AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1087380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1087380 MtrunA17_Chr2g0284621 94.891 137 7 0 1 137 1 137 4.16e-98 277
Msa1087380 MtrunA17_Chr4g0020691 86.861 137 18 0 1 137 1 137 6.36e-89 254
Msa1087380 MtrunA17_Chr8g0371681 54.464 112 48 2 10 119 13 123 2.24e-38 126
Msa1087380 MtrunA17_Chr5g0405631 55.556 108 45 2 10 115 30 136 4.38e-35 118
Msa1087380 MtrunA17_Chr5g0406281 40.179 112 66 1 12 123 75 185 4.16e-27 99.4
Msa1087380 MtrunA17_Chr7g0258361 28.448 116 60 2 18 110 55 170 7.72e-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
Msa1087380 AT2G21045.1 64.029 139 46 3 1 137 30 166 2.76e-63 191
Msa1087380 AT5G66170.3 44.628 121 64 2 1 119 5 124 3.09e-33 114
Msa1087380 AT2G17850.1 50.000 112 53 2 10 119 32 142 4.02e-33 114
Msa1087380 AT5G66170.2 44.715 123 63 3 1 119 5 126 9.67e-32 110
Msa1087380 AT5G66040.1 46.296 108 57 1 12 119 10 116 6.61e-28 100
Msa1087380 AT4G35770.1 38.983 118 66 2 11 128 71 182 1.45e-26 98.2
Msa1087380 AT2G17850.3 38.889 144 53 3 10 119 32 174 3.05e-26 97.8
Msa1087380 AT2G17850.2 50.588 85 39 2 10 92 32 115 1.03e-23 89.7
Msa1087380 AT5G66170.1 43.878 98 52 2 1 96 5 101 2.20e-23 89.0
Msa1087380 AT4G35770.3 39.785 93 55 1 11 103 71 162 4.09e-19 79.0
Msa1087380 AT4G35770.2 42.353 85 48 1 12 96 72 155 8.38e-19 77.8
Msa1087380 AT4G35770.5 40.541 74 43 1 12 85 72 144 1.43e-14 66.6
Msa1087380 AT5G66040.2 45.763 59 32 0 61 119 3 61 6.21e-13 60.1

Find 30 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTGTTTGGAACATATA+GGG 0.248410 7_3:+67864 None:intergenic
GCAACTTGGTTAACAAAATC+AGG 0.314294 7_3:+67690 None:intergenic
AGATATTACCTTCTTCTGTT+TGG 0.320745 7_3:+67853 None:intergenic
TTTGAACACTTACTCCTTTG+TGG 0.354183 7_3:+68204 None:intergenic
TGGGTGGACGCTGGATTTGC+AGG 0.388509 7_3:-67303 Msa1087380:CDS
TTCTTCTGTTTGGAACATAT+AGG 0.391220 7_3:+67863 None:intergenic
TTAATTCAGGCTTGCAATAG+TGG 0.393156 7_3:-67549 Msa1087380:intron
AGATGAATGTAATAGATCTT+TGG 0.398666 7_3:+68067 None:intergenic
AAAGATCTATTACATTCATC+TGG 0.432420 7_3:-68065 Msa1087380:CDS
TTTGGCAGCATGGACATCTA+AGG 0.433360 7_3:+68085 None:intergenic
GGGAGGCTATTCTGCGTGGG+TGG 0.453900 7_3:-67319 Msa1087380:CDS
GTCATAGACTTACTGAATCA+TGG 0.464191 7_3:+67496 None:intergenic
TATATGTTCCAAACAGAAGA+AGG 0.504174 7_3:-67861 Msa1087380:intron
CTTCTGTTTGGAACATATAG+GGG 0.513278 7_3:+67865 None:intergenic
TCTTACATATTGCTGCAACT+TGG 0.515579 7_3:+67676 None:intergenic
CATTAATAGCATTCTCAACA+TGG 0.531780 7_3:+67889 None:intergenic
ATTTCAACATATTGTGAACA+TGG 0.543412 7_3:-67343 Msa1087380:CDS
TATTCTGCGTGGGTGGACGC+TGG 0.551007 7_3:-67312 Msa1087380:CDS
GTAATAGATCTTTGGCAGCA+TGG 0.556298 7_3:+68075 None:intergenic
TTTCAACATATTGTGAACAT+GGG 0.587874 7_3:-67342 Msa1087380:CDS
CATATATATAACATTATGGA+CGG 0.597708 7_3:+67238 None:intergenic
GTTACAATTATCTTGATGTG+AGG 0.616591 7_3:-68043 Msa1087380:intron
GAAAATAATGGACTCCACAA+AGG 0.616932 7_3:-68218 None:intergenic
GAGTGAGGATCACTTAGTTG+TGG 0.619130 7_3:-67655 Msa1087380:intron
ATTCAGGCTTGCAATAGTGG+AGG 0.624070 7_3:-67546 Msa1087380:intron
CAACATATTGTGAACATGGG+GGG 0.627212 7_3:-67339 Msa1087380:CDS
TGAATCATGGAGATCAACGC+AGG 0.638826 7_3:+67509 None:intergenic
TGCAGCAATATGTAAGAGTG+AGG 0.640119 7_3:-67670 Msa1087380:CDS
TTCAACATATTGTGAACATG+GGG 0.642487 7_3:-67341 Msa1087380:CDS
TCAACATATTGTGAACATGG+GGG 0.699731 7_3:-67340 Msa1087380:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATGTAACATAATATTGAA+AGG + chr7_3:67291-67310 None:intergenic 15.0%
!! TTTCAATATTATGTTACATA+TGG - chr7_3:67290-67309 Msa1087380:CDS 15.0%
!!! TTATGTTCTAGAAAATTAAA+AGG + chr7_3:67839-67858 None:intergenic 15.0%
!! ATATGTAACATAATATTGAA+AGG + chr7_3:67291-67310 None:intergenic 15.0%
!! TTTCAATATTATGTTACATA+TGG - chr7_3:67290-67309 Msa1087380:CDS 15.0%
!!! TTATGTTCTAGAAAATTAAA+AGG + chr7_3:67839-67858 None:intergenic 15.0%
!!! CCTAATTCTTTTAAAATTTG+AGG + chr7_3:68001-68020 None:intergenic 20.0%
!!! CCTCAAATTTTAAAAGAATT+AGG - chr7_3:67998-68017 Msa1087380:intron 20.0%
!!! CCTAATTCTTTTAAAATTTG+AGG + chr7_3:68001-68020 None:intergenic 20.0%
!!! CCTCAAATTTTAAAAGAATT+AGG - chr7_3:67998-68017 Msa1087380:intron 20.0%
! AGATGAATGTAATAGATCTT+TGG + chr7_3:67398-67417 None:intergenic 25.0%
! AAAGATCTATTACATTCATC+TGG - chr7_3:67397-67416 Msa1087380:intron 25.0%
! AAATTACAAATGATCGAAGA+AGG + chr7_3:67476-67495 None:intergenic 25.0%
!! CGATCATTTGTAATTTTCAA+AGG - chr7_3:67480-67499 Msa1087380:intron 25.0%
! ATATGCAAGCATCATAAAAT+AGG - chr7_3:67863-67882 Msa1087380:CDS 25.0%
! TAATGGAGTACAATTAATTC+AGG - chr7_3:67900-67919 Msa1087380:CDS 25.0%
!! AAAGCATTTGTAATATGATG+TGG - chr7_3:68085-68104 Msa1087380:CDS 25.0%
! ATTTCAACATATTGTGAACA+TGG - chr7_3:68119-68138 Msa1087380:intron 25.0%
! TTTCAACATATTGTGAACAT+GGG - chr7_3:68120-68139 Msa1087380:intron 25.0%
! AGATGAATGTAATAGATCTT+TGG + chr7_3:67398-67417 None:intergenic 25.0%
! AAAGATCTATTACATTCATC+TGG - chr7_3:67397-67416 Msa1087380:intron 25.0%
! AAATTACAAATGATCGAAGA+AGG + chr7_3:67476-67495 None:intergenic 25.0%
!! CGATCATTTGTAATTTTCAA+AGG - chr7_3:67480-67499 Msa1087380:intron 25.0%
! ATATGCAAGCATCATAAAAT+AGG - chr7_3:67863-67882 Msa1087380:CDS 25.0%
! TAATGGAGTACAATTAATTC+AGG - chr7_3:67900-67919 Msa1087380:CDS 25.0%
!! AAAGCATTTGTAATATGATG+TGG - chr7_3:68085-68104 Msa1087380:CDS 25.0%
! ATTTCAACATATTGTGAACA+TGG - chr7_3:68119-68138 Msa1087380:intron 25.0%
! TTTCAACATATTGTGAACAT+GGG - chr7_3:68120-68139 Msa1087380:intron 25.0%
GTTACAATTATCTTGATGTG+AGG - chr7_3:67419-67438 Msa1087380:intron 30.0%
TGATGTGAGGTAATTAACAA+AGG - chr7_3:67432-67451 Msa1087380:intron 30.0%
AAATGATCGAAGAAGGAAAT+TGG + chr7_3:67469-67488 None:intergenic 30.0%
GAAAGAAAATGACTTCAGTT+AGG + chr7_3:67510-67529 None:intergenic 30.0%
CATTAATAGCATTCTCAACA+TGG + chr7_3:67576-67595 None:intergenic 30.0%
! TCTTCTGTTTGGAACATATA+GGG + chr7_3:67601-67620 None:intergenic 30.0%
! TTCTTCTGTTTGGAACATAT+AGG + chr7_3:67602-67621 None:intergenic 30.0%
TATATGTTCCAAACAGAAGA+AGG - chr7_3:67601-67620 Msa1087380:intron 30.0%
AGATATTACCTTCTTCTGTT+TGG + chr7_3:67612-67631 None:intergenic 30.0%
ATGTATTCCAAATGATCAAC+AGG - chr7_3:67736-67755 Msa1087380:intron 30.0%
TTCAACATATTGTGAACATG+GGG - chr7_3:68121-68140 Msa1087380:intron 30.0%
GTTACAATTATCTTGATGTG+AGG - chr7_3:67419-67438 Msa1087380:intron 30.0%
TGATGTGAGGTAATTAACAA+AGG - chr7_3:67432-67451 Msa1087380:intron 30.0%
AAATGATCGAAGAAGGAAAT+TGG + chr7_3:67469-67488 None:intergenic 30.0%
GAAAGAAAATGACTTCAGTT+AGG + chr7_3:67510-67529 None:intergenic 30.0%
CATTAATAGCATTCTCAACA+TGG + chr7_3:67576-67595 None:intergenic 30.0%
! TCTTCTGTTTGGAACATATA+GGG + chr7_3:67601-67620 None:intergenic 30.0%
! TTCTTCTGTTTGGAACATAT+AGG + chr7_3:67602-67621 None:intergenic 30.0%
TATATGTTCCAAACAGAAGA+AGG - chr7_3:67601-67620 Msa1087380:intron 30.0%
AGATATTACCTTCTTCTGTT+TGG + chr7_3:67612-67631 None:intergenic 30.0%
ATGTATTCCAAATGATCAAC+AGG - chr7_3:67736-67755 Msa1087380:intron 30.0%
TTCAACATATTGTGAACATG+GGG - chr7_3:68121-68140 Msa1087380:intron 30.0%
TTTGAACACTTACTCCTTTG+TGG + chr7_3:67261-67280 None:intergenic 35.0%
!! TTCTTTTGCCCCTTTTGTTT+AGG - chr7_3:67527-67546 Msa1087380:CDS 35.0%
TCAACTGACCTAAACAAAAG+GGG + chr7_3:67538-67557 None:intergenic 35.0%
CTCAACTGACCTAAACAAAA+GGG + chr7_3:67539-67558 None:intergenic 35.0%
! CTTCTGTTTGGAACATATAG+GGG + chr7_3:67600-67619 None:intergenic 35.0%
ATTCCAAATGATCAACAGGA+AGG - chr7_3:67740-67759 Msa1087380:intron 35.0%
TTCCAAATGATCAACAGGAA+GGG - chr7_3:67741-67760 Msa1087380:intron 35.0%
GCAACTTGGTTAACAAAATC+AGG + chr7_3:67775-67794 None:intergenic 35.0%
TCTTACATATTGCTGCAACT+TGG + chr7_3:67789-67808 None:intergenic 35.0%
!! AGGTTGATGTGTGACTATAA+TGG - chr7_3:67883-67902 Msa1087380:CDS 35.0%
TTAATTCAGGCTTGCAATAG+TGG - chr7_3:67913-67932 Msa1087380:CDS 35.0%
GTCATAGACTTACTGAATCA+TGG + chr7_3:67969-67988 None:intergenic 35.0%
TAATATGATGTGGTAAACGC+AGG - chr7_3:68095-68114 Msa1087380:CDS 35.0%
AATATGATGTGGTAAACGCA+GGG - chr7_3:68096-68115 Msa1087380:CDS 35.0%
TCAACATATTGTGAACATGG+GGG - chr7_3:68122-68141 Msa1087380:intron 35.0%
TTTGAACACTTACTCCTTTG+TGG + chr7_3:67261-67280 None:intergenic 35.0%
!! TTCTTTTGCCCCTTTTGTTT+AGG - chr7_3:67527-67546 Msa1087380:CDS 35.0%
TCAACTGACCTAAACAAAAG+GGG + chr7_3:67538-67557 None:intergenic 35.0%
CTCAACTGACCTAAACAAAA+GGG + chr7_3:67539-67558 None:intergenic 35.0%
! CTTCTGTTTGGAACATATAG+GGG + chr7_3:67600-67619 None:intergenic 35.0%
ATTCCAAATGATCAACAGGA+AGG - chr7_3:67740-67759 Msa1087380:intron 35.0%
TTCCAAATGATCAACAGGAA+GGG - chr7_3:67741-67760 Msa1087380:intron 35.0%
GCAACTTGGTTAACAAAATC+AGG + chr7_3:67775-67794 None:intergenic 35.0%
TCTTACATATTGCTGCAACT+TGG + chr7_3:67789-67808 None:intergenic 35.0%
!! AGGTTGATGTGTGACTATAA+TGG - chr7_3:67883-67902 Msa1087380:CDS 35.0%
TTAATTCAGGCTTGCAATAG+TGG - chr7_3:67913-67932 Msa1087380:CDS 35.0%
GTCATAGACTTACTGAATCA+TGG + chr7_3:67969-67988 None:intergenic 35.0%
TAATATGATGTGGTAAACGC+AGG - chr7_3:68095-68114 Msa1087380:CDS 35.0%
AATATGATGTGGTAAACGCA+GGG - chr7_3:68096-68115 Msa1087380:CDS 35.0%
TCAACATATTGTGAACATGG+GGG - chr7_3:68122-68141 Msa1087380:intron 35.0%
GTAATAGATCTTTGGCAGCA+TGG + chr7_3:67390-67409 None:intergenic 40.0%
CCTCAACTGACCTAAACAAA+AGG + chr7_3:67540-67559 None:intergenic 40.0%
!! CCTTTTGTTTAGGTCAGTTG+AGG - chr7_3:67537-67556 Msa1087380:CDS 40.0%
TGCAGCAATATGTAAGAGTG+AGG - chr7_3:67792-67811 Msa1087380:intron 40.0%
CAACATATTGTGAACATGGG+GGG - chr7_3:68123-68142 Msa1087380:intron 40.0%
GTAATAGATCTTTGGCAGCA+TGG + chr7_3:67390-67409 None:intergenic 40.0%
CCTCAACTGACCTAAACAAA+AGG + chr7_3:67540-67559 None:intergenic 40.0%
!! CCTTTTGTTTAGGTCAGTTG+AGG - chr7_3:67537-67556 Msa1087380:CDS 40.0%
TGCAGCAATATGTAAGAGTG+AGG - chr7_3:67792-67811 Msa1087380:intron 40.0%
CAACATATTGTGAACATGGG+GGG - chr7_3:68123-68142 Msa1087380:intron 40.0%
TTTGGCAGCATGGACATCTA+AGG + chr7_3:67380-67399 None:intergenic 45.0%
CACCCTTCCTGTTGATCATT+TGG + chr7_3:67746-67765 None:intergenic 45.0%
GAGTGAGGATCACTTAGTTG+TGG - chr7_3:67807-67826 Msa1087380:intron 45.0%
ATTCAGGCTTGCAATAGTGG+AGG - chr7_3:67916-67935 Msa1087380:CDS 45.0%
TGAATCATGGAGATCAACGC+AGG + chr7_3:67956-67975 None:intergenic 45.0%
TTTGGCAGCATGGACATCTA+AGG + chr7_3:67380-67399 None:intergenic 45.0%
CACCCTTCCTGTTGATCATT+TGG + chr7_3:67746-67765 None:intergenic 45.0%
GAGTGAGGATCACTTAGTTG+TGG - chr7_3:67807-67826 Msa1087380:intron 45.0%
ATTCAGGCTTGCAATAGTGG+AGG - chr7_3:67916-67935 Msa1087380:CDS 45.0%
TGAATCATGGAGATCAACGC+AGG + chr7_3:67956-67975 None:intergenic 45.0%
CATATTGTGAACATGGGGGG+AGG - chr7_3:68126-68145 Msa1087380:intron 50.0%
CATATTGTGAACATGGGGGG+AGG - chr7_3:68126-68145 Msa1087380:intron 50.0%
!! GCTGTTTTGAGCTCGTCTGC+AGG + chr7_3:68195-68214 None:intergenic 55.0%
!! GCTGTTTTGAGCTCGTCTGC+AGG + chr7_3:68195-68214 None:intergenic 55.0%
TATTCTGCGTGGGTGGACGC+TGG - chr7_3:68150-68169 Msa1087380:intron 60.0%
TGGGTGGACGCTGGATTTGC+AGG - chr7_3:68159-68178 Msa1087380:intron 60.0%
TATTCTGCGTGGGTGGACGC+TGG - chr7_3:68150-68169 Msa1087380:intron 60.0%
TGGGTGGACGCTGGATTTGC+AGG - chr7_3:68159-68178 Msa1087380:intron 60.0%
TGGGGGGAGGCTATTCTGCG+TGG - chr7_3:68139-68158 Msa1087380:intron 65.0%
GGGGGGAGGCTATTCTGCGT+GGG - chr7_3:68140-68159 Msa1087380:intron 65.0%
GGGAGGCTATTCTGCGTGGG+TGG - chr7_3:68143-68162 Msa1087380:intron 65.0%
TGGGGGGAGGCTATTCTGCG+TGG - chr7_3:68139-68158 Msa1087380:intron 65.0%
GGGGGGAGGCTATTCTGCGT+GGG - chr7_3:68140-68159 Msa1087380:intron 65.0%
GGGAGGCTATTCTGCGTGGG+TGG - chr7_3:68143-68162 Msa1087380:intron 65.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 67251 68233 67251 ID=Msa1087380;Name=Msa1087380
chr7_3 mRNA 67251 68233 67251 ID=Msa1087380-mRNA-1;Parent=Msa1087380;Name=Msa1087380-mRNA-1;_AED=0.30;_eAED=0.31;_QI=0|0|0|0.83|1|1|6|0|137
chr7_3 exon 68217 68233 68217 ID=Msa1087380-mRNA-1:exon:38;Parent=Msa1087380-mRNA-1
chr7_3 exon 68044 68124 68044 ID=Msa1087380-mRNA-1:exon:37;Parent=Msa1087380-mRNA-1
chr7_3 exon 67862 67935 67862 ID=Msa1087380-mRNA-1:exon:36;Parent=Msa1087380-mRNA-1
chr7_3 exon 67656 67726 67656 ID=Msa1087380-mRNA-1:exon:35;Parent=Msa1087380-mRNA-1
chr7_3 exon 67509 67562 67509 ID=Msa1087380-mRNA-1:exon:34;Parent=Msa1087380-mRNA-1
chr7_3 exon 67251 67367 67251 ID=Msa1087380-mRNA-1:exon:33;Parent=Msa1087380-mRNA-1
chr7_3 CDS 68217 68233 68217 ID=Msa1087380-mRNA-1:cds;Parent=Msa1087380-mRNA-1
chr7_3 CDS 68044 68124 68044 ID=Msa1087380-mRNA-1:cds;Parent=Msa1087380-mRNA-1
chr7_3 CDS 67862 67935 67862 ID=Msa1087380-mRNA-1:cds;Parent=Msa1087380-mRNA-1
chr7_3 CDS 67656 67726 67656 ID=Msa1087380-mRNA-1:cds;Parent=Msa1087380-mRNA-1
chr7_3 CDS 67509 67562 67509 ID=Msa1087380-mRNA-1:cds;Parent=Msa1087380-mRNA-1
chr7_3 CDS 67251 67367 67251 ID=Msa1087380-mRNA-1:cds;Parent=Msa1087380-mRNA-1
Gene Sequence

>Msa1087380

ATGGACTCCACAAAGGATCATCAAAATGTTGTTACCTTAGATGTCCATGCTGCCAAAGATCTATTACATTCATCTGGTTACAATTATCTTGATGTGAGGTCAGTTGAGGAATTCAATAAAAGCCATGTTGAGAATGCTATTAATGTCCCCTATATGTTCCAAACAGAAGAAGGAAGGGTGAAAAATCCTGATTTTGTTAACCAAGTTGCAGCAATATGTAAGAGTGAGGATCACTTAGTTGTGGCTTGCAATAGTGGAGGAAGATCAAGTCAAGCCTGCGTTGATCTCCATGATTCAGGATTTCAACATATTGTGAACATGGGGGGAGGCTATTCTGCGTGGGTGGACGCTGGATTTGCAGGTGATGACAAGCCTGCAGACGAGCTCAAAACAGCTTGCAAGTTCCGTCCATAA

Protein sequence

>Msa1087380

MDSTKDHQNVVTLDVHAAKDLLHSSGYNYLDVRSVEEFNKSHVENAINVPYMFQTEEGRVKNPDFVNQVAAICKSEDHLVVACNSGGRSSQACVDLHDSGFQHIVNMGGGYSAWVDAGFAGDDKPADELKTACKFRP*