AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene87454

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene87454.t1 MTR_8g077510 89.627 241 15 3 1 234 1 238 8.39e-128 361
MS.gene87454.t1 MTR_5g020230 54.878 246 78 12 1 224 1 235 3.76e-68 209
MS.gene87454.t1 MTR_4g126350 52.308 65 29 1 89 153 153 215 3.23e-14 70.9
MS.gene87454.t1 MTR_1g016170 59.322 59 21 2 114 172 179 234 1.45e-13 68.9
MS.gene87454.t1 MTR_7g112330 65.789 38 13 0 120 157 18 55 2.04e-13 65.5
MS.gene87454.t1 MTR_4g121110 50.820 61 30 0 100 160 6 66 2.57e-13 65.5
MS.gene87454.t1 MTR_2g094600 37.500 104 50 3 68 156 145 248 1.03e-12 66.6
MS.gene87454.t1 MTR_4g058910 56.098 41 18 0 116 156 306 346 6.98e-12 64.7
MS.gene87454.t1 MTR_1g116010 65.714 35 12 0 122 156 162 196 8.34e-12 63.2
MS.gene87454.t1 MTR_1g094930 64.865 37 13 0 120 156 143 179 1.38e-11 62.8
MS.gene87454.t1 MTR_1g094930 64.865 37 13 0 120 156 238 274 2.38e-11 62.8
MS.gene87454.t1 MTR_3g117380 52.273 44 21 0 113 156 218 261 7.50e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene87454.t1 AT3G50870 38.889 288 94 12 20 234 17 295 3.83e-45 152
MS.gene87454.t1 AT2G18380 49.693 163 58 5 23 178 1 146 1.26e-37 130
MS.gene87454.t1 AT4G36620 41.346 208 83 6 52 233 16 210 9.65e-34 120
MS.gene87454.t1 AT5G56860 64.583 48 15 1 110 157 218 263 8.06e-14 70.5
MS.gene87454.t1 AT4G26150 46.970 66 35 0 89 154 164 229 3.20e-13 68.6
MS.gene87454.t1 AT5G26930 68.571 35 11 0 126 160 28 62 6.51e-13 63.9
MS.gene87454.t1 AT5G49300 71.429 35 10 0 126 160 38 72 1.33e-12 63.5
MS.gene87454.t1 AT3G06740 71.429 35 10 0 126 160 43 77 2.23e-12 63.2
MS.gene87454.t1 AT1G08010 58.537 41 16 1 116 156 213 252 2.15e-11 62.8
MS.gene87454.t1 AT1G08010 58.537 41 16 1 116 156 213 252 2.15e-11 62.8
MS.gene87454.t1 AT1G08010 58.537 41 16 1 116 156 213 252 2.15e-11 62.8
MS.gene87454.t1 AT3G54810 48.571 70 31 2 109 174 215 283 3.31e-11 62.4
MS.gene87454.t1 AT3G54810 48.571 70 31 2 109 174 215 283 3.31e-11 62.4
MS.gene87454.t1 AT4G32890 69.697 33 10 0 124 156 197 229 7.74e-11 61.2
MS.gene87454.t1 AT3G20750 66.667 33 11 0 129 161 164 196 8.18e-11 60.1
MS.gene87454.t1 AT3G60530 40.964 83 41 2 79 156 111 190 8.90e-11 60.5

Find 47 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTCCAAATTTCCTTTCT+TGG 0.186888 8.3:+26744185 MS.gene87454:CDS
AGTCTCCAAGAAAGGAAATT+TGG 0.258564 8.3:-26744190 None:intergenic
GATGGAGTAGTGTAAGAGTA+AGG 0.348845 8.3:-26743401 None:intergenic
ATTGTTTCCTTTGCTTGACT+TGG 0.380199 8.3:-26743567 None:intergenic
TCTACAACAACAACAATTCA+TGG 0.388097 8.3:+26744086 MS.gene87454:CDS
TCAAGCAAAGGAAACAATAA+TGG 0.415727 8.3:+26743572 MS.gene87454:CDS
AGTCACTATGCAATGCTTGC+GGG 0.430912 8.3:+26743975 MS.gene87454:intron
CGCGACTAACAGCAGCATAA+TGG 0.440251 8.3:+26744051 MS.gene87454:CDS
ACACCACTTCTACACCCCTT+TGG 0.442678 8.3:+26743645 MS.gene87454:CDS
AGCGACGGTTTCGTTTATCT+TGG 0.447089 8.3:-26743481 None:intergenic
TCTCAACAAGGTCACATAAT+GGG 0.447815 8.3:+26743281 MS.gene87454:CDS
CTCTCAACAAGGTCACATAA+TGG 0.454874 8.3:+26743280 MS.gene87454:CDS
CCACTTCTACACCCCTTTGG+AGG 0.484365 8.3:+26743648 MS.gene87454:CDS
GAGTAGTTAGAATTTGTTTG+AGG 0.488131 8.3:-26743332 None:intergenic
TTGAGAATTATGTTTAGTGT+TGG 0.488709 8.3:-26743537 None:intergenic
ACGAGGACCATTCCTCCAAA+GGG 0.492453 8.3:-26743660 None:intergenic
AACAGCAGCATAATGGAGTC+AGG 0.496113 8.3:+26744058 MS.gene87454:CDS
TGGCAGTGAGCTAAATTTCA+TGG 0.499631 8.3:+26744135 MS.gene87454:CDS
TCTACACCCCTTTGGAGGAA+TGG 0.501186 8.3:+26743653 MS.gene87454:CDS
TTCAGATAAACGTGTGGAAG+GGG 0.521943 8.3:-26743456 None:intergenic
TTGTGTTGAGTCTCCAAGAA+AGG 0.529190 8.3:-26744198 None:intergenic
ATGGAGTAGTGTAAGAGTAA+GGG 0.532615 8.3:-26743400 None:intergenic
CAGTCACTATGCAATGCTTG+CGG 0.541543 8.3:+26743974 MS.gene87454:intron
CACGAGGACCATTCCTCCAA+AGG 0.545071 8.3:-26743661 None:intergenic
CTTCAGATAAACGTGTGGAA+GGG 0.558291 8.3:-26743457 None:intergenic
GTGCAATCAACAGAAGAAGA+TGG 0.561538 8.3:-26743419 None:intergenic
CAACCACAGAGTCAAATGTA+TGG 0.561677 8.3:+26744115 MS.gene87454:CDS
CCTCCAAAGGGGTGTAGAAG+TGG 0.563224 8.3:-26743648 None:intergenic
GCTGTTAGTCGCGGCTGTAG+TGG 0.564500 8.3:-26744041 None:intergenic
AACGTGTGGAAGGGGTAGCA+AGG 0.566554 8.3:-26743448 None:intergenic
TCAGATGCAGAATCAGAGAA+TGG 0.577226 8.3:+26744163 MS.gene87454:CDS
TCTTCAGATAAACGTGTGGA+AGG 0.585551 8.3:-26743458 None:intergenic
GAATGGTCCTCGTGGCCCAA+AGG 0.595177 8.3:+26743670 MS.gene87454:CDS
CGCGGCTGTAGTGGCAACCG+CGG 0.597888 8.3:-26744032 None:intergenic
CATTATGCTGCTGTTAGTCG+CGG 0.600615 8.3:-26744050 None:intergenic
TCTCAATCCAAGTCAAGCAA+AGG 0.601871 8.3:+26743560 MS.gene87454:CDS
CTGCCATACATTTGACTCTG+TGG 0.604113 8.3:-26744118 None:intergenic
ACGTGTGGAAGGGGTAGCAA+GGG 0.615165 8.3:-26743447 None:intergenic
AATTAGCAAGAGAAGAGCGA+CGG 0.619540 8.3:-26743496 None:intergenic
ATGGGAGGAACATGCACATG+TGG 0.624656 8.3:+26743299 MS.gene87454:CDS
TTGCGGGATTAGATACAAGA+AGG 0.629096 8.3:+26743991 MS.gene87454:CDS
AGAGAGAAGAGCGAACGCCG+CGG 0.661922 8.3:+26744015 MS.gene87454:CDS
CTTTGGAGGAATGGTCCTCG+TGG 0.675633 8.3:+26743662 MS.gene87454:CDS
CAACAAGGTCACATAATGGG+AGG 0.680593 8.3:+26743284 MS.gene87454:CDS
TTGGTCTTCAGATAAACGTG+TGG 0.689873 8.3:-26743462 None:intergenic
CGAGGACCATTCCTCCAAAG+GGG 0.705344 8.3:-26743659 None:intergenic
TGTTGTAGTAGCTCTCAACA+AGG 0.711133 8.3:+26743269 MS.gene87454:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACATTTATAGTCTATT+TGG + chr8.3:26743772-26743791 MS.gene87454:intron 15.0%
!!! TTAAGAATGTTTTGTAATAA+TGG + chr8.3:26743937-26743956 MS.gene87454:intron 15.0%
!!! AATCATAATGATCATTTTGT+TGG - chr8.3:26743376-26743395 None:intergenic 20.0%
!!! AGTAATGTATTTTTACCTTT+GGG - chr8.3:26743688-26743707 None:intergenic 20.0%
!!! TAGTAATGTATTTTTACCTT+TGG - chr8.3:26743689-26743708 None:intergenic 20.0%
! TTGAGAATTATGTTTAGTGT+TGG - chr8.3:26743540-26743559 None:intergenic 25.0%
AACATTTATAGTCTACTACG+AGG - chr8.3:26743747-26743766 None:intergenic 30.0%
TCAAGCAAAGGAAACAATAA+TGG + chr8.3:26743572-26743591 MS.gene87454:CDS 30.0%
TCTACAACAACAACAATTCA+TGG + chr8.3:26744086-26744105 MS.gene87454:CDS 30.0%
! GAGTAGTTAGAATTTGTTTG+AGG - chr8.3:26743335-26743354 None:intergenic 30.0%
AGTCTCCAAGAAAGGAAATT+TGG - chr8.3:26744193-26744212 None:intergenic 35.0%
ATGGAGTAGTGTAAGAGTAA+GGG - chr8.3:26743403-26743422 None:intergenic 35.0%
ATTGTTTCCTTTGCTTGACT+TGG - chr8.3:26743570-26743589 None:intergenic 35.0%
GCATTCCAAATTTCCTTTCT+TGG + chr8.3:26744185-26744204 MS.gene87454:CDS 35.0%
TCTCAACAAGGTCACATAAT+GGG + chr8.3:26743281-26743300 MS.gene87454:CDS 35.0%
! CTGACTTTGACTTTGTTAGT+GGG + chr8.3:26743816-26743835 MS.gene87454:intron 35.0%
! TCTGACTTTGACTTTGTTAG+TGG + chr8.3:26743815-26743834 MS.gene87454:intron 35.0%
AATTAGCAAGAGAAGAGCGA+CGG - chr8.3:26743499-26743518 None:intergenic 40.0%
CAACCACAGAGTCAAATGTA+TGG + chr8.3:26744115-26744134 MS.gene87454:CDS 40.0%
CTCTCAACAAGGTCACATAA+TGG + chr8.3:26743280-26743299 MS.gene87454:CDS 40.0%
CTTCAGATAAACGTGTGGAA+GGG - chr8.3:26743460-26743479 None:intergenic 40.0%
GATGGAGTAGTGTAAGAGTA+AGG - chr8.3:26743404-26743423 None:intergenic 40.0%
GTCAGACTCTTACTACTGAA+CGG - chr8.3:26743801-26743820 None:intergenic 40.0%
GTGCAATCAACAGAAGAAGA+TGG - chr8.3:26743422-26743441 None:intergenic 40.0%
TATAGTCTACTACGAGGTCT+CGG - chr8.3:26743741-26743760 None:intergenic 40.0%
TCAGATGCAGAATCAGAGAA+TGG + chr8.3:26744163-26744182 MS.gene87454:CDS 40.0%
TCTCAATCCAAGTCAAGCAA+AGG + chr8.3:26743560-26743579 MS.gene87454:CDS 40.0%
TCTTCAGATAAACGTGTGGA+AGG - chr8.3:26743461-26743480 None:intergenic 40.0%
TGGCAGTGAGCTAAATTTCA+TGG + chr8.3:26744135-26744154 MS.gene87454:CDS 40.0%
TGTTGTAGTAGCTCTCAACA+AGG + chr8.3:26743269-26743288 MS.gene87454:CDS 40.0%
TTCAGATAAACGTGTGGAAG+GGG - chr8.3:26743459-26743478 None:intergenic 40.0%
TTGCGGGATTAGATACAAGA+AGG + chr8.3:26743991-26744010 MS.gene87454:CDS 40.0%
TTGTGTTGAGTCTCCAAGAA+AGG - chr8.3:26744201-26744220 None:intergenic 40.0%
! TTGGTCTTCAGATAAACGTG+TGG - chr8.3:26743465-26743484 None:intergenic 40.0%
AGCGACGGTTTCGTTTATCT+TGG - chr8.3:26743484-26743503 None:intergenic 45.0%
AGTCACTATGCAATGCTTGC+GGG + chr8.3:26743975-26743994 MS.gene87454:intron 45.0%
CAGTCACTATGCAATGCTTG+CGG + chr8.3:26743974-26743993 MS.gene87454:intron 45.0%
CATTATGCTGCTGTTAGTCG+CGG - chr8.3:26744053-26744072 None:intergenic 45.0%
CTGCCATACATTTGACTCTG+TGG - chr8.3:26744121-26744140 None:intergenic 45.0%
! AACAGCAGCATAATGGAGTC+AGG + chr8.3:26744058-26744077 MS.gene87454:CDS 45.0%
! ATTTTTACCTTTGGGCCACG+AGG - chr8.3:26743680-26743699 None:intergenic 45.0%
! CAACAAGGTCACATAATGGG+AGG + chr8.3:26743284-26743303 MS.gene87454:CDS 45.0%
!! CAAAAAATTATTATTAATAA+CGG - chr8.3:26743881-26743900 None:intergenic 5.0%
ACACCACTTCTACACCCCTT+TGG + chr8.3:26743645-26743664 MS.gene87454:CDS 50.0%
ACGAGGACCATTCCTCCAAA+GGG - chr8.3:26743663-26743682 None:intergenic 50.0%
ATGGGAGGAACATGCACATG+TGG + chr8.3:26743299-26743318 MS.gene87454:CDS 50.0%
CGCGACTAACAGCAGCATAA+TGG + chr8.3:26744051-26744070 MS.gene87454:CDS 50.0%
! TCTACACCCCTTTGGAGGAA+TGG + chr8.3:26743653-26743672 MS.gene87454:CDS 50.0%
AACGTGTGGAAGGGGTAGCA+AGG - chr8.3:26743451-26743470 None:intergenic 55.0%
ACGTGTGGAAGGGGTAGCAA+GGG - chr8.3:26743450-26743469 None:intergenic 55.0%
CACGAGGACCATTCCTCCAA+AGG - chr8.3:26743664-26743683 None:intergenic 55.0%
CCACTTCTACACCCCTTTGG+AGG + chr8.3:26743648-26743667 MS.gene87454:CDS 55.0%
CGAGGACCATTCCTCCAAAG+GGG - chr8.3:26743662-26743681 None:intergenic 55.0%
! CCTCCAAAGGGGTGTAGAAG+TGG - chr8.3:26743651-26743670 None:intergenic 55.0%
! CTTTGGAGGAATGGTCCTCG+TGG + chr8.3:26743662-26743681 MS.gene87454:CDS 55.0%
AGAGAGAAGAGCGAACGCCG+CGG + chr8.3:26744015-26744034 MS.gene87454:CDS 60.0%
GAATGGTCCTCGTGGCCCAA+AGG + chr8.3:26743670-26743689 MS.gene87454:CDS 60.0%
GCTGTTAGTCGCGGCTGTAG+TGG - chr8.3:26744044-26744063 None:intergenic 60.0%
CGCGGCTGTAGTGGCAACCG+CGG - chr8.3:26744035-26744054 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr8.3 gene 26743257 26744246 26743257 ID=MS.gene87454
chr8.3 mRNA 26743257 26744246 26743257 ID=MS.gene87454.t1;Parent=MS.gene87454
chr8.3 exon 26743257 26743691 26743257 ID=MS.gene87454.t1.exon1;Parent=MS.gene87454.t1
chr8.3 CDS 26743257 26743691 26743257 ID=cds.MS.gene87454.t1;Parent=MS.gene87454.t1
chr8.3 exon 26743977 26744246 26743977 ID=MS.gene87454.t1.exon2;Parent=MS.gene87454.t1
chr8.3 CDS 26743977 26744246 26743977 ID=cds.MS.gene87454.t1;Parent=MS.gene87454.t1
Gene Sequence

>MS.gene87454

ATGATGCATCATTGTTGTAGTAGCTCTCAACAAGGTCACATAATGGGAGGAACATGCACATGTGGTATGTTTCATCCTCAAACAAATTCTAACTACTCGTTGCTTTACTCTAACTACCAACAAAATGATCATTATGATTTTGACCCTTACTCTTACACTACTCCATCTTCTTCTGTTGATTGCACACTCTCCCTTGCTACCCCTTCCACACGTTTATCTGAAGACCAAGATAAACGAAACCGTCGCTCTTCTCTTGCTAATTTTTTCTGTAGCAAATCTTCCAACACTAAACATAATTCTCAATCTCAATCCAAGTCAAGCAAAGGAAACAATAATGGTAGTAACTCTAACAATGATTCTCTTCTTTCTCGTCGATGTGCTAGCTGTGACACCACTTCTACACCCCTTTGGAGGAATGGTCCTCGTGGCCCAAAGGTAAAAATACATTACTATCTTTGTGTCTATGTTCAAAATATATGAGCCGAGACCTCGTAGTAGACTATAAATGTTCGACAAAAAACATTTATAGTCTATTTGGTCTCCGTTCAGTAGTAAGAGTCTGACTTTGACTTTGTTAGTGGGAGACAAAATTTTATAGAGTACGAGACAATGTCATTGTCACCGTTATTAATAATAATTTTTTGTTTCTTGATGTTATTCTTGTTTTTTTTTATCTTCTTTTAAGAATGTTTTGTAATAATGGTTGAATTGAATTTGCAGTCACTATGCAATGCTTGCGGGATTAGATACAAGAAGGAAGAGAGAAGAGCGAACGCCGCGGTTGCCACTACAGCCGCGACTAACAGCAGCATAATGGAGTCAGGAAACTTCTACAACAACAACAATTCATGGTACTCACAACCACAGAGTCAAATGTATGGCAGTGAGCTAAATTTCATGGATGATTCAGATGCAGAATCAGAGAATGGCATTCCAAATTTCCTTTCTTGGAGACTCAACACAAGTCTTGTTCACGATTACACAAGATGA
Protein sequence

>MS.gene87454.t1

MMHHCCSSSQQGHIMGGTCTCGMFHPQTNSNYSLLYSNYQQNDHYDFDPYSYTTPSSSVDCTLSLATPSTRLSEDQDKRNRRSSLANFFCSKSSNTKHNSQSQSKSSKGNNNGSNSNNDSLLSRRCASCDTTSTPLWRNGPRGPKSLCNACGIRYKKEERRANAAVATTAATNSSIMESGNFYNNNNSWYSQPQSQMYGSELNFMDDSDAESENGIPNFLSWRLNTSLVHDYTR