AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21514


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21514.t1 MTR_5g013530 86.957 184 13 3 1 184 1 173 6.13e-113 318
MS.gene21514.t1 MTR_5g013530 85.256 156 12 3 29 184 7 151 1.13e-89 259
MS.gene21514.t1 MTR_5g013520 82.895 152 19 3 30 181 1 145 8.89e-87 251
MS.gene21514.t1 MTR_5g013515 70.345 145 28 5 31 168 1 137 6.63e-64 193
MS.gene21514.t1 MTR_2g042900 46.667 165 44 7 25 163 99 245 2.60e-34 122
MS.gene21514.t1 MTR_4g124960 32.941 170 69 5 5 169 73 202 3.17e-19 81.3
MS.gene21514.t1 MTR_2g042900 36.905 168 40 7 25 136 99 256 3.20e-19 82.4
MS.gene21514.t1 MTR_4g124960 33.099 142 50 5 5 141 73 174 1.05e-14 68.9
MS.gene21514.t1 MTR_8g021380 30.534 131 85 3 19 144 79 208 5.19e-14 68.2
MS.gene21514.t1 MTR_2g044910 29.310 116 73 1 40 146 11 126 7.68e-13 63.5
MS.gene21514.t1 MTR_2g044910 29.310 116 73 1 40 146 54 169 1.49e-12 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21514.t1 AT1G19180 43.284 134 70 4 37 166 53 184 1.20e-27 102
MS.gene21514.t1 AT1G19180 43.284 134 70 4 37 166 119 250 9.54e-27 102
MS.gene21514.t1 AT1G19180 43.284 134 70 4 37 166 119 250 9.54e-27 102
MS.gene21514.t1 AT1G74950 39.130 138 72 3 37 164 112 247 1.46e-22 91.3
MS.gene21514.t1 AT1G74950 40.000 110 56 2 37 136 112 221 3.15e-17 76.6
MS.gene21514.t1 AT5G20900 35.664 143 70 5 24 147 28 167 9.26e-16 72.0
MS.gene21514.t1 AT1G72450 36.885 122 65 4 39 152 101 218 1.12e-15 73.2
MS.gene21514.t1 AT1G17380 35.714 126 73 2 33 150 58 183 1.20e-15 72.8
MS.gene21514.t1 AT1G17380 35.714 126 73 2 33 150 87 212 3.92e-15 71.6
MS.gene21514.t1 AT1G70700 36.538 104 62 2 44 144 119 221 1.59e-12 64.3
MS.gene21514.t1 AT4G14720 33.121 157 85 7 40 181 153 304 7.18e-11 60.1
MS.gene21514.t1 AT1G17380 33.929 112 66 2 33 136 87 198 7.36e-11 59.3
MS.gene21514.t1 AT4G14720 33.121 157 85 7 40 181 153 304 7.50e-11 60.1

Find 36 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTACAAGAGATTCCTATTT+TGG 0.046444 5.3:+6713791 MS.gene21514:CDS
CCATCTATGCCTGTTATTTA+TGG 0.102905 5.3:+6714209 MS.gene21514:CDS
ATTCATCAATTGACTTATTT+AGG 0.185988 5.3:-6715248 None:intergenic
AGCTTCACTTCATCGGTTCT+TGG 0.292747 5.3:+6714353 MS.gene21514:CDS
CCAAAATAGGAATCTCTTGT+AGG 0.331403 5.3:-6713791 None:intergenic
TACCTGGAGTTTCCCAAAAT+AGG 0.395618 5.3:-6713804 None:intergenic
GGAAAAGTCCATGATGTCTT+TGG 0.411671 5.3:-6714072 None:intergenic
ATGTCTTTGGCTTTATCAGC+TGG 0.417227 5.3:-6714059 None:intergenic
GCTGGATTACTTGTTTGATA+AGG 0.423471 5.3:-6715219 None:intergenic
AGTGAAGCTTTCCTAGTCAT+TGG 0.425048 5.3:-6714339 None:intergenic
GACTTATTTAGGAATGCTGC+TGG 0.431039 5.3:-6715237 None:intergenic
GTAGTCTTGAAGAGAATTGT+TGG 0.442893 5.3:-6714177 None:intergenic
CCATAAATAACAGGCATAGA+TGG 0.445007 5.3:-6714209 None:intergenic
CAAATGACAATCTTCTATGA+TGG 0.453411 5.3:+6714011 MS.gene21514:CDS
TGAAGTACTAGTAATTCCTT+TGG 0.455465 5.3:-6714096 None:intergenic
TTCATCGGTTCTTGGAGAAA+AGG 0.463618 5.3:+6714361 MS.gene21514:CDS
GGAAGCTGTTGAAAATTCAT+AGG 0.469618 5.3:-6713759 None:intergenic
AGTACTAGTAATTCCTTTGG+TGG 0.499055 5.3:-6714093 None:intergenic
ATCCATGTCATGGCTATCCT+TGG 0.509457 5.3:+6715269 MS.gene21514:CDS
AATGAAGGCTAATGTTAAGA+AGG 0.511094 5.3:+6713971 MS.gene21514:CDS
AGCAAGCATAGTTGTTATTG+TGG 0.514503 5.3:-6714130 None:intergenic
CTAGGAAAGCTTCACTTCAT+CGG 0.529148 5.3:+6714346 MS.gene21514:CDS
AAATGACAATCTTCTATGAT+GGG 0.538308 5.3:+6714012 MS.gene21514:CDS
CTACATTTAGATTTGTGTTG+CGG 0.547996 5.3:-6715303 None:intergenic
ATCTCTTGTAGGAAGAGATG+AGG 0.564072 5.3:-6713780 None:intergenic
TCTTGGAGAAAAGGAAGGAT+AGG 0.567398 5.3:+6714370 MS.gene21514:CDS
GGCTAATGTTAAGAAGGAAG+AGG 0.580916 5.3:+6713977 MS.gene21514:CDS
TGATAAAGCCAAAGACATCA+TGG 0.585378 5.3:+6714064 MS.gene21514:CDS
TCGGTTCTTGGAGAAAAGGA+AGG 0.585705 5.3:+6714365 MS.gene21514:CDS
GTTTCTGCAGAATTGCTGCA+AGG 0.606526 5.3:+6715193 MS.gene21514:intron
TTTCTGCAGAATTGCTGCAA+GGG 0.611240 5.3:+6715194 MS.gene21514:intron
CAATTGATGAATCCATGTCA+TGG 0.612586 5.3:+6715259 MS.gene21514:CDS
TGCCAAGGATAGCCATGACA+TGG 0.617530 5.3:-6715271 None:intergenic
GATTTGTGTTGCGGTGAATG+TGG 0.627153 5.3:-6715294 None:intergenic
TTGCGGTGAATGTGGTGCCA+AGG 0.648709 5.3:-6715286 None:intergenic
ATACAGATTTACCAATGACT+AGG 0.658525 5.3:+6714328 MS.gene21514:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTATGGTATTTTTTTT+TGG + chr5.3:6714222-6714241 MS.gene21514:intron 10.0%
!! AAAAAAATACCATAAATAAC+AGG - chr5.3:6714221-6714240 None:intergenic 15.0%
!!! TACACTATTATAATCAATTT+TGG + chr5.3:6714987-6715006 MS.gene21514:intron 15.0%
!!! TGATAGATAAATCAATTTTA+AGG + chr5.3:6714628-6714647 MS.gene21514:intron 15.0%
!!! TTTTTGTTTATAATAGTGAT+TGG + chr5.3:6714753-6714772 MS.gene21514:intron 15.0%
!! GATAACCAATTTACTAAAAT+TGG - chr5.3:6715083-6715102 None:intergenic 20.0%
!!! AATTTTAAGGAACCAATTTT+AGG + chr5.3:6714641-6714660 MS.gene21514:intron 20.0%
!!! AGTGTAATTTTGTGTATTTT+AGG + chr5.3:6714597-6714616 MS.gene21514:intron 20.0%
!!! ATTCATCAATTGACTTATTT+AGG - chr5.3:6715251-6715270 None:intergenic 20.0%
!!! TATAGTTTTTTTCTCTACAT+TGG - chr5.3:6714867-6714886 None:intergenic 20.0%
! AAACATCATACTAGTAGAAA+AGG - chr5.3:6715139-6715158 None:intergenic 25.0%
! AAATGACAATCTTCTATGAT+GGG + chr5.3:6714012-6714031 MS.gene21514:CDS 25.0%
! AACATCATACTAGTAGAAAA+GGG - chr5.3:6715138-6715157 None:intergenic 25.0%
! CATACTAGTAGTATATAACA+TGG + chr5.3:6713903-6713922 MS.gene21514:intron 25.0%
! GTTACAAAAATTGATTGAAC+TGG + chr5.3:6714496-6714515 MS.gene21514:intron 25.0%
! TCCTCTCAAAACTATATATA+TGG + chr5.3:6715108-6715127 MS.gene21514:intron 25.0%
! TGGATATATTATGTTTGAGA+GGG + chr5.3:6714242-6714261 MS.gene21514:intron 25.0%
! TTATAGTTTCAATCAGTTTC+TGG + chr5.3:6714889-6714908 MS.gene21514:intron 25.0%
! TTGCGTTTATATAATAGTGA+CGG - chr5.3:6714675-6714694 None:intergenic 25.0%
! TTGGATATATTATGTTTGAG+AGG + chr5.3:6714241-6714260 MS.gene21514:intron 25.0%
!! TTTTCTACTAGTATGATGTT+TGG + chr5.3:6715138-6715157 MS.gene21514:intron 25.0%
!! TTTTCTCTACATTGGATTTT+TGG - chr5.3:6714859-6714878 None:intergenic 25.0%
!!! ATATAGTTTTGAGAGGATAA+CGG - chr5.3:6715105-6715124 None:intergenic 25.0%
!!! GTTTTATTACAGTGTAATGA+AGG + chr5.3:6713956-6713975 MS.gene21514:intron 25.0%
AAAAAGAACATGTATGTACC+TGG - chr5.3:6713823-6713842 None:intergenic 30.0%
AACACACTACTTAACAATTG+AGG - chr5.3:6714466-6714485 None:intergenic 30.0%
AAGTAGTGTGTTTGATTCTA+CGG + chr5.3:6714474-6714493 MS.gene21514:intron 30.0%
AATGAAGGCTAATGTTAAGA+AGG + chr5.3:6713971-6713990 MS.gene21514:CDS 30.0%
ATACAGATTTACCAATGACT+AGG + chr5.3:6714328-6714347 MS.gene21514:intron 30.0%
ATATTTGATTGAGAGAGATC+TGG - chr5.3:6714404-6714423 None:intergenic 30.0%
ATCCAAATTCTCTACCTTTA+AGG - chr5.3:6714836-6714855 None:intergenic 30.0%
CAAATGACAATCTTCTATGA+TGG + chr5.3:6714011-6714030 MS.gene21514:CDS 30.0%
CTACATTTAGATTTGTGTTG+CGG - chr5.3:6715306-6715325 None:intergenic 30.0%
GACAAACTTATCAGTCAATA+TGG - chr5.3:6715170-6715189 None:intergenic 30.0%
TGCGTTTATATAATAGTGAC+GGG - chr5.3:6714674-6714693 None:intergenic 30.0%
! CTACAAGAGATTCCTATTTT+GGG + chr5.3:6713792-6713811 MS.gene21514:CDS 30.0%
! GTGATTTTGCTAAAAGTGAA+TGG + chr5.3:6714529-6714548 MS.gene21514:intron 30.0%
! TGAAGTACTAGTAATTCCTT+TGG - chr5.3:6714099-6714118 None:intergenic 30.0%
! TTTATATAATAGTGACGGGA+GGG - chr5.3:6714670-6714689 None:intergenic 30.0%
!! AGGAGCCAATTTTAGTAAAT+TGG + chr5.3:6715075-6715094 MS.gene21514:intron 30.0%
!!! GCCATATATATAGTTTTGAG+AGG - chr5.3:6715112-6715131 None:intergenic 30.0%
!!! GTCAATAGACTTCACTTTTT+AGG + chr5.3:6714436-6714455 MS.gene21514:intron 30.0%
AGATATAGTGACTTTGGTGA+TGG + chr5.3:6714556-6714575 MS.gene21514:intron 35.0%
AGTACTAGTAATTCCTTTGG+TGG - chr5.3:6714096-6714115 None:intergenic 35.0%
CAATTGATGAATCCATGTCA+TGG + chr5.3:6715259-6715278 MS.gene21514:CDS 35.0%
CCAAAATAGGAATCTCTTGT+AGG - chr5.3:6713794-6713813 None:intergenic 35.0%
CCATAAATAACAGGCATAGA+TGG - chr5.3:6714212-6714231 None:intergenic 35.0%
CTACAAAAATAACACAGAGG+TGG - chr5.3:6715331-6715350 None:intergenic 35.0%
GATACCATGAACAAAAGTGA+AGG + chr5.3:6715055-6715074 MS.gene21514:intron 35.0%
GCTGGATTACTTGTTTGATA+AGG - chr5.3:6715222-6715241 None:intergenic 35.0%
GGAAGCTGTTGAAAATTCAT+AGG - chr5.3:6713762-6713781 None:intergenic 35.0%
GGATTGAGATATAGTGACTT+TGG + chr5.3:6714550-6714569 MS.gene21514:intron 35.0%
TGATAAAGCCAAAGACATCA+TGG + chr5.3:6714064-6714083 MS.gene21514:CDS 35.0%
TTAAGGCGAAAAAGTCATCA+TGG - chr5.3:6714819-6714838 None:intergenic 35.0%
! AGCAAGCATAGTTGTTATTG+TGG - chr5.3:6714133-6714152 None:intergenic 35.0%
! CCATCTATGCCTGTTATTTA+TGG + chr5.3:6714209-6714228 MS.gene21514:CDS 35.0%
! CCTACAAGAGATTCCTATTT+TGG + chr5.3:6713791-6713810 MS.gene21514:CDS 35.0%
! GATATAGTGACTTTGGTGAT+GGG + chr5.3:6714557-6714576 MS.gene21514:intron 35.0%
! GTAGTCTTGAAGAGAATTGT+TGG - chr5.3:6714180-6714199 None:intergenic 35.0%
! GTTTATATAATAGTGACGGG+AGG - chr5.3:6714671-6714690 None:intergenic 35.0%
!!! TGATGACTTTTTCGCCTTAA+AGG + chr5.3:6714819-6714838 MS.gene21514:intron 35.0%
AGTGAAGCTTTCCTAGTCAT+TGG - chr5.3:6714342-6714361 None:intergenic 40.0%
ATCTCTTGTAGGAAGAGATG+AGG - chr5.3:6713783-6713802 None:intergenic 40.0%
CGCCTTAAAGGTAGAGAATT+TGG + chr5.3:6714831-6714850 MS.gene21514:intron 40.0%
CTAGGAAAGCTTCACTTCAT+CGG + chr5.3:6714346-6714365 MS.gene21514:CDS 40.0%
GACTTATTTAGGAATGCTGC+TGG - chr5.3:6715240-6715259 None:intergenic 40.0%
GGAAAAGTCCATGATGTCTT+TGG - chr5.3:6714075-6714094 None:intergenic 40.0%
GGCTAATGTTAAGAAGGAAG+AGG + chr5.3:6713977-6713996 MS.gene21514:CDS 40.0%
TACCTGGAGTTTCCCAAAAT+AGG - chr5.3:6713807-6713826 None:intergenic 40.0%
TCTTGGAGAAAAGGAAGGAT+AGG + chr5.3:6714370-6714389 MS.gene21514:CDS 40.0%
TTTCTGCAGAATTGCTGCAA+GGG + chr5.3:6715194-6715213 MS.gene21514:intron 40.0%
! ATCATGGACTTTTCCACCAA+AGG + chr5.3:6714080-6714099 MS.gene21514:CDS 40.0%
!! AGGGTGTTTGATTTGTGTCA+TGG + chr5.3:6714261-6714280 MS.gene21514:intron 40.0%
!! ATGTCTTTGGCTTTATCAGC+TGG - chr5.3:6714062-6714081 None:intergenic 40.0%
!! TTCATCGGTTCTTGGAGAAA+AGG + chr5.3:6714361-6714380 MS.gene21514:CDS 40.0%
!! TTCCTATTTTGGGAAACTCC+AGG + chr5.3:6713802-6713821 MS.gene21514:CDS 40.0%
ATCCATGTCATGGCTATCCT+TGG + chr5.3:6715269-6715288 MS.gene21514:CDS 45.0%
GACATGACTCAGTGTATCCT+CGG - chr5.3:6715030-6715049 None:intergenic 45.0%
GATTTGTGTTGCGGTGAATG+TGG - chr5.3:6715297-6715316 None:intergenic 45.0%
GTTTCTGCAGAATTGCTGCA+AGG + chr5.3:6715193-6715212 MS.gene21514:intron 45.0%
TCGGTTCTTGGAGAAAAGGA+AGG + chr5.3:6714365-6714384 MS.gene21514:CDS 45.0%
TTGATTGAGAGAGATCTGGC+AGG - chr5.3:6714400-6714419 None:intergenic 45.0%
!! AGCTTCACTTCATCGGTTCT+TGG + chr5.3:6714353-6714372 MS.gene21514:CDS 45.0%
!! GGCTCCTTCACTTTTGTTCA+TGG - chr5.3:6715062-6715081 None:intergenic 45.0%
ACGGGAGGGAGTCCTAAAAT+TGG - chr5.3:6714656-6714675 None:intergenic 50.0%
TGCCAAGGATAGCCATGACA+TGG - chr5.3:6715274-6715293 None:intergenic 50.0%
! TGTATCCTCGGCTCGACTTT+AGG - chr5.3:6715018-6715037 None:intergenic 50.0%
CTCATCCTAAAGTCGAGCCG+AGG + chr5.3:6715010-6715029 MS.gene21514:intron 55.0%
! TTGCGGTGAATGTGGTGCCA+AGG - chr5.3:6715289-6715308 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 6713738 6715350 6713738 ID=MS.gene21514
chr5.3 mRNA 6713738 6715350 6713738 ID=MS.gene21514.t1;Parent=MS.gene21514
chr5.3 exon 6713738 6713823 6713738 ID=MS.gene21514.t1.exon1;Parent=MS.gene21514.t1
chr5.3 CDS 6713738 6713823 6713738 ID=cds.MS.gene21514.t1;Parent=MS.gene21514.t1
chr5.3 exon 6713968 6714230 6713968 ID=MS.gene21514.t1.exon2;Parent=MS.gene21514.t1
chr5.3 CDS 6713968 6714230 6713968 ID=cds.MS.gene21514.t1;Parent=MS.gene21514.t1
chr5.3 exon 6714334 6714391 6714334 ID=MS.gene21514.t1.exon3;Parent=MS.gene21514.t1
chr5.3 CDS 6714334 6714391 6714334 ID=cds.MS.gene21514.t1;Parent=MS.gene21514.t1
chr5.3 exon 6715203 6715350 6715203 ID=MS.gene21514.t1.exon4;Parent=MS.gene21514.t1
chr5.3 CDS 6715203 6715350 6715203 ID=cds.MS.gene21514.t1;Parent=MS.gene21514.t1
Gene Sequence

>MS.gene21514

ATGAATCATCACAACATAACACCTATGAATTTTCAACAGCTTCCTCATCTCTTCCTACAAGAGATTCCTATTTTGGGAAACTCCAGGTACATACATGTTCTTTTTTCTACTTTAACTTGTTTAAGTACATCAACATTTTTTTAGCAAAATTCAAATTCATTAATTCATACTAGTAGTATATAACATGGTCAGTTTGCATTAAATTAATTTTTAATGTTGTTTTATTACAGTGTAATGAAGGCTAATGTTAAGAAGGAAGAGGCTAGATGTGCACAAATGACAATCTTCTATGATGGGAAAGTAATTGTGTTTGATGATGTTCCAGCTGATAAAGCCAAAGACATCATGGACTTTTCCACCAAAGGAATTACTAGTACTTCACAAGCACAAAACCACAATAACAACTATGCTTGCTCTTCATTTCTTGCTAGAAATTCTGCCAACAATTCTCTTCAAGACTACTATCAAGTACCATCTATGCCTGTTATTTATGGTATTTTTTTTTGGATATATTATGTTTGAGAGGGTGTTTGATTTGTGTCATGGTTTTGTTTTTTGTGTGTTTTTAACTCATGAAATTCTTTTTATGTATACAGATTTACCAATGACTAGGAAAGCTTCACTTCATCGGTTCTTGGAGAAAAGGAAGGATAGGTAAGCCTGCCAGATCTCTCTCAATCAAATATTGTTTGATCTTTGTCAATAGACTTCACTTTTTAGGAAAACCTCAATTGTTAAGTAGTGTGTTTGATTCTACGGTTACAAAAATTGATTGAACTGGTTATTTAAAAGTGATTTTGCTAAAAGTGAATGGATTGAGATATAGTGACTTTGGTGATGGGAAAGTAATTATTACTATAGTGTAATTTTGTGTATTTTAGGAAAGAAAATGATAGATAAATCAATTTTAAGGAACCAATTTTAGGACTCCCTCCCGTCACTATTATATAAACGCAAAAAATCACTTTTAAATTTATTCAATAACTAATGTATTGAATGAATCTTAAAAGTTGTTTTTTTGTTTATAATAGTGATTGGATGAAGTATATATATATAAAAGTGAAAGATAAACACAAAGCCATGATGACTTTTTCGCCTTAAAGGTAGAGAATTTGGATCCAAAAATCCAATGTAGAGAAAAAAACTATAAATTATAGTTTCAATCAGTTTCTGGAAGCAAAATCAATTTCACTTCAAAAACATTCAAACATTTGTTTTTGAAAGAAAGAAAACATGTCAAAATCAATTCTACACTATTATAATCAATTTTGGCTCATCCTAAAGTCGAGCCGAGGATACACTGAGTCATGTCAAATTGATACCATGAACAAAAGTGAAGGAGCCAATTTTAGTAAATTGGTTATCCGTTATCCTCTCAAAACTATATATATGGCTGACCCTTTTCTACTAGTATGATGTTTGGAATTATCCATATTGACTGATAAGTTTGTCTATGTTTCTGCAGAATTGCTGCAAGGGCACCTTATCAAACAAGTAATCCAGCAGCATTCCTAAATAAGTCAATTGATGAATCCATGTCATGGCTATCCTTGGCACCACATTCACCGCAACACAAATCTAAATGTAGCTCCACCTCTGTGTTATTTTTGTAG

Protein sequence

>MS.gene21514.t1

MNHHNITPMNFQQLPHLFLQEIPILGNSSVMKANVKKEEARCAQMTIFYDGKVIVFDDVPADKAKDIMDFSTKGITSTSQAQNHNNNYACSSFLARNSANNSLQDYYQVPSMPVIYDLPMTRKASLHRFLEKRKDRIAARAPYQTSNPAAFLNKSIDESMSWLSLAPHSPQHKSKCSSTSVLFL