AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015366


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015366.t1 MTR_5g013530 89.011 182 11 2 1 182 1 173 1.08e-115 325
MS.gene015366.t1 MTR_5g013530 87.662 154 10 2 29 182 7 151 1.45e-92 266
MS.gene015366.t1 MTR_5g013520 85.333 150 17 2 30 179 1 145 9.50e-90 259
MS.gene015366.t1 MTR_5g013515 72.028 143 27 5 31 166 1 137 4.53e-64 194
MS.gene015366.t1 MTR_2g042900 45.963 161 49 5 25 161 99 245 3.12e-34 121
MS.gene015366.t1 MTR_2g042900 35.976 164 45 5 25 134 99 256 4.06e-19 82.0
MS.gene015366.t1 MTR_4g124960 32.143 168 71 5 5 167 73 202 7.75e-19 80.5
MS.gene015366.t1 MTR_4g124960 32.143 140 52 5 5 139 73 174 2.62e-14 67.8
MS.gene015366.t1 MTR_8g021380 32.824 131 80 4 19 142 79 208 1.24e-13 67.0
MS.gene015366.t1 MTR_4g124950 32.624 141 67 4 5 145 7 119 2.20e-13 64.3
MS.gene015366.t1 MTR_2g044910 29.310 116 71 3 40 144 11 126 2.64e-12 62.0
MS.gene015366.t1 MTR_2g044910 29.310 116 71 3 40 144 54 169 4.24e-12 62.4
MS.gene015366.t1 MTR_4g124360 27.928 111 65 2 44 141 7 115 8.17e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015366.t1 AT1G19180 42.105 133 71 4 37 164 53 184 5.88e-27 101
MS.gene015366.t1 AT1G19180 42.105 133 71 4 37 164 119 250 3.27e-26 100
MS.gene015366.t1 AT1G19180 42.105 133 71 4 37 164 119 250 3.27e-26 100
MS.gene015366.t1 AT1G74950 40.580 138 68 3 37 162 112 247 1.20e-23 94.0
MS.gene015366.t1 AT1G74950 41.818 110 52 2 37 134 112 221 2.34e-18 79.3
MS.gene015366.t1 AT1G17380 37.302 126 69 3 33 148 58 183 3.84e-16 73.9
MS.gene015366.t1 AT1G17380 37.302 126 69 3 33 148 87 212 1.22e-15 73.2
MS.gene015366.t1 AT1G72450 37.288 118 68 2 39 150 101 218 2.36e-15 72.4
MS.gene015366.t1 AT5G20900 32.394 142 74 5 24 145 28 167 1.16e-13 66.2
MS.gene015366.t1 AT1G70700 34.615 104 62 3 44 142 119 221 1.73e-11 61.2
MS.gene015366.t1 AT1G17380 34.821 112 63 2 33 134 87 198 2.65e-11 60.5

Find 37 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTACAAGAGATTCCTATTT+TGG 0.046444 5.4:+7404375 MS.gene015366:CDS
CCATCTATACCTGTTATTTA+TGG 0.164541 5.4:+7404787 MS.gene015366:CDS
ATTCATCAATTGACTTATTT+AGG 0.185988 5.4:-7405822 None:intergenic
AGCTTCACTTCATCGGTTCT+TGG 0.292747 5.4:+7404930 MS.gene015366:CDS
CCAAAATAGGAATCTCTTGT+AGG 0.331403 5.4:-7404375 None:intergenic
TACCTGGAGTTTCCCAAAAT+AGG 0.395618 5.4:-7404388 None:intergenic
GGAAAAGTCCATGATGTCTT+TGG 0.411671 5.4:-7404656 None:intergenic
ATGTCTTTGGCTTTATCAGC+TGG 0.417227 5.4:-7404643 None:intergenic
GCTGGATTACTTGTTTGATA+AGG 0.423471 5.4:-7405793 None:intergenic
AGTGAAGCTTTCCTAGTCAT+TGG 0.425048 5.4:-7404916 None:intergenic
GACTTATTTAGGAATGCTGC+TGG 0.431039 5.4:-7405811 None:intergenic
TGAAGTACTAGTAATTCCTT+TGG 0.431697 5.4:-7404680 None:intergenic
GTAGTCTTGAAGAGAATTGT+TGG 0.447616 5.4:-7404755 None:intergenic
CAAATGACAATCTTCTATGA+TGG 0.453411 5.4:+7404595 MS.gene015366:CDS
TTCATCGGTTCTTGGAGAAA+AGG 0.463618 5.4:+7404938 MS.gene015366:CDS
GGAAGCTGTTGAAAATTCAT+AGG 0.469618 5.4:-7404343 None:intergenic
CCATAAATAACAGGTATAGA+TGG 0.477854 5.4:-7404787 None:intergenic
AGTACTAGTAATTCCTTTGG+TGG 0.499055 5.4:-7404677 None:intergenic
TAGTCTTGAAGAGAATTGTT+GGG 0.502082 5.4:-7404754 None:intergenic
ATCCATGTCATGGCTATCCT+TGG 0.509457 5.4:+7405843 MS.gene015366:CDS
AATGAAGGCTAATGTTAAGA+AGG 0.511094 5.4:+7404555 MS.gene015366:CDS
AGCAAGCATAGTTGTTATTG+TGG 0.514503 5.4:-7404708 None:intergenic
CTAGGAAAGCTTCACTTCAT+CGG 0.529148 5.4:+7404923 MS.gene015366:CDS
AAATGACAATCTTCTATGAT+GGG 0.538308 5.4:+7404596 MS.gene015366:CDS
CTACATTCAGATTTGTGTTG+CGG 0.544643 5.4:-7405877 None:intergenic
ATCTCTTGTAGGAAGAGATG+AGG 0.564072 5.4:-7404364 None:intergenic
TCTTGGAGAAAAGGAAGGAT+AGG 0.567398 5.4:+7404947 MS.gene015366:CDS
GGCTAATGTTAAGAAGGAAG+AGG 0.580916 5.4:+7404561 MS.gene015366:CDS
TGATAAAGCCAAAGACATCA+TGG 0.585378 5.4:+7404648 MS.gene015366:CDS
TCGGTTCTTGGAGAAAAGGA+AGG 0.585705 5.4:+7404942 MS.gene015366:CDS
GTTTCTGCAGAATTGCTGCA+AGG 0.606526 5.4:+7405767 MS.gene015366:intron
ATTCAGATTTACCAATGACT+AGG 0.608086 5.4:+7404905 MS.gene015366:intron
TTTCTGCAGAATTGCTGCAA+GGG 0.611240 5.4:+7405768 MS.gene015366:intron
CAATTGATGAATCCATGTCA+TGG 0.612586 5.4:+7405833 MS.gene015366:CDS
TGCCAAGGATAGCCATGACA+TGG 0.617530 5.4:-7405845 None:intergenic
GATTTGTGTTGCGGTGAATG+TGG 0.622415 5.4:-7405868 None:intergenic
TTGCGGTGAATGTGGTGCCA+AGG 0.648709 5.4:-7405860 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACACTATTATAATCAATTT+TGG + chr5.4:7405572-7405591 MS.gene015366:intron 15.0%
!!! TGATAGATAAATCAATTTTA+AGG + chr5.4:7405205-7405224 MS.gene015366:intron 15.0%
!! AAAAACTTACCATAAATAAC+AGG - chr5.4:7404799-7404818 None:intergenic 20.0%
!! GATAACCAATTTACTAAAAT+TGG - chr5.4:7405668-7405687 None:intergenic 20.0%
!!! AATTTTAAGGAACCAATTTT+AGG + chr5.4:7405218-7405237 MS.gene015366:intron 20.0%
!!! AGTGTAATTTTGTGTATTTT+AGG + chr5.4:7405174-7405193 MS.gene015366:intron 20.0%
!!! ATTCATCAATTGACTTATTT+AGG - chr5.4:7405825-7405844 None:intergenic 20.0%
!!! GTTATTTATGGTAAGTTTTT+TGG + chr5.4:7404799-7404818 MS.gene015366:intron 20.0%
!!! TTTTTGCTTATAATAGTGAT+TGG + chr5.4:7405330-7405349 MS.gene015366:intron 20.0%
! AAATGACAATCTTCTATGAT+GGG + chr5.4:7404596-7404615 MS.gene015366:CDS 25.0%
! ATCCTCTCAAAACTAATATA+TGG + chr5.4:7405685-7405704 MS.gene015366:intron 25.0%
! CATACTAGTAGTATATAACA+TGG + chr5.4:7404487-7404506 MS.gene015366:intron 25.0%
! GTTACAAAAATTGATTGAAC+TGG + chr5.4:7405073-7405092 MS.gene015366:intron 25.0%
! TGGATATATTATGTTTGAGA+GGG + chr5.4:7404819-7404838 MS.gene015366:intron 25.0%
! TTGCGTTTATATAATAGTGA+CGG - chr5.4:7405252-7405271 None:intergenic 25.0%
! TTGGATATATTATGTTTGAG+AGG + chr5.4:7404818-7404837 MS.gene015366:intron 25.0%
!! ATTAATTTTGCTTCCAGAAA+CGG - chr5.4:7405490-7405509 None:intergenic 25.0%
!!! GTTTTATTACAGTGTAATGA+AGG + chr5.4:7404540-7404559 MS.gene015366:intron 25.0%
AAAAAGAACATGTATGTACC+TGG - chr5.4:7404407-7404426 None:intergenic 30.0%
AACACACTACTTAACAATTG+AGG - chr5.4:7405043-7405062 None:intergenic 30.0%
AAGTAGTGTGTTTGATTCTA+CGG + chr5.4:7405051-7405070 MS.gene015366:intron 30.0%
AATGAAGGCTAATGTTAAGA+AGG + chr5.4:7404555-7404574 MS.gene015366:CDS 30.0%
ATATTTGATTGAGAGAGATC+TGG - chr5.4:7404981-7405000 None:intergenic 30.0%
ATTCAGATTTACCAATGACT+AGG + chr5.4:7404905-7404924 MS.gene015366:intron 30.0%
CAAATGACAATCTTCTATGA+TGG + chr5.4:7404595-7404614 MS.gene015366:CDS 30.0%
CCAAACATCACAATAGAAAA+GGG - chr5.4:7405715-7405734 None:intergenic 30.0%
CCATAAATAACAGGTATAGA+TGG - chr5.4:7404790-7404809 None:intergenic 30.0%
GACAAACATATCAGTCAATA+TGG - chr5.4:7405744-7405763 None:intergenic 30.0%
TCCAAACATCACAATAGAAA+AGG - chr5.4:7405716-7405735 None:intergenic 30.0%
TGATGACTTTCTCACTTTAA+AGG + chr5.4:7405404-7405423 MS.gene015366:intron 30.0%
TGCGTTTATATAATAGTGAC+GGG - chr5.4:7405251-7405270 None:intergenic 30.0%
TTAAAGTGAGAAAGTCATCA+TGG - chr5.4:7405404-7405423 None:intergenic 30.0%
! CCATCTATACCTGTTATTTA+TGG + chr5.4:7404787-7404806 MS.gene015366:CDS 30.0%
! CTACAAGAGATTCCTATTTT+GGG + chr5.4:7404376-7404395 MS.gene015366:CDS 30.0%
! GTGATTTTGCTAAAAGTGAA+TGG + chr5.4:7405106-7405125 MS.gene015366:intron 30.0%
! TAGTCTTGAAGAGAATTGTT+GGG - chr5.4:7404757-7404776 None:intergenic 30.0%
! TGAAGTACTAGTAATTCCTT+TGG - chr5.4:7404683-7404702 None:intergenic 30.0%
! TTTATATAATAGTGACGGGA+GGG - chr5.4:7405247-7405266 None:intergenic 30.0%
!! AACGGATTGAAGCTATAATT+TGG - chr5.4:7405472-7405491 None:intergenic 30.0%
!! AGGAGCCAATTTTAGTAAAT+TGG + chr5.4:7405660-7405679 MS.gene015366:intron 30.0%
!!! AGCCATATATTAGTTTTGAG+AGG - chr5.4:7405690-7405709 None:intergenic 30.0%
!!! GTCAATAGACTTCACTTTTT+AGG + chr5.4:7405013-7405032 MS.gene015366:intron 30.0%
AGATATAGTGACTTTGGTGA+TGG + chr5.4:7405133-7405152 MS.gene015366:intron 35.0%
AGTACTAGTAATTCCTTTGG+TGG - chr5.4:7404680-7404699 None:intergenic 35.0%
CAATTGATGAATCCATGTCA+TGG + chr5.4:7405833-7405852 MS.gene015366:CDS 35.0%
CCAAAATAGGAATCTCTTGT+AGG - chr5.4:7404378-7404397 None:intergenic 35.0%
CTACAAAAATAACACAGAGG+TGG - chr5.4:7405905-7405924 None:intergenic 35.0%
CTACATTCAGATTTGTGTTG+CGG - chr5.4:7405880-7405899 None:intergenic 35.0%
GATACCATGAACAAAAGTGA+AGG + chr5.4:7405640-7405659 MS.gene015366:intron 35.0%
GCTGGATTACTTGTTTGATA+AGG - chr5.4:7405796-7405815 None:intergenic 35.0%
GGAAGCTGTTGAAAATTCAT+AGG - chr5.4:7404346-7404365 None:intergenic 35.0%
GGATTGAGATATAGTGACTT+TGG + chr5.4:7405127-7405146 MS.gene015366:intron 35.0%
TGATAAAGCCAAAGACATCA+TGG + chr5.4:7404648-7404667 MS.gene015366:CDS 35.0%
TTATAGCTTCAATCCGTTTC+TGG + chr5.4:7405474-7405493 MS.gene015366:intron 35.0%
! ACTTTCTCACTTTAAAGGCA+GGG + chr5.4:7405409-7405428 MS.gene015366:intron 35.0%
! AGCAAGCATAGTTGTTATTG+TGG - chr5.4:7404711-7404730 None:intergenic 35.0%
! CCCTTTTCTATTGTGATGTT+TGG + chr5.4:7405712-7405731 MS.gene015366:intron 35.0%
! CCTACAAGAGATTCCTATTT+TGG + chr5.4:7404375-7404394 MS.gene015366:CDS 35.0%
! GATATAGTGACTTTGGTGAT+GGG + chr5.4:7405134-7405153 MS.gene015366:intron 35.0%
! GTAGTCTTGAAGAGAATTGT+TGG - chr5.4:7404758-7404777 None:intergenic 35.0%
! GTTTATATAATAGTGACGGG+AGG - chr5.4:7405248-7405267 None:intergenic 35.0%
! TGGAGTTTTTGTCTCTACAT+TGG - chr5.4:7405452-7405471 None:intergenic 35.0%
AGTGAAGCTTTCCTAGTCAT+TGG - chr5.4:7404919-7404938 None:intergenic 40.0%
ATCTCTTGTAGGAAGAGATG+AGG - chr5.4:7404367-7404386 None:intergenic 40.0%
CTAGGAAAGCTTCACTTCAT+CGG + chr5.4:7404923-7404942 MS.gene015366:CDS 40.0%
GACATGACTCTTTGTATCCT+CGG - chr5.4:7405615-7405634 None:intergenic 40.0%
GACTTATTTAGGAATGCTGC+TGG - chr5.4:7405814-7405833 None:intergenic 40.0%
GGAAAAGTCCATGATGTCTT+TGG - chr5.4:7404659-7404678 None:intergenic 40.0%
GGCTAATGTTAAGAAGGAAG+AGG + chr5.4:7404561-7404580 MS.gene015366:CDS 40.0%
TACCTGGAGTTTCCCAAAAT+AGG - chr5.4:7404391-7404410 None:intergenic 40.0%
TCTTGGAGAAAAGGAAGGAT+AGG + chr5.4:7404947-7404966 MS.gene015366:CDS 40.0%
TTTCTGCAGAATTGCTGCAA+GGG + chr5.4:7405768-7405787 MS.gene015366:intron 40.0%
! ATCATGGACTTTTCCACCAA+AGG + chr5.4:7404664-7404683 MS.gene015366:CDS 40.0%
! CACTTTAAAGGCAGGGAATT+TGG + chr5.4:7405416-7405435 MS.gene015366:intron 40.0%
! GACTTTCTCACTTTAAAGGC+AGG + chr5.4:7405408-7405427 MS.gene015366:intron 40.0%
!! AGGGTGTTTGATTTGTGTCA+TGG + chr5.4:7404838-7404857 MS.gene015366:intron 40.0%
!! ATGTCTTTGGCTTTATCAGC+TGG - chr5.4:7404646-7404665 None:intergenic 40.0%
!! TTCATCGGTTCTTGGAGAAA+AGG + chr5.4:7404938-7404957 MS.gene015366:CDS 40.0%
!! TTCCTATTTTGGGAAACTCC+AGG + chr5.4:7404386-7404405 MS.gene015366:CDS 40.0%
ATCCATGTCATGGCTATCCT+TGG + chr5.4:7405843-7405862 MS.gene015366:CDS 45.0%
GATTTGTGTTGCGGTGAATG+TGG - chr5.4:7405871-7405890 None:intergenic 45.0%
GTTTCTGCAGAATTGCTGCA+AGG + chr5.4:7405767-7405786 MS.gene015366:intron 45.0%
TCGGTTCTTGGAGAAAAGGA+AGG + chr5.4:7404942-7404961 MS.gene015366:CDS 45.0%
TTGATTGAGAGAGATCTGGC+AGG - chr5.4:7404977-7404996 None:intergenic 45.0%
!! AGCTTCACTTCATCGGTTCT+TGG + chr5.4:7404930-7404949 MS.gene015366:CDS 45.0%
!! GGCTCCTTCACTTTTGTTCA+TGG - chr5.4:7405647-7405666 None:intergenic 45.0%
ACGGGAGGGAGTCCTAAAAT+TGG - chr5.4:7405233-7405252 None:intergenic 50.0%
TGCCAAGGATAGCCATGACA+TGG - chr5.4:7405848-7405867 None:intergenic 50.0%
! TGTATCCTCGGCTCGACTTT+AGG - chr5.4:7405603-7405622 None:intergenic 50.0%
CTCATCCTAAAGTCGAGCCG+AGG + chr5.4:7405595-7405614 MS.gene015366:intron 55.0%
! TTGCGGTGAATGTGGTGCCA+AGG - chr5.4:7405863-7405882 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 7404322 7405924 7404322 ID=MS.gene015366
chr5.4 mRNA 7404322 7405924 7404322 ID=MS.gene015366.t1;Parent=MS.gene015366
chr5.4 exon 7404322 7404407 7404322 ID=MS.gene015366.t1.exon1;Parent=MS.gene015366.t1
chr5.4 CDS 7404322 7404407 7404322 ID=cds.MS.gene015366.t1;Parent=MS.gene015366.t1
chr5.4 exon 7404552 7404808 7404552 ID=MS.gene015366.t1.exon2;Parent=MS.gene015366.t1
chr5.4 CDS 7404552 7404808 7404552 ID=cds.MS.gene015366.t1;Parent=MS.gene015366.t1
chr5.4 exon 7404911 7404968 7404911 ID=MS.gene015366.t1.exon3;Parent=MS.gene015366.t1
chr5.4 CDS 7404911 7404968 7404911 ID=cds.MS.gene015366.t1;Parent=MS.gene015366.t1
chr5.4 exon 7405777 7405924 7405777 ID=MS.gene015366.t1.exon4;Parent=MS.gene015366.t1
chr5.4 CDS 7405777 7405924 7405777 ID=cds.MS.gene015366.t1;Parent=MS.gene015366.t1
Gene Sequence

>MS.gene015366

ATGAATCATCACAACATAACACCTATGAATTTTCAACAGCTTCCTCATCTCTTCCTACAAGAGATTCCTATTTTGGGAAACTCCAGGTACATACATGTTCTTTTTTCTACTATAACTTGTTTAAGTACATCAACATTTTTTTAGCAAAATTCAAATTCATTAATTCATACTAGTAGTATATAACATGGTCAATTTGCATTAAATTAATTTTTAATGTTGTTTTATTACAGTGTAATGAAGGCTAATGTTAAGAAGGAAGAGGCTAGATGTGCACAAATGACAATCTTCTATGATGGGAAAGTAATTGTGTTTGATGATGTTCCAGCTGATAAAGCCAAAGACATCATGGACTTTTCCACCAAAGGAATTACTAGTACTTCACAAAACCACAATAACAACTATGCTTGCTCTTCATTTCTTGCTAGAAATTCTCCCAACAATTCTCTTCAAGACTACTATCAAGTACCATCTATACCTGTTATTTATGGTAAGTTTTTTGGATATATTATGTTTGAGAGGGTGTTTGATTTGTGTCATGGTTTTGTTTTTTGTGTGTTTTTAACTCATGAAATTCTTTTTATGTATTCAGATTTACCAATGACTAGGAAAGCTTCACTTCATCGGTTCTTGGAGAAAAGGAAGGATAGGTAAGCCTGCCAGATCTCTCTCAATCAAATATTGTTTGATCTTTGTCAATAGACTTCACTTTTTAGGAAAACCTCAATTGTTAAGTAGTGTGTTTGATTCTACGGTTACAAAAATTGATTGAACTGGTTATTTAAAAGTGATTTTGCTAAAAGTGAATGGATTGAGATATAGTGACTTTGGTGATGGGAAAGTAATTATTACTATAGTGTAATTTTGTGTATTTTAGGAAAGAAAATGATAGATAAATCAATTTTAAGGAACCAATTTTAGGACTCCCTCCCGTCACTATTATATAAACGCAAAAAATCACTTTTAAATTTATTCAATAACTAATGTATTGAATGAATCTTAAAAGTTGTTTTTTTGCTTATAATAGTGATTGGATGAAGTATATATATATATATATATAAAAGAGAAAGATAAACACAAAGCCATGATGACTTTCTCACTTTAAAGGCAGGGAATTTGGATCTGAAAATCCAATGTAGAGACAAAAACTCCAAATTATAGCTTCAATCCGTTTCTGGAAGCAAAATTAATTTCACTTCAAAAACATTCAAACATTTGTTTTTGAAAGAAAGAAAACATGTCAAAATCAATTCTACACTATTATAATCAATTTTGGCTCATCCTAAAGTCGAGCCGAGGATACAAAGAGTCATGTCAAATTGATACCATGAACAAAAGTGAAGGAGCCAATTTTAGTAAATTGGTTATCCTCTCAAAACTAATATATGGCTGACCCTTTTCTATTGTGATGTTTGGAATTATCCATATTGACTGATATGTTTGTCTATGTTTCTGCAGAATTGCTGCAAGGGCACCTTATCAAACAAGTAATCCAGCAGCATTCCTAAATAAGTCAATTGATGAATCCATGTCATGGCTATCCTTGGCACCACATTCACCGCAACACAAATCTGAATGTAGCTCCACCTCTGTGTTATTTTTGTAG

Protein sequence

>MS.gene015366.t1

MNHHNITPMNFQQLPHLFLQEIPILGNSSVMKANVKKEEARCAQMTIFYDGKVIVFDDVPADKAKDIMDFSTKGITSTSQNHNNNYACSSFLARNSPNNSLQDYYQVPSIPVIYDLPMTRKASLHRFLEKRKDRIAARAPYQTSNPAAFLNKSIDESMSWLSLAPHSPQHKSECSSTSVLFL