AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028905

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028905.t1 MTR_2g090365 92.500 200 15 0 1 200 254 453 1.52e-140 400
MS.gene028905.t1 MTR_2g078310 63.874 191 64 3 10 197 1 189 1.03e-74 224
MS.gene028905.t1 MTR_3g117270 51.562 192 85 5 10 195 1 190 1.09e-62 193
MS.gene028905.t1 MTR_3g117270 51.562 192 85 5 10 195 1 190 1.87e-62 193
MS.gene028905.t1 MTR_3g117270 54.601 163 68 4 10 166 1 163 8.08e-56 174
MS.gene028905.t1 MTR_3g117270 54.601 163 68 4 10 166 1 163 8.80e-56 174
MS.gene028905.t1 MTR_3g117280 50.568 176 81 3 25 199 2 172 1.45e-55 175
MS.gene028905.t1 MTR_5g097190 40.476 126 65 4 82 198 20 144 2.61e-20 87.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028905.t1 AT4G22140 59.296 199 68 3 10 197 1 197 1.38e-75 227
MS.gene028905.t1 AT4G22140 59.296 199 68 3 10 197 1 197 1.71e-75 227
MS.gene028905.t1 AT4G22140 59.296 199 68 3 10 197 1 197 1.71e-75 227
MS.gene028905.t1 AT4G39100 51.099 182 85 3 21 200 14 193 2.78e-61 191
MS.gene028905.t1 AT4G04260 56.970 165 67 3 34 197 10 171 1.18e-54 173
MS.gene028905.t1 AT4G04260 57.895 152 61 2 46 197 10 158 4.32e-52 166
MS.gene028905.t1 AT4G39100 54.362 149 66 2 21 167 14 162 7.71e-52 164
MS.gene028905.t1 AT4G04260 54.286 140 60 3 10 145 1 140 6.13e-41 136

Find 45 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAATGTTCACCTGATTTAA+AGG 0.193987 2.3:-10153754 MS.gene028905:CDS
AAAGGCATGCCCACGCATTT+AGG 0.253844 2.3:+10153819 None:intergenic
TTCACCTGATTTAAAGGATT+AGG 0.322143 2.3:-10153748 None:intergenic
TCACCTGATTTAAAGGATTA+GGG 0.322613 2.3:-10153747 None:intergenic
ACGATTACTTTAGCAGGTTC+TGG 0.332292 2.3:-10154261 MS.gene028905:CDS
ATTAACCTATCCGGGTTATA+AGG 0.334701 2.3:+10154065 None:intergenic
TTATAACCCGGATAGGTTAA+TGG 0.355817 2.3:-10154063 MS.gene028905:CDS
GATTTCATTGCTTCATCAAA+AGG 0.383487 2.3:+10153801 None:intergenic
ACTTACACTTCAACGCGTTC+AGG 0.403385 2.3:+10154211 None:intergenic
CACAGCACCATTAACCTATC+CGG 0.404617 2.3:+10154056 None:intergenic
AGTCCCTAATCCTTTAAATC+AGG 0.432271 2.3:+10153744 None:intergenic
TTGGTTTGTTCCTGCCAGTA+TGG 0.439578 2.3:+10154512 None:intergenic
CGACAACAAGGCAAGGGAAA+AGG 0.450024 2.3:-10155010 MS.gene028905:CDS
AAAACATACGCGTCCTTCAA+TGG 0.453876 2.3:+10154405 None:intergenic
GGCACCAACACGGTCGTTAG+AGG 0.459119 2.3:-10154969 MS.gene028905:intron
GTGCTAACGATTACTTTAGC+AGG 0.480077 2.3:-10154267 MS.gene028905:CDS
CAGCAACCTACAGAACATAA+TGG 0.494473 2.3:-10155033 MS.gene028905:CDS
AGGATAATATGAACAGAATG+AGG 0.500778 2.3:-10154462 MS.gene028905:CDS
CGTCCTTCAATGGTTTCCTC+AGG 0.503827 2.3:+10154415 None:intergenic
AAAAGGAACAAATACACAAT+CGG 0.520774 2.3:-10154993 MS.gene028905:CDS
CATAGTGCTGACACAATTGA+AGG 0.525786 2.3:-10154340 MS.gene028905:CDS
TACATGAAGCTTGAAGTTGT+AGG 0.537934 2.3:-10154289 MS.gene028905:CDS
TTGTCGCCATTATGTTCTGT+AGG 0.543808 2.3:+10155027 None:intergenic
CGACCTGAGGAAACCATTGA+AGG 0.551081 2.3:-10154418 MS.gene028905:CDS
GAATGAGGGTCTATGTAAGA+AGG 0.562196 2.3:-10154447 MS.gene028905:CDS
CCGTGTGGAAAAGATTGAGC+AGG 0.565789 2.3:-10154482 MS.gene028905:CDS
TTATGTTCTGTAGGTTGCTG+CGG 0.575653 2.3:+10155036 None:intergenic
CAGGTACCATCCTAAATGCG+TGG 0.581382 2.3:-10153829 MS.gene028905:CDS
ACAGCACCATTAACCTATCC+GGG 0.588194 2.3:+10154057 None:intergenic
AGATGCCTTATAACCCGGAT+AGG 0.594661 2.3:-10154070 MS.gene028905:CDS
GCATGCCCACGCATTTAGGA+TGG 0.615056 2.3:+10153823 None:intergenic
ATAATGGCGACAACAAGGCA+AGG 0.623162 2.3:-10155017 MS.gene028905:CDS
ATGTGAGATGCCTTATAACC+CGG 0.623493 2.3:-10154075 MS.gene028905:CDS
AGGTACCATCCTAAATGCGT+GGG 0.636148 2.3:-10153828 MS.gene028905:CDS
AGAACATAATGGCGACAACA+AGG 0.636635 2.3:-10155022 MS.gene028905:CDS
TGTGTGGAAGTTGCAATCAA+AGG 0.645860 2.3:-10154037 MS.gene028905:intron
GGATAATATGAACAGAATGA+GGG 0.654950 2.3:-10154461 MS.gene028905:CDS
ATAGTGCTGACACAATTGAA+GGG 0.668881 2.3:-10154339 MS.gene028905:CDS
ATTACCTCTAACGACCGTGT+TGG 0.672565 2.3:+10154965 None:intergenic
CACAATCGGAGGCACCAACA+CGG 0.673961 2.3:-10154979 MS.gene028905:CDS
TAATGGCGACAACAAGGCAA+GGG 0.678546 2.3:-10155016 MS.gene028905:CDS
AGGAACAAATACACAATCGG+AGG 0.686184 2.3:-10154990 MS.gene028905:CDS
CAAACCAATCATAGCCCGTG+TGG 0.703357 2.3:-10154497 MS.gene028905:CDS
AAGAAGGTATTATCGACCTG+AGG 0.704026 2.3:-10154431 MS.gene028905:CDS
GATAGGTTAATGGTGCTGTG+TGG 0.736018 2.3:-10154053 MS.gene028905:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTATAATGAATTATTATGC+AGG - chr2.3:10154800-10154819 MS.gene028905:intron 20.0%
!!! AAACACTGATATTTTTTTCT+AGG - chr2.3:10154604-10154623 MS.gene028905:intron 20.0%
!!! AACACTGATATTTTTTTCTA+GGG - chr2.3:10154605-10154624 MS.gene028905:intron 20.0%
!!! ATTTTACTTTTATGTTTCGA+AGG - chr2.3:10154684-10154703 MS.gene028905:intron 20.0%
! AAAAGGAACAAATACACAAT+CGG - chr2.3:10153797-10153816 MS.gene028905:CDS 25.0%
! AAAATGTTCACCTGATTTAA+AGG - chr2.3:10155036-10155055 MS.gene028905:CDS 25.0%
! AAGTAGATAGTTCAAAAACA+TGG - chr2.3:10153924-10153943 MS.gene028905:intron 25.0%
! GAAATATTTCAATTTCTTGC+AGG - chr2.3:10154942-10154961 MS.gene028905:intron 25.0%
!! ATCAAAGGTAAATTGGATTT+TGG - chr2.3:10154768-10154787 MS.gene028905:intron 25.0%
!! ATTTGAAGCAATTTGCTTAA+CGG + chr2.3:10153881-10153900 None:intergenic 25.0%
!! TCAAAGGTAAATTGGATTTT+GGG - chr2.3:10154769-10154788 MS.gene028905:intron 25.0%
!!! ACACTGATATTTTTTTCTAG+GGG - chr2.3:10154606-10154625 MS.gene028905:intron 25.0%
AGATCTGTAAGGAAATAAAC+TGG + chr2.3:10154915-10154934 None:intergenic 30.0%
AGGATAATATGAACAGAATG+AGG - chr2.3:10154328-10154347 MS.gene028905:CDS 30.0%
AGTTGCAATCAAAGGTAAAT+TGG - chr2.3:10154761-10154780 MS.gene028905:intron 30.0%
GATTTCATTGCTTCATCAAA+AGG + chr2.3:10154992-10155011 None:intergenic 30.0%
GGATAATATGAACAGAATGA+GGG - chr2.3:10154329-10154348 MS.gene028905:CDS 30.0%
TGAATGTATGATGCCAAATA+AGG + chr2.3:10154827-10154846 None:intergenic 30.0%
TTATTATGCAGGACCTTATT+TGG - chr2.3:10154811-10154830 MS.gene028905:intron 30.0%
TTTCTGTCATAAGATCTGTA+AGG + chr2.3:10154926-10154945 None:intergenic 30.0%
! TTTGAAGCAATTTGCTTAAC+GGG + chr2.3:10153880-10153899 None:intergenic 30.0%
!!! GTTTTAAATTGCACTGATTG+TGG + chr2.3:10154170-10154189 None:intergenic 30.0%
ATTAACCTATCCGGGTTATA+AGG + chr2.3:10154728-10154747 None:intergenic 35.0%
TACATGAAGCTTGAAGTTGT+AGG - chr2.3:10154501-10154520 MS.gene028905:CDS 35.0%
TCTAAGAAGTAATGCTGTGT+TGG - chr2.3:10154880-10154899 MS.gene028905:intron 35.0%
TTATAACCCGGATAGGTTAA+TGG - chr2.3:10154727-10154746 MS.gene028905:intron 35.0%
! CGTATGTTTTCATGGAGATA+AGG - chr2.3:10154398-10154417 MS.gene028905:CDS 35.0%
! TCTGGTACAATGCTTTTACT+GGG - chr2.3:10154547-10154566 MS.gene028905:intron 35.0%
! TTCTGGTACAATGCTTTTAC+TGG - chr2.3:10154546-10154565 MS.gene028905:intron 35.0%
!! ATAGTGCTGACACAATTGAA+GGG - chr2.3:10154451-10154470 MS.gene028905:CDS 35.0%
AAAACATACGCGTCCTTCAA+TGG + chr2.3:10154388-10154407 None:intergenic 40.0%
ACGATTACTTTAGCAGGTTC+TGG - chr2.3:10154529-10154548 MS.gene028905:CDS 40.0%
AGAACATAATGGCGACAACA+AGG - chr2.3:10153768-10153787 MS.gene028905:CDS 40.0%
AGGAACAAATACACAATCGG+AGG - chr2.3:10153800-10153819 MS.gene028905:CDS 40.0%
ATGTGAGATGCCTTATAACC+CGG - chr2.3:10154715-10154734 MS.gene028905:intron 40.0%
ATTGCAGTGCAATGTTGAAG+AGG + chr2.3:10154004-10154023 None:intergenic 40.0%
CAGCAACCTACAGAACATAA+TGG - chr2.3:10153757-10153776 MS.gene028905:CDS 40.0%
CTATGTAAACGACGCTGATA+TGG + chr2.3:10154204-10154223 None:intergenic 40.0%
GAATGAGGGTCTATGTAAGA+AGG - chr2.3:10154343-10154362 MS.gene028905:CDS 40.0%
GTGCTAACGATTACTTTAGC+AGG - chr2.3:10154523-10154542 MS.gene028905:CDS 40.0%
TGGTGTGGTTACGAATAATG+TGG + chr2.3:10154057-10154076 None:intergenic 40.0%
TGTGTGGAAGTTGCAATCAA+AGG - chr2.3:10154753-10154772 MS.gene028905:intron 40.0%
TTATGTTCTGTAGGTTGCTG+CGG + chr2.3:10153757-10153776 None:intergenic 40.0%
TTGTCGCCATTATGTTCTGT+AGG + chr2.3:10153766-10153785 None:intergenic 40.0%
! AAGCAATTTGCTTAACGGGA+AGG + chr2.3:10153876-10153895 None:intergenic 40.0%
! AGTTTGCTCCACAGTTGTTA+GGG + chr2.3:10154092-10154111 None:intergenic 40.0%
! CTGGTACAATGCTTTTACTG+GGG - chr2.3:10154548-10154567 MS.gene028905:intron 40.0%
! GCTTCAAATCGTTCCTTTTG+CGG - chr2.3:10153892-10153911 MS.gene028905:intron 40.0%
! TCCACAGTTGTTAGGGTTTT+GGG + chr2.3:10154085-10154104 None:intergenic 40.0%
!! AAGAAGGTATTATCGACCTG+AGG - chr2.3:10154359-10154378 MS.gene028905:CDS 40.0%
!! CATAGTGCTGACACAATTGA+AGG - chr2.3:10154450-10154469 MS.gene028905:CDS 40.0%
!! TAAGGAGAGAAGGGTTTTGA+GGG + chr2.3:10153851-10153870 None:intergenic 40.0%
ACAGCACCATTAACCTATCC+GGG + chr2.3:10154736-10154755 None:intergenic 45.0%
ACTTACACTTCAACGCGTTC+AGG + chr2.3:10154582-10154601 None:intergenic 45.0%
ACTTCACTCGATTCCGCAAA+AGG + chr2.3:10153908-10153927 None:intergenic 45.0%
AGATGCCTTATAACCCGGAT+AGG - chr2.3:10154720-10154739 MS.gene028905:intron 45.0%
AGGTACCATCCTAAATGCGT+GGG - chr2.3:10154962-10154981 MS.gene028905:intron 45.0%
ATAATGGCGACAACAAGGCA+AGG - chr2.3:10153773-10153792 MS.gene028905:CDS 45.0%
ATTACCTCTAACGACCGTGT+TGG + chr2.3:10153828-10153847 None:intergenic 45.0%
CACAGCACCATTAACCTATC+CGG + chr2.3:10154737-10154756 None:intergenic 45.0%
CTGCCATAACAGCGAAATTG+CGG + chr2.3:10153981-10154000 None:intergenic 45.0%
TAATGGCGACAACAAGGCAA+GGG - chr2.3:10153774-10153793 MS.gene028905:CDS 45.0%
! CAGTTTGCTCCACAGTTGTT+AGG + chr2.3:10154093-10154112 None:intergenic 45.0%
! CCACAGTTGTTAGGGTTTTG+GGG + chr2.3:10154084-10154103 None:intergenic 45.0%
! CCTGCTCAATCTTTTCCACA+CGG + chr2.3:10154311-10154330 None:intergenic 45.0%
! CTCCACAGTTGTTAGGGTTT+TGG + chr2.3:10154086-10154105 None:intergenic 45.0%
! CTGCTCAATCTTTTCCACAC+GGG + chr2.3:10154310-10154329 None:intergenic 45.0%
! GAAGGACGCGTATGTTTTCA+TGG - chr2.3:10154390-10154409 MS.gene028905:CDS 45.0%
! GTAAGGAGAGAAGGGTTTTG+AGG + chr2.3:10153852-10153871 None:intergenic 45.0%
! TGTGTTTTGCTACGCCATAC+TGG - chr2.3:10154264-10154283 MS.gene028905:CDS 45.0%
! TTGCTTAACGGGAAGGTGTA+AGG + chr2.3:10153869-10153888 None:intergenic 45.0%
!! GATAGGTTAATGGTGCTGTG+TGG - chr2.3:10154737-10154756 MS.gene028905:intron 45.0%
!! TTGGTTTGTTCCTGCCAGTA+TGG + chr2.3:10154281-10154300 None:intergenic 45.0%
!! TTTTCCACACGGGCTATGAT+TGG + chr2.3:10154300-10154319 None:intergenic 45.0%
!!! TGTTAGGGTTTTGGGGTAGT+TGG + chr2.3:10154077-10154096 None:intergenic 45.0%
CAAACCAATCATAGCCCGTG+TGG - chr2.3:10154293-10154312 MS.gene028905:CDS 50.0%
CAGCCGCAATTTCGCTGTTA+TGG - chr2.3:10153975-10153994 MS.gene028905:intron 50.0%
CAGGTACCATCCTAAATGCG+TGG - chr2.3:10154961-10154980 MS.gene028905:intron 50.0%
CCCCAAAACCCTAACAACTG+TGG - chr2.3:10154081-10154100 MS.gene028905:CDS 50.0%
CCGTGTGGAAAAGATTGAGC+AGG - chr2.3:10154308-10154327 MS.gene028905:CDS 50.0%
CGAAATTGCGGCTGCAATTG+CGG + chr2.3:10153969-10153988 None:intergenic 50.0%
CGACAACAAGGCAAGGGAAA+AGG - chr2.3:10153780-10153799 MS.gene028905:CDS 50.0%
CGACCTGAGGAAACCATTGA+AGG - chr2.3:10154372-10154391 MS.gene028905:CDS 50.0%
CGTCCTTCAATGGTTTCCTC+AGG + chr2.3:10154378-10154397 None:intergenic 50.0%
GACACACATTGCGGTCATTG+TGG + chr2.3:10154140-10154159 None:intergenic 50.0%
! AAAGGCATGCCCACGCATTT+AGG + chr2.3:10154974-10154993 None:intergenic 50.0%
! GGGAAGGTGTAAGGAGAGAA+GGG + chr2.3:10153860-10153879 None:intergenic 50.0%
! TTTTGCTACGCCATACTGGC+AGG - chr2.3:10154268-10154287 MS.gene028905:CDS 50.0%
GCATGCCCACGCATTTAGGA+TGG + chr2.3:10154970-10154989 None:intergenic 55.0%
GGATGCTGCGACACACATTG+CGG + chr2.3:10154149-10154168 None:intergenic 55.0%
! CGGGAAGGTGTAAGGAGAGA+AGG + chr2.3:10153861-10153880 None:intergenic 55.0%
!! CACAATCGGAGGCACCAACA+CGG - chr2.3:10153811-10153830 MS.gene028905:CDS 55.0%
!!! GGGTTTTGGGGTAGTTGGTG+TGG + chr2.3:10154072-10154091 None:intergenic 55.0%
GGCACCAACACGGTCGTTAG+AGG - chr2.3:10153821-10153840 MS.gene028905:CDS 60.0%
TGCGGCTGCAATTGCGGTTG+CGG + chr2.3:10153963-10153982 None:intergenic 60.0%
GCGGCTGCAATTGCGGTTGC+GGG + chr2.3:10153962-10153981 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 10153749 10155063 10153749 ID=MS.gene028905
chr2.3 mRNA 10153749 10155063 10153749 ID=MS.gene028905.t1;Parent=MS.gene028905
chr2.3 exon 10154970 10155063 10154970 ID=MS.gene028905.t1.exon1;Parent=MS.gene028905.t1
chr2.3 CDS 10154970 10155063 10154970 ID=cds.MS.gene028905.t1;Parent=MS.gene028905.t1
chr2.3 exon 10154217 10154556 10154217 ID=MS.gene028905.t1.exon2;Parent=MS.gene028905.t1
chr2.3 CDS 10154217 10154556 10154217 ID=cds.MS.gene028905.t1;Parent=MS.gene028905.t1
chr2.3 exon 10154038 10154106 10154038 ID=MS.gene028905.t1.exon3;Parent=MS.gene028905.t1
chr2.3 CDS 10154038 10154106 10154038 ID=cds.MS.gene028905.t1;Parent=MS.gene028905.t1
chr2.3 exon 10153749 10153848 10153749 ID=MS.gene028905.t1.exon4;Parent=MS.gene028905.t1
chr2.3 CDS 10153749 10153848 10153749 ID=cds.MS.gene028905.t1;Parent=MS.gene028905.t1
Gene Sequence

>MS.gene028905

ATGCGCCGCAGCAACCTACAGAACATAATGGCGACAACAAGGCAAGGGAAAAGGAACAAATACACAATCGGAGGCACCAACACGGTCGTTAGAGGTAATCCCTCAAAACCCTTCTCTCCTTACACCTTCCCGTTAAGCAAATTGCTTCAAATCGTTCCTTTTGCGGAATCGAGTGAAGTAGATAGTTCAAAAACATGGTTTCAAATTGCACCCGCAACCGCAATTGCAGCCGCAATTTCGCTGTTATGGCAGCCTCTTCAACATTGCACTGCAATTGCGATGTGATCTTCAATCACGTGTGTGTACCACATTATTCGTAACCACACCAACTACCCCAAAACCCTAACAACTGTGGAGCAAACTGAAACTTCTAAAAATTTATTTCACGCCACAATGACCGCAATGTGTGTCGCAGCATCCACAATCAGTGCAATTTAAAACAATATTCAAAACCATATCAGCGTCGTTTACATAGATTATGATTTTGCTTTTTTGTTTTTGTTGCAGCTAAAGACTGTGTTTTGCTACGCCATACTGGCAGGAACAAACCAATCATAGCCCGTGTGGAAAAGATTGAGCAGGATAATATGAACAGAATGAGGGTCTATGTAAGAAGGTATTATCGACCTGAGGAAACCATTGAAGGACGCGTATGTTTTCATGGAGATAAGGAGCTGTTTTTGTCTAATCATTATGATGTTCATAGTGCTGACACAATTGAAGGGAAGTGTTTTGTGCACACTTTGAAGAACTACATGAAGCTTGAAGTTGTAGGTGCTAACGATTACTTTAGCAGGTTCTGGTACAATGCTTTTACTGGGGCTATGACACCTGAACGCGTTGAAGTGTAAGTCTAAACACTGATATTTTTTTCTAGGGGAATTTTGAGTATTTGATAAGTTTTTTTTTTTTTTTTTTTTAAATAAATTTTGTTGATTTTACTTTTATGTTTCGAAGGTTGTGCAAATGTGAGATGCCTTATAACCCGGATAGGTTAATGGTGCTGTGTGGAAGTTGCAATCAAAGGTAAATTGGATTTTGGGTTTATGTATGTATAATGAATTATTATGCAGGACCTTATTTGGCATCATACATTCATTAAAACAAAAAATTTGTTGTATTTACAGAGAATCTAAGAAGTAATGCTGTGTTGGTTTTATGAACCAGTTTATTTCCTTACAGATCTTATGACAGAAATATTTCAATTTCTTGCAGGTACCATCCTAAATGCGTGGGCATGCCTTTTGATGAAGCAATGAAATCAGAAGATTTTAGATTTGTTTGTTCAAAATGTTCACCTGATTTAAAGGATTAG
Protein sequence

>MS.gene028905.t1

MRRSNLQNIMATTRQGKRNKYTIGGTNTVVRAKDCVLLRHTGRNKPIIARVEKIEQDNMNRMRVYVRRYYRPEETIEGRVCFHGDKELFLSNHYDVHSADTIEGKCFVHTLKNYMKLEVVGANDYFSRFWYNAFTGAMTPERVEVLCKCEMPYNPDRLMVLCGSCNQRYHPKCVGMPFDEAMKSEDFRFVCSKCSPDLKD