAAGGGAGATTCAAGCATTGAAACAAGTGTAGCAGAATATAAATTTTTCACAAAGAAGATGAAGAAGAATGTCACAAAGTTGATCACATCTTTAAAACATATGGAAACTAAATTTGGAGCTTCCTCACTTTCGAATCAAGATCAAGACCTTGTTGCAGTGATTACAGTTCTTAGAGAGGTCATTGCAATGAACTTGTCTATCTTTCAATCTGTTTTGTCTTTCTTGGTTGGATCTTCATAA
Protein sequence

>MS.gene67539.t1

MASTNYHVRSNSFPSQSHPNSTRIEQELCKMKTWVATSTSTSDSITNGLYLLEDLYISLENLLNMTSTQKLVSHHQGEKFVEELLDGSVKVLDICGITRDTMLQIKENVQSLHSSLRRRKGDSSIETSVAEYKFFTKKMKKNVTKLITSLKHMETKFGASSLSNQDQDLVAVITVLREVIAMNLSIFQSVLSFLVGSS