AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0316080


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0316080 MtrunA17_Chr2g0288361 97.403 77 2 0 1 77 1 77 4.48e-53 159
Msa0316080 MtrunA17_Chr4g0024181 49.333 75 35 2 1 74 1 73 3.57e-20 76.3
Msa0316080 MtrunA17_Chr2g0322831 59.184 49 20 0 27 75 32 80 9.03e-18 70.5
Msa0316080 MtrunA17_Chr5g0396771 42.647 68 36 1 7 74 20 84 7.08e-15 63.2
Msa0316080 MtrunA17_Chr3g0121241 51.111 45 22 0 28 72 99 143 1.78e-12 60.5
Msa0316080 MtrunA17_Chr4g0055981 51.163 43 21 0 29 71 113 155 6.65e-12 58.2
Msa0316080 MtrunA17_Chr7g0275911 51.163 43 21 0 30 72 71 113 1.19e-11 57.8
Msa0316080 MtrunA17_Chr7g0240821 47.727 44 23 0 29 72 59 102 1.20e-11 57.8
Msa0316080 MtrunA17_Chr8g0360111 47.727 44 23 0 29 72 83 126 1.78e-11 57.4
Msa0316080 MtrunA17_Chr4g0070641 44.444 45 25 0 28 72 69 113 1.98e-11 56.2
Msa0316080 MtrunA17_Chr7g0229101 45.455 44 24 0 28 71 29 72 2.60e-11 56.6
Msa0316080 MtrunA17_Chr5g0435101 48.837 43 22 0 29 71 69 111 2.98e-11 56.2
Msa0316080 MtrunA17_Chr7g0228991 46.000 50 24 1 18 67 79 125 6.08e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0316080 AT2G46410.1 63.636 44 16 0 27 70 36 79 1.70e-17 70.5
Msa0316080 AT4G01060.1 50.000 64 29 1 7 70 16 76 5.71e-16 65.9
Msa0316080 AT1G01380.1 56.818 44 19 0 27 70 32 75 1.51e-15 65.1
Msa0316080 AT5G53200.1 52.000 50 24 0 27 76 31 80 2.03e-15 65.5
Msa0316080 AT4G01060.2 60.000 45 18 0 26 70 29 73 2.10e-15 64.3
Msa0316080 AT4G01060.3 60.000 45 18 0 26 70 30 74 2.71e-15 64.3
Msa0316080 AT2G30420.1 36.111 72 43 1 1 72 15 83 1.74e-12 58.2
Msa0316080 AT2G30424.1 50.000 44 22 0 27 70 34 77 4.93e-12 56.6
Msa0316080 AT5G52600.1 45.455 44 24 0 29 72 70 113 1.09e-11 57.8
Msa0316080 AT5G14750.4 43.182 44 25 0 29 72 13 56 2.21e-11 55.8
Msa0316080 AT5G14750.2 43.182 44 25 0 29 72 13 56 2.21e-11 55.8
Msa0316080 AT2G30432.1 44.262 61 31 2 10 70 19 76 4.10e-11 53.9
Msa0316080 AT3G13540.1 52.500 40 19 0 30 69 82 121 8.08e-11 55.8

Find 32 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAACGATATCTTCCTCTTC+TGG 0.165562 2_4:-12908014 None:intergenic
ATATCTTCTGGGGTTCTTCC+AGG 0.255062 2_4:-12908230 None:intergenic
GGATCAATATAATAGGAAAA+AGG 0.355165 2_4:-12908535 None:intergenic
TGCATATGGATCAATATAAT+AGG 0.358516 2_4:-12908542 None:intergenic
CAACGATATCTTCCTCTTCT+GGG 0.371629 2_4:-12908013 None:intergenic
ATAATTTCAAACCATGCATA+TGG 0.386582 2_4:-12908556 None:intergenic
TGTAGATGGCATCTCATTGC+TGG 0.392405 2_4:+12908200 Msa0316080:intron
TTGTTATTACATCATATTTG+TGG 0.396920 2_4:-12908630 None:intergenic
CTCATTGCTGGGAGAATCCC+TGG 0.434907 2_4:+12908212 Msa0316080:CDS
CAGAAGATATTGAAAAGTAT+TGG 0.446559 2_4:+12908243 Msa0316080:CDS
TCAGTTTATGTGTGCAGTGC+AGG 0.449820 2_4:-12907684 None:intergenic
TATCTTCTGGGGTTCTTCCA+GGG 0.463656 2_4:-12908229 None:intergenic
GATGAAACGTGAGGCTGTGC+TGG 0.475255 2_4:+12907983 Msa0316080:CDS
AATGGCCAGTATGTCTCTTC+AGG 0.479277 2_4:+12907772 Msa0316080:CDS
AAGTACCATTCTAAGTTCCT+AGG 0.489489 2_4:+12908314 Msa0316080:three_prime_UTR
TTGTTTAGAAATAGACATGT+AGG 0.497435 2_4:-12907599 None:intergenic
ATATTTGTGGATAAAGATGT+AGG 0.506418 2_4:-12908617 None:intergenic
ATTTGCCTAGGAACTTAGAA+TGG 0.512782 2_4:-12908319 None:intergenic
TGTTTAGATTGGTCGGAAAG+AGG 0.513739 2_4:+12908042 Msa0316080:CDS
TGGTACCTGAAGAGACATAC+TGG 0.523534 2_4:-12907777 None:intergenic
AGGAACTTAGAATGGTACTT+AGG 0.533310 2_4:-12908311 None:intergenic
AATTACACAATAATTTGCCT+AGG 0.552512 2_4:-12908331 None:intergenic
TGTTTAGAAATAGACATGTA+GGG 0.567975 2_4:-12907598 None:intergenic
GTAGATGGCATCTCATTGCT+GGG 0.572643 2_4:+12908201 Msa0316080:intron
ATTATATTGATCCATATGCA+TGG 0.574143 2_4:+12908545 Msa0316080:three_prime_UTR
TATGTGTGCAGTGCAGGCAT+TGG 0.585896 2_4:-12907678 None:intergenic
TATTTGTGGATAAAGATGTA+GGG 0.588008 2_4:-12908616 None:intergenic
CATTGGTATTGAGATAAGCA+TGG 0.590027 2_4:-12907661 None:intergenic
AACGATATCTTCCTCTTCTG+GGG 0.611771 2_4:-12908012 None:intergenic
TATGCAACCACTGCAAACAA+TGG 0.637268 2_4:+12907754 Msa0316080:CDS
ATACTGGCCATTGTTTGCAG+TGG 0.645184 2_4:-12907761 None:intergenic
CTCAGATCAGATGAAACGTG+AGG 0.650176 2_4:+12907974 Msa0316080:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATATATATATATAT+AGG + chr2_4:12907820-12907839 Msa0316080:intron 0.0%
!! TATATATATATATATATATA+GGG + chr2_4:12907819-12907838 Msa0316080:intron 0.0%
!! ATATATATATATATATATAT+AGG + chr2_4:12907820-12907839 Msa0316080:intron 0.0%
!! TATATATATATATATATATA+GGG + chr2_4:12907819-12907838 Msa0316080:intron 0.0%
!! ATATATATATATATACAAGA+TGG - chr2_4:12907814-12907833 None:intergenic 10.0%
!! ATATATATATATATACAAGA+TGG - chr2_4:12907814-12907833 None:intergenic 10.0%
!! TATACAGATTCATATGATTT+GGG - chr2_4:12907938-12907957 None:intergenic 20.0%
!! ATATACAGATTCATATGATT+TGG - chr2_4:12907939-12907958 None:intergenic 20.0%
!! TATATGTTAATTAACTTCGT+TGG + chr2_4:12908083-12908102 Msa0316080:intron 20.0%
!!! AATACTTTTCAATATCTTCT+GGG - chr2_4:12908244-12908263 None:intergenic 20.0%
!!! TTTATATATGCATCTTTTGT+TGG + chr2_4:12908494-12908513 Msa0316080:three_prime_UTR 20.0%
!!! TTGTTATTACATCATATTTG+TGG - chr2_4:12908633-12908652 None:intergenic 20.0%
!! TATACAGATTCATATGATTT+GGG - chr2_4:12907938-12907957 None:intergenic 20.0%
!! ATATACAGATTCATATGATT+TGG - chr2_4:12907939-12907958 None:intergenic 20.0%
!! TATATGTTAATTAACTTCGT+TGG + chr2_4:12908083-12908102 Msa0316080:intron 20.0%
!!! AATACTTTTCAATATCTTCT+GGG - chr2_4:12908244-12908263 None:intergenic 20.0%
!!! TTTATATATGCATCTTTTGT+TGG + chr2_4:12908494-12908513 Msa0316080:three_prime_UTR 20.0%
!!! TTGTTATTACATCATATTTG+TGG - chr2_4:12908633-12908652 None:intergenic 20.0%
! TGTTTAGAAATAGACATGTA+GGG - chr2_4:12907601-12907620 None:intergenic 25.0%
! TTGTTTAGAAATAGACATGT+AGG - chr2_4:12907602-12907621 None:intergenic 25.0%
! TTTGACATGTTAATTGTAGA+TGG + chr2_4:12908186-12908205 Msa0316080:intron 25.0%
!! ATACTTTTCAATATCTTCTG+GGG - chr2_4:12908243-12908262 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG - chr2_4:12908245-12908264 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG + chr2_4:12908243-12908262 Msa0316080:CDS 25.0%
!! AATTACACAATAATTTGCCT+AGG - chr2_4:12908334-12908353 None:intergenic 25.0%
! TTTATCCATCAACAAAAAGT+CGG + chr2_4:12908352-12908371 Msa0316080:three_prime_UTR 25.0%
! GGATCAATATAATAGGAAAA+AGG - chr2_4:12908538-12908557 None:intergenic 25.0%
! TGCATATGGATCAATATAAT+AGG - chr2_4:12908545-12908564 None:intergenic 25.0%
! ATTATATTGATCCATATGCA+TGG + chr2_4:12908545-12908564 Msa0316080:three_prime_UTR 25.0%
! ATAATTTCAAACCATGCATA+TGG - chr2_4:12908559-12908578 None:intergenic 25.0%
! TATTTGTGGATAAAGATGTA+GGG - chr2_4:12908619-12908638 None:intergenic 25.0%
! ATATTTGTGGATAAAGATGT+AGG - chr2_4:12908620-12908639 None:intergenic 25.0%
! TGTTTAGAAATAGACATGTA+GGG - chr2_4:12907601-12907620 None:intergenic 25.0%
! TTGTTTAGAAATAGACATGT+AGG - chr2_4:12907602-12907621 None:intergenic 25.0%
! TTTGACATGTTAATTGTAGA+TGG + chr2_4:12908186-12908205 Msa0316080:intron 25.0%
!! ATACTTTTCAATATCTTCTG+GGG - chr2_4:12908243-12908262 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG - chr2_4:12908245-12908264 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG + chr2_4:12908243-12908262 Msa0316080:CDS 25.0%
!! AATTACACAATAATTTGCCT+AGG - chr2_4:12908334-12908353 None:intergenic 25.0%
! TTTATCCATCAACAAAAAGT+CGG + chr2_4:12908352-12908371 Msa0316080:three_prime_UTR 25.0%
! GGATCAATATAATAGGAAAA+AGG - chr2_4:12908538-12908557 None:intergenic 25.0%
! TGCATATGGATCAATATAAT+AGG - chr2_4:12908545-12908564 None:intergenic 25.0%
! ATTATATTGATCCATATGCA+TGG + chr2_4:12908545-12908564 Msa0316080:three_prime_UTR 25.0%
! ATAATTTCAAACCATGCATA+TGG - chr2_4:12908559-12908578 None:intergenic 25.0%
! TATTTGTGGATAAAGATGTA+GGG - chr2_4:12908619-12908638 None:intergenic 25.0%
! ATATTTGTGGATAAAGATGT+AGG - chr2_4:12908620-12908639 None:intergenic 25.0%
! AGATTCATATGATTTGGGAA+GGG - chr2_4:12907933-12907952 None:intergenic 30.0%
CGTTGCAAAAATGTTTAGAT+TGG + chr2_4:12908031-12908050 Msa0316080:CDS 30.0%
GCAAAAATGTTTAGATTGGT+CGG + chr2_4:12908035-12908054 Msa0316080:CDS 30.0%
TCATGTGTTTGTATTGTAGA+AGG + chr2_4:12908148-12908167 Msa0316080:intron 30.0%
! ATATATGCATCTTTTGTTGG+TGG + chr2_4:12908497-12908516 Msa0316080:three_prime_UTR 30.0%
! AGATTCATATGATTTGGGAA+GGG - chr2_4:12907933-12907952 None:intergenic 30.0%
CGTTGCAAAAATGTTTAGAT+TGG + chr2_4:12908031-12908050 Msa0316080:CDS 30.0%
GCAAAAATGTTTAGATTGGT+CGG + chr2_4:12908035-12908054 Msa0316080:CDS 30.0%
TCATGTGTTTGTATTGTAGA+AGG + chr2_4:12908148-12908167 Msa0316080:intron 30.0%
! ATATATGCATCTTTTGTTGG+TGG + chr2_4:12908497-12908516 Msa0316080:three_prime_UTR 30.0%
! CATTGGTATTGAGATAAGCA+TGG - chr2_4:12907664-12907683 None:intergenic 35.0%
!!! CACTCATGATTTTTTGAGCT+GGG - chr2_4:12907726-12907745 None:intergenic 35.0%
!!! TCACTCATGATTTTTTGAGC+TGG - chr2_4:12907727-12907746 None:intergenic 35.0%
! GATTCATATGATTTGGGAAG+GGG - chr2_4:12907932-12907951 None:intergenic 35.0%
! CAGATTCATATGATTTGGGA+AGG - chr2_4:12907934-12907953 None:intergenic 35.0%
AGGAACTTAGAATGGTACTT+AGG - chr2_4:12908314-12908333 None:intergenic 35.0%
AAGTACCATTCTAAGTTCCT+AGG + chr2_4:12908314-12908333 Msa0316080:three_prime_UTR 35.0%
ATTTGCCTAGGAACTTAGAA+TGG - chr2_4:12908322-12908341 None:intergenic 35.0%
! CATTGGTATTGAGATAAGCA+TGG - chr2_4:12907664-12907683 None:intergenic 35.0%
!!! CACTCATGATTTTTTGAGCT+GGG - chr2_4:12907726-12907745 None:intergenic 35.0%
!!! TCACTCATGATTTTTTGAGC+TGG - chr2_4:12907727-12907746 None:intergenic 35.0%
! GATTCATATGATTTGGGAAG+GGG - chr2_4:12907932-12907951 None:intergenic 35.0%
! CAGATTCATATGATTTGGGA+AGG - chr2_4:12907934-12907953 None:intergenic 35.0%
AGGAACTTAGAATGGTACTT+AGG - chr2_4:12908314-12908333 None:intergenic 35.0%
AAGTACCATTCTAAGTTCCT+AGG + chr2_4:12908314-12908333 Msa0316080:three_prime_UTR 35.0%
ATTTGCCTAGGAACTTAGAA+TGG - chr2_4:12908322-12908341 None:intergenic 35.0%
TATGCAACCACTGCAAACAA+TGG + chr2_4:12907754-12907773 Msa0316080:CDS 40.0%
ACAAGATGGTCAACTTGAAG+TGG - chr2_4:12907800-12907819 None:intergenic 40.0%
AACGATATCTTCCTCTTCTG+GGG - chr2_4:12908015-12908034 None:intergenic 40.0%
CAACGATATCTTCCTCTTCT+GGG - chr2_4:12908016-12908035 None:intergenic 40.0%
! TGTTTAGATTGGTCGGAAAG+AGG + chr2_4:12908042-12908061 Msa0316080:CDS 40.0%
ATCAAGTTTGCGCAAATGCA+AGG - chr2_4:12908115-12908134 None:intergenic 40.0%
!!! CTCTACCGACTTTTTGTTGA+TGG - chr2_4:12908360-12908379 None:intergenic 40.0%
TATGCAACCACTGCAAACAA+TGG + chr2_4:12907754-12907773 Msa0316080:CDS 40.0%
ACAAGATGGTCAACTTGAAG+TGG - chr2_4:12907800-12907819 None:intergenic 40.0%
AACGATATCTTCCTCTTCTG+GGG - chr2_4:12908015-12908034 None:intergenic 40.0%
CAACGATATCTTCCTCTTCT+GGG - chr2_4:12908016-12908035 None:intergenic 40.0%
! TGTTTAGATTGGTCGGAAAG+AGG + chr2_4:12908042-12908061 Msa0316080:CDS 40.0%
ATCAAGTTTGCGCAAATGCA+AGG - chr2_4:12908115-12908134 None:intergenic 40.0%
!!! CTCTACCGACTTTTTGTTGA+TGG - chr2_4:12908360-12908379 None:intergenic 40.0%
TCAGTTTATGTGTGCAGTGC+AGG - chr2_4:12907687-12907706 None:intergenic 45.0%
ATACTGGCCATTGTTTGCAG+TGG - chr2_4:12907764-12907783 None:intergenic 45.0%
AATGGCCAGTATGTCTCTTC+AGG + chr2_4:12907772-12907791 Msa0316080:CDS 45.0%
TGGTACCTGAAGAGACATAC+TGG - chr2_4:12907780-12907799 None:intergenic 45.0%
CTCAGATCAGATGAAACGTG+AGG + chr2_4:12907974-12907993 Msa0316080:intron 45.0%
GCAACGATATCTTCCTCTTC+TGG - chr2_4:12908017-12908036 None:intergenic 45.0%
GCATTTGCGCAAACTTGATG+AGG + chr2_4:12908116-12908135 Msa0316080:intron 45.0%
TGTAGATGGCATCTCATTGC+TGG + chr2_4:12908200-12908219 Msa0316080:intron 45.0%
GTAGATGGCATCTCATTGCT+GGG + chr2_4:12908201-12908220 Msa0316080:intron 45.0%
!! TATCTTCTGGGGTTCTTCCA+GGG - chr2_4:12908232-12908251 None:intergenic 45.0%
!! ATATCTTCTGGGGTTCTTCC+AGG - chr2_4:12908233-12908252 None:intergenic 45.0%
TCAGTTTATGTGTGCAGTGC+AGG - chr2_4:12907687-12907706 None:intergenic 45.0%
ATACTGGCCATTGTTTGCAG+TGG - chr2_4:12907764-12907783 None:intergenic 45.0%
AATGGCCAGTATGTCTCTTC+AGG + chr2_4:12907772-12907791 Msa0316080:CDS 45.0%
TGGTACCTGAAGAGACATAC+TGG - chr2_4:12907780-12907799 None:intergenic 45.0%
CTCAGATCAGATGAAACGTG+AGG + chr2_4:12907974-12907993 Msa0316080:intron 45.0%
GCAACGATATCTTCCTCTTC+TGG - chr2_4:12908017-12908036 None:intergenic 45.0%
GCATTTGCGCAAACTTGATG+AGG + chr2_4:12908116-12908135 Msa0316080:intron 45.0%
TGTAGATGGCATCTCATTGC+TGG + chr2_4:12908200-12908219 Msa0316080:intron 45.0%
GTAGATGGCATCTCATTGCT+GGG + chr2_4:12908201-12908220 Msa0316080:intron 45.0%
!! TATCTTCTGGGGTTCTTCCA+GGG - chr2_4:12908232-12908251 None:intergenic 45.0%
!! ATATCTTCTGGGGTTCTTCC+AGG - chr2_4:12908233-12908252 None:intergenic 45.0%
TATGTGTGCAGTGCAGGCAT+TGG - chr2_4:12907681-12907700 None:intergenic 50.0%
! GCTGGAATTTTCCCCAGAAG+AGG + chr2_4:12908001-12908020 Msa0316080:CDS 50.0%
TATGTGTGCAGTGCAGGCAT+TGG - chr2_4:12907681-12907700 None:intergenic 50.0%
! GCTGGAATTTTCCCCAGAAG+AGG + chr2_4:12908001-12908020 Msa0316080:CDS 50.0%
GATGAAACGTGAGGCTGTGC+TGG + chr2_4:12907983-12908002 Msa0316080:CDS 55.0%
CTCATTGCTGGGAGAATCCC+TGG + chr2_4:12908212-12908231 Msa0316080:CDS 55.0%
GATGAAACGTGAGGCTGTGC+TGG + chr2_4:12907983-12908002 Msa0316080:CDS 55.0%
CTCATTGCTGGGAGAATCCC+TGG + chr2_4:12908212-12908231 Msa0316080:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 12907592 12908771 12907592 ID=Msa0316080;Name=Msa0316080
chr2_4 mRNA 12907592 12908771 12907592 ID=Msa0316080-mRNA-1;Parent=Msa0316080;Name=Msa0316080-mRNA-1;_AED=0.07;_eAED=0.07;_QI=147|1|1|1|1|1|3|473|77
chr2_4 exon 12907592 12907793 12907592 ID=Msa0316080-mRNA-1:exon:4906;Parent=Msa0316080-mRNA-1
chr2_4 exon 12907979 12908063 12907979 ID=Msa0316080-mRNA-1:exon:4907;Parent=Msa0316080-mRNA-1
chr2_4 exon 12908205 12908771 12908205 ID=Msa0316080-mRNA-1:exon:4908;Parent=Msa0316080-mRNA-1
chr2_4 five_prime_UTR 12907592 12907738 12907592 ID=Msa0316080-mRNA-1:five_prime_utr;Parent=Msa0316080-mRNA-1
chr2_4 CDS 12907739 12907793 12907739 ID=Msa0316080-mRNA-1:cds;Parent=Msa0316080-mRNA-1
chr2_4 CDS 12907979 12908063 12907979 ID=Msa0316080-mRNA-1:cds;Parent=Msa0316080-mRNA-1
chr2_4 CDS 12908205 12908298 12908205 ID=Msa0316080-mRNA-1:cds;Parent=Msa0316080-mRNA-1
chr2_4 three_prime_UTR 12908299 12908771 12908299 ID=Msa0316080-mRNA-1:three_prime_utr;Parent=Msa0316080-mRNA-1
Gene Sequence

>Msa0316080

ATGAGTGACTCGAAGTATGCAACCACTGCAAACAATGGCCAGTATGTCTCTTCAGATCAGATGAAACGTGAGGCTGTGCTGGAATTTTCCCCAGAAGAGGAAGATATCGTTGCAAAAATGTTTAGATTGGTCGGAAAGAGATGGCATCTCATTGCTGGGAGAATCCCTGGAAGAACCCCAGAAGATATTGAAAAGTATTGGACATCAAAGTTCTCATCATCAACTGCATGCTAA

Protein sequence

>Msa0316080

MSDSKYATTANNGQYVSSDQMKREAVLEFSPEEEDIVAKMFRLVGKRWHLIAGRIPGRTPEDIEKYWTSKFSSSTAC*