AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015368


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015368.t1 MTR_5g013530 89.011 182 11 2 1 182 1 173 1.08e-115 325
MS.gene015368.t1 MTR_5g013530 87.662 154 10 2 29 182 7 151 1.45e-92 266
MS.gene015368.t1 MTR_5g013520 85.333 150 17 2 30 179 1 145 9.50e-90 259
MS.gene015368.t1 MTR_5g013515 72.028 143 27 5 31 166 1 137 4.53e-64 194
MS.gene015368.t1 MTR_2g042900 45.963 161 49 5 25 161 99 245 3.12e-34 121
MS.gene015368.t1 MTR_2g042900 35.976 164 45 5 25 134 99 256 4.06e-19 82.0
MS.gene015368.t1 MTR_4g124960 32.143 168 71 5 5 167 73 202 7.75e-19 80.5
MS.gene015368.t1 MTR_4g124960 32.143 140 52 5 5 139 73 174 2.62e-14 67.8
MS.gene015368.t1 MTR_8g021380 32.824 131 80 4 19 142 79 208 1.24e-13 67.0
MS.gene015368.t1 MTR_4g124950 32.624 141 67 4 5 145 7 119 2.20e-13 64.3
MS.gene015368.t1 MTR_2g044910 29.310 116 71 3 40 144 11 126 2.64e-12 62.0
MS.gene015368.t1 MTR_2g044910 29.310 116 71 3 40 144 54 169 4.24e-12 62.4
MS.gene015368.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.gene015368.t1 AT1G19180 42.105 133 71 4 37 164 53 184 5.88e-27 101
MS.gene015368.t1 AT1G19180 42.105 133 71 4 37 164 119 250 3.27e-26 100
MS.gene015368.t1 AT1G19180 42.105 133 71 4 37 164 119 250 3.27e-26 100
MS.gene015368.t1 AT1G74950 40.580 138 68 3 37 162 112 247 1.20e-23 94.0
MS.gene015368.t1 AT1G74950 41.818 110 52 2 37 134 112 221 2.34e-18 79.3
MS.gene015368.t1 AT1G17380 37.302 126 69 3 33 148 58 183 3.84e-16 73.9
MS.gene015368.t1 AT1G17380 37.302 126 69 3 33 148 87 212 1.22e-15 73.2
MS.gene015368.t1 AT1G72450 37.288 118 68 2 39 150 101 218 2.36e-15 72.4
MS.gene015368.t1 AT5G20900 32.394 142 74 5 24 145 28 167 1.16e-13 66.2
MS.gene015368.t1 AT1G70700 34.615 104 62 3 44 142 119 221 1.73e-11 61.2
MS.gene015368.t1 AT1G17380 34.821 112 63 2 33 134 87 198 2.65e-11 60.5

Find 37 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTACAAGAGATTCCTATTT+TGG 0.046444 5.4:+7389085 MS.gene015368:CDS
CCATCTATACCTGTTATTTA+TGG 0.164541 5.4:+7389497 MS.gene015368:CDS
ATTCATCAATTGACTTATTT+AGG 0.185988 5.4:-7390599 None:intergenic
AGCTTCACTTCATCGGTTCT+TGG 0.292747 5.4:+7389640 MS.gene015368:CDS
CCAAAATAGGAATCTCTTGT+AGG 0.331403 5.4:-7389085 None:intergenic
TACCTGGAGTTTCCCAAAAT+AGG 0.395618 5.4:-7389098 None:intergenic
GGAAAAGTCCATGATGTCTT+TGG 0.411671 5.4:-7389366 None:intergenic
ATGTCTTTGGCTTTATCAGC+TGG 0.417227 5.4:-7389353 None:intergenic
GCTGGATTACTTGTTTGATA+AGG 0.423471 5.4:-7390570 None:intergenic
AGTGAAGCTTTCCTAGTCAT+TGG 0.425048 5.4:-7389626 None:intergenic
GACTTATTTAGGAATGCTGC+TGG 0.431039 5.4:-7390588 None:intergenic
TGAAGTACTAGTAATTCCTT+TGG 0.431697 5.4:-7389390 None:intergenic
GTAGTCTTGAAGAGAATTGT+TGG 0.447616 5.4:-7389465 None:intergenic
CAAATGACAATCTTCTATGA+TGG 0.453411 5.4:+7389305 MS.gene015368:CDS
TTCATCGGTTCTTGGAGAAA+AGG 0.463618 5.4:+7389648 MS.gene015368:CDS
GGAAGCTGTTGAAAATTCAT+AGG 0.469618 5.4:-7389053 None:intergenic
CCATAAATAACAGGTATAGA+TGG 0.477854 5.4:-7389497 None:intergenic
AGTACTAGTAATTCCTTTGG+TGG 0.499055 5.4:-7389387 None:intergenic
TAGTCTTGAAGAGAATTGTT+GGG 0.502082 5.4:-7389464 None:intergenic
ATCCATGTCATGGCTATCCT+TGG 0.509457 5.4:+7390620 MS.gene015368:CDS
AATGAAGGCTAATGTTAAGA+AGG 0.511094 5.4:+7389265 MS.gene015368:CDS
AGCAAGCATAGTTGTTATTG+TGG 0.514503 5.4:-7389418 None:intergenic
CTAGGAAAGCTTCACTTCAT+CGG 0.529148 5.4:+7389633 MS.gene015368:CDS
AAATGACAATCTTCTATGAT+GGG 0.538308 5.4:+7389306 MS.gene015368:CDS
CTACATTCAGATTTGTGTTG+CGG 0.544643 5.4:-7390654 None:intergenic
ATCTCTTGTAGGAAGAGATG+AGG 0.564072 5.4:-7389074 None:intergenic
TCTTGGAGAAAAGGAAGGAT+AGG 0.567398 5.4:+7389657 MS.gene015368:CDS
GGCTAATGTTAAGAAGGAAG+AGG 0.580916 5.4:+7389271 MS.gene015368:CDS
TGATAAAGCCAAAGACATCA+TGG 0.585378 5.4:+7389358 MS.gene015368:CDS
TCGGTTCTTGGAGAAAAGGA+AGG 0.585705 5.4:+7389652 MS.gene015368:CDS
GTTTCTGCAGAATTGCTGCA+AGG 0.606526 5.4:+7390544 MS.gene015368:intron
ATTCAGATTTACCAATGACT+AGG 0.608086 5.4:+7389615 MS.gene015368:intron
TTTCTGCAGAATTGCTGCAA+GGG 0.611240 5.4:+7390545 MS.gene015368:intron
CAATTGATGAATCCATGTCA+TGG 0.612586 5.4:+7390610 MS.gene015368:CDS
TGCCAAGGATAGCCATGACA+TGG 0.617530 5.4:-7390622 None:intergenic
GATTTGTGTTGCGGTGAATG+TGG 0.622415 5.4:-7390645 None:intergenic
TTGCGGTGAATGTGGTGCCA+AGG 0.648709 5.4:-7390637 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACACTATTATAATCAATTT+TGG + chr5.4:7390338-7390357 MS.gene015368:intron 15.0%
!!! TGATAGATAAATCAATTTTA+AGG + chr5.4:7389915-7389934 MS.gene015368:intron 15.0%
!! AAAAACTTACCATAAATAAC+AGG - chr5.4:7389509-7389528 None:intergenic 20.0%
!! GATAACCAATTTACTAAAAT+TGG - chr5.4:7390434-7390453 None:intergenic 20.0%
!!! AATTTTAAGGAACCAATTTT+AGG + chr5.4:7389928-7389947 MS.gene015368:intron 20.0%
!!! AGTGTAATTTTGTGTATTTT+AGG + chr5.4:7389884-7389903 MS.gene015368:intron 20.0%
!!! ATTCATCAATTGACTTATTT+AGG - chr5.4:7390602-7390621 None:intergenic 20.0%
!!! GTTATTTATGGTAAGTTTTT+TGG + chr5.4:7389509-7389528 MS.gene015368:intron 20.0%
! AAACATCATACTAGTAGAAA+AGG - chr5.4:7390490-7390509 None:intergenic 25.0%
! AAATGACAATCTTCTATGAT+GGG + chr5.4:7389306-7389325 MS.gene015368:CDS 25.0%
! AACATCATACTAGTAGAAAA+GGG - chr5.4:7390489-7390508 None:intergenic 25.0%
! CATACTAGTAGTATATAACA+TGG + chr5.4:7389197-7389216 MS.gene015368:intron 25.0%
! GTTACAAAAATTGATTGAAC+TGG + chr5.4:7389783-7389802 MS.gene015368:intron 25.0%
! TCCTCTCAAAACTATATATA+TGG + chr5.4:7390459-7390478 MS.gene015368:intron 25.0%
! TGGATATATTATGTTTGAGA+GGG + chr5.4:7389529-7389548 MS.gene015368:intron 25.0%
! TTGCGTTTATATAATAGTGA+CGG - chr5.4:7389962-7389981 None:intergenic 25.0%
! TTGGATATATTATGTTTGAG+AGG + chr5.4:7389528-7389547 MS.gene015368:intron 25.0%
!! TTTTCTACTAGTATGATGTT+TGG + chr5.4:7390489-7390508 MS.gene015368:intron 25.0%
!! TTTTTGCTCATAATAGTGAT+TGG + chr5.4:7390040-7390059 MS.gene015368:intron 25.0%
!!! ATATAGTTTTGAGAGGATAA+CGG - chr5.4:7390456-7390475 None:intergenic 25.0%
!!! GTTTTATTACAGTGTAATGA+AGG + chr5.4:7389250-7389269 MS.gene015368:intron 25.0%
AAAAAGAACATGTATGTACC+TGG - chr5.4:7389117-7389136 None:intergenic 30.0%
AACACACTACTTAACAATTG+AGG - chr5.4:7389753-7389772 None:intergenic 30.0%
AAGTAGTGTGTTTGATTCTA+CGG + chr5.4:7389761-7389780 MS.gene015368:intron 30.0%
AATGAAGGCTAATGTTAAGA+AGG + chr5.4:7389265-7389284 MS.gene015368:CDS 30.0%
ATATTTGATTGAGAGAGATC+TGG - chr5.4:7389691-7389710 None:intergenic 30.0%
ATTCAGATTTACCAATGACT+AGG + chr5.4:7389615-7389634 MS.gene015368:intron 30.0%
CAAATGACAATCTTCTATGA+TGG + chr5.4:7389305-7389324 MS.gene015368:CDS 30.0%
CCATAAATAACAGGTATAGA+TGG - chr5.4:7389500-7389519 None:intergenic 30.0%
GACAAACTTATCAGTCAATA+TGG - chr5.4:7390521-7390540 None:intergenic 30.0%
TGATGACTTTCTCACTTTAA+AGG + chr5.4:7390170-7390189 MS.gene015368:intron 30.0%
TGCGTTTATATAATAGTGAC+GGG - chr5.4:7389961-7389980 None:intergenic 30.0%
TTAAAGTGAGAAAGTCATCA+TGG - chr5.4:7390170-7390189 None:intergenic 30.0%
! CCATCTATACCTGTTATTTA+TGG + chr5.4:7389497-7389516 MS.gene015368:CDS 30.0%
! CTACAAGAGATTCCTATTTT+GGG + chr5.4:7389086-7389105 MS.gene015368:CDS 30.0%
! GTGATTTTGCTAAAAGTGAA+TGG + chr5.4:7389816-7389835 MS.gene015368:intron 30.0%
! TAGTCTTGAAGAGAATTGTT+GGG - chr5.4:7389467-7389486 None:intergenic 30.0%
! TGAAGTACTAGTAATTCCTT+TGG - chr5.4:7389393-7389412 None:intergenic 30.0%
! TTTATATAATAGTGACGGGA+GGG - chr5.4:7389957-7389976 None:intergenic 30.0%
!! AACGGATTGAAGCTATAATT+TGG - chr5.4:7390238-7390257 None:intergenic 30.0%
!! AGGAGCCAATTTTAGTAAAT+TGG + chr5.4:7390426-7390445 MS.gene015368:intron 30.0%
!! ATTGATTTTGCTTCCAGAAA+CGG - chr5.4:7390256-7390275 None:intergenic 30.0%
!!! GCCATATATATAGTTTTGAG+AGG - chr5.4:7390463-7390482 None:intergenic 30.0%
!!! GTCAATAGACTTCACTTTTT+AGG + chr5.4:7389723-7389742 MS.gene015368:intron 30.0%
AGATATAGTGACTTTGGTGA+TGG + chr5.4:7389843-7389862 MS.gene015368:intron 35.0%
AGTACTAGTAATTCCTTTGG+TGG - chr5.4:7389390-7389409 None:intergenic 35.0%
CAATTGATGAATCCATGTCA+TGG + chr5.4:7390610-7390629 MS.gene015368:CDS 35.0%
CCAAAATAGGAATCTCTTGT+AGG - chr5.4:7389088-7389107 None:intergenic 35.0%
CTACAAAAATAACACAGAGG+TGG - chr5.4:7390682-7390701 None:intergenic 35.0%
CTACATTCAGATTTGTGTTG+CGG - chr5.4:7390657-7390676 None:intergenic 35.0%
GATACCATGAACAAAAGTGA+AGG + chr5.4:7390406-7390425 MS.gene015368:intron 35.0%
GCTGGATTACTTGTTTGATA+AGG - chr5.4:7390573-7390592 None:intergenic 35.0%
GGAAGCTGTTGAAAATTCAT+AGG - chr5.4:7389056-7389075 None:intergenic 35.0%
GGATTGAGATATAGTGACTT+TGG + chr5.4:7389837-7389856 MS.gene015368:intron 35.0%
TGATAAAGCCAAAGACATCA+TGG + chr5.4:7389358-7389377 MS.gene015368:CDS 35.0%
TTATAGCTTCAATCCGTTTC+TGG + chr5.4:7390240-7390259 MS.gene015368:intron 35.0%
! ACTTTCTCACTTTAAAGGCA+GGG + chr5.4:7390175-7390194 MS.gene015368:intron 35.0%
! AGCAAGCATAGTTGTTATTG+TGG - chr5.4:7389421-7389440 None:intergenic 35.0%
! CCTACAAGAGATTCCTATTT+TGG + chr5.4:7389085-7389104 MS.gene015368:CDS 35.0%
! GATATAGTGACTTTGGTGAT+GGG + chr5.4:7389844-7389863 MS.gene015368:intron 35.0%
! GTAGTCTTGAAGAGAATTGT+TGG - chr5.4:7389468-7389487 None:intergenic 35.0%
! GTTTATATAATAGTGACGGG+AGG - chr5.4:7389958-7389977 None:intergenic 35.0%
! TGGAGTTTTTGTCTCTACAT+TGG - chr5.4:7390218-7390237 None:intergenic 35.0%
AGTGAAGCTTTCCTAGTCAT+TGG - chr5.4:7389629-7389648 None:intergenic 40.0%
ATCTCTTGTAGGAAGAGATG+AGG - chr5.4:7389077-7389096 None:intergenic 40.0%
CTAGGAAAGCTTCACTTCAT+CGG + chr5.4:7389633-7389652 MS.gene015368:CDS 40.0%
GACTTATTTAGGAATGCTGC+TGG - chr5.4:7390591-7390610 None:intergenic 40.0%
GGAAAAGTCCATGATGTCTT+TGG - chr5.4:7389369-7389388 None:intergenic 40.0%
GGCTAATGTTAAGAAGGAAG+AGG + chr5.4:7389271-7389290 MS.gene015368:CDS 40.0%
TACCTGGAGTTTCCCAAAAT+AGG - chr5.4:7389101-7389120 None:intergenic 40.0%
TCTTGGAGAAAAGGAAGGAT+AGG + chr5.4:7389657-7389676 MS.gene015368:CDS 40.0%
TTTCTGCAGAATTGCTGCAA+GGG + chr5.4:7390545-7390564 MS.gene015368:intron 40.0%
! ATCATGGACTTTTCCACCAA+AGG + chr5.4:7389374-7389393 MS.gene015368:CDS 40.0%
! CACTTTAAAGGCAGGGAATT+TGG + chr5.4:7390182-7390201 MS.gene015368:intron 40.0%
! GACTTTCTCACTTTAAAGGC+AGG + chr5.4:7390174-7390193 MS.gene015368:intron 40.0%
!! AGGGTGTTTGATTTGTGTCA+TGG + chr5.4:7389548-7389567 MS.gene015368:intron 40.0%
!! ATGTCTTTGGCTTTATCAGC+TGG - chr5.4:7389356-7389375 None:intergenic 40.0%
!! TTCATCGGTTCTTGGAGAAA+AGG + chr5.4:7389648-7389667 MS.gene015368:CDS 40.0%
!! TTCCTATTTTGGGAAACTCC+AGG + chr5.4:7389096-7389115 MS.gene015368:CDS 40.0%
ATCCATGTCATGGCTATCCT+TGG + chr5.4:7390620-7390639 MS.gene015368:CDS 45.0%
GACATGACTCAGTGTATCCT+CGG - chr5.4:7390381-7390400 None:intergenic 45.0%
GATTTGTGTTGCGGTGAATG+TGG - chr5.4:7390648-7390667 None:intergenic 45.0%
GTTTCTGCAGAATTGCTGCA+AGG + chr5.4:7390544-7390563 MS.gene015368:intron 45.0%
TCGGTTCTTGGAGAAAAGGA+AGG + chr5.4:7389652-7389671 MS.gene015368:CDS 45.0%
TTGATTGAGAGAGATCTGGC+AGG - chr5.4:7389687-7389706 None:intergenic 45.0%
!! AGCTTCACTTCATCGGTTCT+TGG + chr5.4:7389640-7389659 MS.gene015368:CDS 45.0%
!! GGCTCCTTCACTTTTGTTCA+TGG - chr5.4:7390413-7390432 None:intergenic 45.0%
ACGGGAGGGAGTCCTAAAAT+TGG - chr5.4:7389943-7389962 None:intergenic 50.0%
TGCCAAGGATAGCCATGACA+TGG - chr5.4:7390625-7390644 None:intergenic 50.0%
! TGTATCCTCGGCTCGACTTT+AGG - chr5.4:7390369-7390388 None:intergenic 50.0%
CTCATCCTAAAGTCGAGCCG+AGG + chr5.4:7390361-7390380 MS.gene015368:intron 55.0%
! TTGCGGTGAATGTGGTGCCA+AGG - chr5.4:7390640-7390659 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 7389032 7390701 7389032 ID=MS.gene015368
chr5.4 mRNA 7389032 7390701 7389032 ID=MS.gene015368.t1;Parent=MS.gene015368
chr5.4 exon 7389032 7389117 7389032 ID=MS.gene015368.t1.exon1;Parent=MS.gene015368.t1
chr5.4 CDS 7389032 7389117 7389032 ID=cds.MS.gene015368.t1;Parent=MS.gene015368.t1
chr5.4 exon 7389262 7389518 7389262 ID=MS.gene015368.t1.exon2;Parent=MS.gene015368.t1
chr5.4 CDS 7389262 7389518 7389262 ID=cds.MS.gene015368.t1;Parent=MS.gene015368.t1
chr5.4 exon 7389621 7389678 7389621 ID=MS.gene015368.t1.exon3;Parent=MS.gene015368.t1
chr5.4 CDS 7389621 7389678 7389621 ID=cds.MS.gene015368.t1;Parent=MS.gene015368.t1
chr5.4 exon 7390554 7390701 7390554 ID=MS.gene015368.t1.exon4;Parent=MS.gene015368.t1
chr5.4 CDS 7390554 7390701 7390554 ID=cds.MS.gene015368.t1;Parent=MS.gene015368.t1
Gene Sequence

>MS.gene015368

ATGAATCATCACAACATAACACCTATGAATTTTCAACAGCTTCCTCATCTCTTCCTACAAGAGATTCCTATTTTGGGAAACTCCAGGTACATACATGTTCTTTTTTCTACTATAACTTGTTTAAGTACATCAACATTTTTTTAGCAAAATTCAAATTCATTAATTCATACTAGTAGTATATAACATGGTCAATTTGCATTAAATTAATTTTTAATGTTGTTTTATTACAGTGTAATGAAGGCTAATGTTAAGAAGGAAGAGGCTAGATGTGCACAAATGACAATCTTCTATGATGGGAAAGTAATTGTGTTTGATGATGTTCCAGCTGATAAAGCCAAAGACATCATGGACTTTTCCACCAAAGGAATTACTAGTACTTCACAAAACCACAATAACAACTATGCTTGCTCTTCATTTCTTGCTAGAAATTCTCCCAACAATTCTCTTCAAGACTACTATCAAGTACCATCTATACCTGTTATTTATGGTAAGTTTTTTGGATATATTATGTTTGAGAGGGTGTTTGATTTGTGTCATGGTTTTGTTTTTTGTGTGTTTTTAACTCATGAAATTCTTTTTATGTATTCAGATTTACCAATGACTAGGAAAGCTTCACTTCATCGGTTCTTGGAGAAAAGGAAGGATAGGTAAGCCTGCCAGATCTCTCTCAATCAAATATTGTTTGATCTTTGTCAATAGACTTCACTTTTTAGGAAAACCTCAATTGTTAAGTAGTGTGTTTGATTCTACGGTTACAAAAATTGATTGAACTGGTTATTTAAAAGTGATTTTGCTAAAAGTGAATGGATTGAGATATAGTGACTTTGGTGATGGGAAAGTAATTATTACTATAGTGTAATTTTGTGTATTTTAGGAAAGAAAATGATAGATAAATCAATTTTAAGGAACCAATTTTAGGACTCCCTCCCGTCACTATTATATAAACGCAAAAAATCACTTTTAAATTTATTCAATAACTAATGTATTGAATGAATCTTAAAAGTTGTTTTTTTGCTCATAATAGTGATTGGATGAAGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAAAGAGAGAGATAAACACAAAGCCATGATGACTTTCTCACTTTAAAGGCAGGGAATTTGGATCTGAAAATCCAATGTAGAGACAAAAACTCCAAATTATAGCTTCAATCCGTTTCTGGAAGCAAAATCAATTTCACTTCAAAAACATTCAAACATTTGTTTTTGAAAGAAAGAAAACATGTCAAAATCAATTCTACACTATTATAATCAATTTTGGCTCATCCTAAAGTCGAGCCGAGGATACACTGAGTCATGTCAAATTGATACCATGAACAAAAGTGAAGGAGCCAATTTTAGTAAATTGGTTATCCGTTATCCTCTCAAAACTATATATATGGCTGACCCTTTTCTACTAGTATGATGTTTGGAATTATCCATATTGACTGATAAGTTTGTCTATGTTTCTGCAGAATTGCTGCAAGGGCACCTTATCAAACAAGTAATCCAGCAGCATTCCTAAATAAGTCAATTGATGAATCCATGTCATGGCTATCCTTGGCACCACATTCACCGCAACACAAATCTGAATGTAGCTCCACCTCTGTGTTATTTTTGTAG

Protein sequence

>MS.gene015368.t1

MNHHNITPMNFQQLPHLFLQEIPILGNSSVMKANVKKEEARCAQMTIFYDGKVIVFDDVPADKAKDIMDFSTKGITSTSQNHNNNYACSSFLARNSPNNSLQDYYQVPSIPVIYDLPMTRKASLHRFLEKRKDRIAARAPYQTSNPAAFLNKSIDESMSWLSLAPHSPQHKSECSSTSVLFL