AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0331780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0331780 MtrunA17_Chr2g0322221 94.872 117 3 1 1 114 1 117 2.26e-72 214
Msa0331780 MtrunA17_Chr4g0025361 61.607 112 36 4 3 114 1 105 4.00e-29 103
Msa0331780 MtrunA17_Chr4g0063931 73.469 49 13 0 9 57 11 59 4.55e-20 81.3
Msa0331780 MtrunA17_Chr4g0011841 69.091 55 15 1 14 68 25 77 5.48e-19 79.0
Msa0331780 MtrunA17_Chr5g0413381 68.627 51 16 0 12 62 12 62 7.39e-19 78.2
Msa0331780 MtrunA17_Chr4g0056521 60.656 61 22 1 8 68 14 72 1.04e-17 75.5
Msa0331780 MtrunA17_Chr5g0419871 55.102 49 21 1 1 49 7 54 5.41e-14 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0331780 AT1G08465.1 47.863 117 48 5 1 114 1 107 5.15e-24 91.7
Msa0331780 AT2G26580.2 68.333 60 17 2 3 62 1 58 2.21e-20 81.6
Msa0331780 AT2G26580.1 68.333 60 17 2 3 62 1 58 2.21e-20 81.6
Msa0331780 AT4G00180.1 59.615 52 21 0 8 59 19 70 1.40e-15 70.9
Msa0331780 AT2G45190.1 57.692 52 22 0 8 59 19 70 1.42e-13 65.1
Msa0331780 AT1G23420.1 59.574 47 19 0 13 59 20 66 7.20e-13 63.2
Msa0331780 AT1G23420.2 59.574 47 19 0 13 59 51 97 1.13e-12 63.2

Find 34 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGACGAATTGGAGGAGTTCT+AGG 0.259388 2_4:+47802096 None:intergenic
GTAAAATTAATTATTATAAG+TGG 0.347625 2_4:+47804552 None:intergenic
AAAACAAGATATTAATAAGT+AGG 0.445391 2_4:+47804529 None:intergenic
TAAAATTAATTATTATAAGT+GGG 0.450249 2_4:+47804553 None:intergenic
GAGTGAGACTCACGACGAAT+TGG 0.463921 2_4:+47802084 None:intergenic
AGAGAGAGAGAAAGAGAGAG+AGG 0.479673 2_4:+47804458 None:intergenic
TAATTTGCTTTCTGTTAACA+TGG 0.488657 2_4:-47802488 Msa0331780:CDS
AAACAAGATATTAATAAGTA+GGG 0.497233 2_4:+47804530 None:intergenic
CTAGGTTGCTCATGGACTAA+AGG 0.498311 2_4:+47802114 None:intergenic
GAGGAGTTCTAGGTTGCTCA+TGG 0.501712 2_4:+47802106 None:intergenic
AAAATTGTGAATGGTTAGGA+TGG 0.505764 2_4:+47804489 None:intergenic
GAAAGCAGGAAGGAAGTTGT+AGG 0.512942 2_4:-47802177 Msa0331780:CDS
AGGATGGGACTAGACTGGTC+GGG 0.530217 2_4:+47804505 None:intergenic
ACTGTCATCAAGAAGAAAGC+AGG 0.549205 2_4:-47802191 Msa0331780:CDS
GTACAAAATTGTGAATGGTT+AGG 0.550311 2_4:+47804485 None:intergenic
GTCAATGGATATGAATATGA+TGG 0.554037 2_4:-47804215 Msa0331780:CDS
AAAAGGTTAATCAATTTAGG+AGG 0.554456 2_4:+47802035 None:intergenic
TGAGACTCACGACGAATTGG+AGG 0.556210 2_4:+47802087 None:intergenic
TCCTCAACAAGATCACCCTC+AGG 0.562715 2_4:-47802440 Msa0331780:intron
ACCTGAGGGTGATCTTGTTG+AGG 0.567055 2_4:+47802439 None:intergenic
AATTTGCTTTCTGTTAACAT+GGG 0.574518 2_4:-47802487 Msa0331780:CDS
TGGTTAGGATGGGACTAGAC+TGG 0.575256 2_4:+47804500 None:intergenic
GATGTGTACAAAATTGTGAA+TGG 0.592715 2_4:+47804480 None:intergenic
GGATGGGACTAGACTGGTCG+GGG 0.594813 2_4:+47804506 None:intergenic
TAGGATGGGACTAGACTGGT+CGG 0.607600 2_4:+47804504 None:intergenic
TGAGGGTGATCTTGTTGAGG+AGG 0.608495 2_4:+47802442 None:intergenic
AGAATTTATAGACTAGCAAG+AGG 0.609308 2_4:+47804356 None:intergenic
ATAGTCAGCAAACTACTGCA+TGG 0.610734 2_4:+47802538 None:intergenic
GATTTATAAGCAGATCAAAG+AGG 0.614597 2_4:+47804292 None:intergenic
AAATTGTGAATGGTTAGGAT+GGG 0.621819 2_4:+47804490 None:intergenic
TCTACTATAAGCACAAACAA+AGG 0.622531 2_4:-47804271 Msa0331780:five_prime_UTR
TCATCAAGAAGAAAGCAGGA+AGG 0.669010 2_4:-47802187 Msa0331780:CDS
ACTATAGTGACAGTTAGATG+TGG 0.681695 2_4:-47802520 Msa0331780:CDS
CTTCTGCAACACTACTCTAG+CGG 0.702590 2_4:-47804158 Msa0331780:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTAAAATTAATTATTATAAG+TGG + chr2_4:47802059-47802078 None:intergenic 10.0%
!!! ATTGATTTATTTAATTATTC+AGG - chr2_4:47802899-47802918 Msa0331780:intron 10.0%
!! AAAAAAAATAAAGATGAAAT+AGG + chr2_4:47803173-47803192 None:intergenic 10.0%
!! AAACAAGATATTAATAAGTA+GGG + chr2_4:47802081-47802100 None:intergenic 15.0%
!! AAAACAAGATATTAATAAGT+AGG + chr2_4:47802082-47802101 None:intergenic 15.0%
!!! TTCTTGTTATTAAGAAATAT+AGG + chr2_4:47802547-47802566 None:intergenic 15.0%
!! AAACAAGTTATTATTATAGA+AGG + chr2_4:47803598-47803617 None:intergenic 15.0%
!! AGAAAGAAAAAAAATGTCAA+TGG - chr2_4:47802378-47802397 Msa0331780:intron 20.0%
!! GTATATATAGTAGAGTTTAT+AGG + chr2_4:47802663-47802682 None:intergenic 20.0%
!! AATCAATTTAAAAAGGGAAA+GGG + chr2_4:47802886-47802905 None:intergenic 20.0%
!! AAATCAATTTAAAAAGGGAA+AGG + chr2_4:47802887-47802906 None:intergenic 20.0%
!!! TCAAGTTTTTTTCACAATTT+TGG - chr2_4:47803086-47803105 Msa0331780:intron 20.0%
!!! TTTCTACCTTTTATCATATA+TGG - chr2_4:47803462-47803481 Msa0331780:intron 20.0%
!! ATTGAAAACATAAACATAAG+TGG + chr2_4:47803721-47803740 None:intergenic 20.0%
!! ACTAATATTGAAGAAAATGA+TGG - chr2_4:47803830-47803849 Msa0331780:intron 20.0%
!!! AATGCTTTTAATTCATACTT+TGG + chr2_4:47803857-47803876 None:intergenic 20.0%
!!! GTAATAAAGTTTTAATTTGC+AGG - chr2_4:47804039-47804058 Msa0331780:intron 20.0%
! TGATGAAAGACATAATAACA+AGG + chr2_4:47802506-47802525 None:intergenic 25.0%
! ATAACAAGAAATAAGTGAAG+TGG - chr2_4:47802557-47802576 Msa0331780:intron 25.0%
! TACATATAGTGCTAATTTGA+AGG - chr2_4:47802696-47802715 Msa0331780:intron 25.0%
! ACATATAGTGCTAATTTGAA+GGG - chr2_4:47802697-47802716 Msa0331780:intron 25.0%
! ATCCAAAATGCATAATTTGA+AGG - chr2_4:47802791-47802810 Msa0331780:intron 25.0%
!!! AGGTTTTTTTTCTTTCTTTC+TGG + chr2_4:47803153-47803172 None:intergenic 25.0%
!! TAGTTTTCAAAGTTTGTGTT+TGG - chr2_4:47803765-47803784 Msa0331780:intron 25.0%
!! AAAGAATCTGTGTCATTAAT+AGG + chr2_4:47803943-47803962 None:intergenic 25.0%
!!! TAATTTGCTTTCTGTTAACA+TGG - chr2_4:47804120-47804139 Msa0331780:intron 25.0%
!! AATTTGCTTTCTGTTAACAT+GGG - chr2_4:47804121-47804140 Msa0331780:intron 25.0%
! GAAAATGAAATTATACCTGA+GGG + chr2_4:47804186-47804205 None:intergenic 25.0%
! TGAAAATGAAATTATACCTG+AGG + chr2_4:47804187-47804206 None:intergenic 25.0%
! CATTTCATTTCCATATATAG+GGG + chr2_4:47804244-47804263 None:intergenic 25.0%
! GCATTTCATTTCCATATATA+GGG + chr2_4:47804245-47804264 None:intergenic 25.0%
! AGCATTTCATTTCCATATAT+AGG + chr2_4:47804246-47804265 None:intergenic 25.0%
AAATTGTGAATGGTTAGGAT+GGG + chr2_4:47802121-47802140 None:intergenic 30.0%
AAAATTGTGAATGGTTAGGA+TGG + chr2_4:47802122-47802141 None:intergenic 30.0%
GTACAAAATTGTGAATGGTT+AGG + chr2_4:47802126-47802145 None:intergenic 30.0%
GATGTGTACAAAATTGTGAA+TGG + chr2_4:47802131-47802150 None:intergenic 30.0%
AGAATTTATAGACTAGCAAG+AGG + chr2_4:47802255-47802274 None:intergenic 30.0%
GATTTATAAGCAGATCAAAG+AGG + chr2_4:47802319-47802338 None:intergenic 30.0%
TCTACTATAAGCACAAACAA+AGG - chr2_4:47802337-47802356 Msa0331780:intron 30.0%
GTCAATGGATATGAATATGA+TGG - chr2_4:47802393-47802412 Msa0331780:intron 30.0%
!! ATTTTATGAGAAAGTGCAAC+TGG - chr2_4:47802629-47802648 Msa0331780:intron 30.0%
!! TTTTATGAGAAAGTGCAACT+GGG - chr2_4:47802630-47802649 Msa0331780:intron 30.0%
TTCTAAACAAACAAACACCT+TGG + chr2_4:47802765-47802784 None:intergenic 30.0%
! AGCCTTCAAATTATGCATTT+TGG + chr2_4:47802796-47802815 None:intergenic 30.0%
! GAGAAAGAGATTTCTTTTCA+TGG + chr2_4:47802993-47803012 None:intergenic 30.0%
GTATTCTGTTCATCATGATT+TGG - chr2_4:47803037-47803056 Msa0331780:intron 30.0%
AAAGATGGTGCTTTCTTAAA+AGG + chr2_4:47803233-47803252 None:intergenic 30.0%
TTTCAACAGAGAAAGAAAGA+TGG + chr2_4:47803248-47803267 None:intergenic 30.0%
AGATCAAAGGATAGCATATA+GGG + chr2_4:47803348-47803367 None:intergenic 30.0%
AAAAGCTATAGACAGATCAA+AGG + chr2_4:47803361-47803380 None:intergenic 30.0%
TGCAAGCCATATATGATAAA+AGG + chr2_4:47803471-47803490 None:intergenic 30.0%
!! AAGGAAGAAGCATTTCATAT+AGG + chr2_4:47803579-47803598 None:intergenic 30.0%
AACATAAGTGGACAAATAAG+AGG + chr2_4:47803709-47803728 None:intergenic 30.0%
ACATCTCTATCCTCTTAATT+GGG + chr2_4:47803886-47803905 None:intergenic 30.0%
TTAATGACACAGATTCTTTG+AGG - chr2_4:47803944-47803963 Msa0331780:intron 30.0%
! TTAGTTTAGTTTATGCTGCT+AGG - chr2_4:47803981-47804000 Msa0331780:intron 30.0%
TATAGTGCTAATTTGAAGGG+TGG - chr2_4:47802700-47802719 Msa0331780:intron 35.0%
TTTGAAGGCTGTGAATGAAT+AGG - chr2_4:47802806-47802825 Msa0331780:intron 35.0%
! ACTCACAGAGAAGGTATATT+AGG - chr2_4:47802838-47802857 Msa0331780:intron 35.0%
! CTCACAGAGAAGGTATATTA+GGG - chr2_4:47802839-47802858 Msa0331780:intron 35.0%
TCTGATATGTCTGTCAAAGT+TGG - chr2_4:47803011-47803030 Msa0331780:intron 35.0%
CTGATATGTCTGTCAAAGTT+GGG - chr2_4:47803012-47803031 Msa0331780:intron 35.0%
CAGATCAAAGGATAGCATAT+AGG + chr2_4:47803349-47803368 None:intergenic 35.0%
AAAAGTTAGCACTCTCACAA+TGG + chr2_4:47803523-47803542 None:intergenic 35.0%
GGATCTGACAAATATGACAT+TGG + chr2_4:47803558-47803577 None:intergenic 35.0%
CATTGAGAATCCCAATTAAG+AGG - chr2_4:47803873-47803892 Msa0331780:intron 35.0%
CACATCTCTATCCTCTTAAT+TGG + chr2_4:47803887-47803906 None:intergenic 35.0%
GGATAGAGATGTGACTATAT+AGG - chr2_4:47803894-47803913 Msa0331780:intron 35.0%
! GAATCTGTGTCATTAATAGG+AGG + chr2_4:47803940-47803959 None:intergenic 35.0%
ACTATAGTGACAGTTAGATG+TGG - chr2_4:47804088-47804107 Msa0331780:intron 35.0%
TTGCAAATGACCCCTATATA+TGG - chr2_4:47804231-47804250 Msa0331780:exon 35.0%
GGTTGAATGAAGCAATTCCA+AGG - chr2_4:47802745-47802764 Msa0331780:intron 40.0%
AAGGCTGTGAATGAATAGGT+AGG - chr2_4:47802810-47802829 Msa0331780:intron 40.0%
AGGCTGTGAATGAATAGGTA+GGG - chr2_4:47802811-47802830 Msa0331780:intron 40.0%
ATATGTCTGTCAAAGTTGGG+TGG - chr2_4:47803015-47803034 Msa0331780:intron 40.0%
! CATCATGATTTGGCAGTGAA+TGG - chr2_4:47803047-47803066 Msa0331780:intron 40.0%
GTGTACTACTGTACAGGTTT+AGG + chr2_4:47803660-47803679 None:intergenic 40.0%
ATAGTCAGCAAACTACTGCA+TGG + chr2_4:47804073-47804092 None:intergenic 40.0%
ACTGTCATCAAGAAGAAAGC+AGG - chr2_4:47804417-47804436 Msa0331780:five_prime_UTR 40.0%
TCATCAAGAAGAAAGCAGGA+AGG - chr2_4:47804421-47804440 Msa0331780:five_prime_UTR 40.0%
AGAGAGAGAGAAAGAGAGAG+AGG + chr2_4:47802153-47802172 None:intergenic 45.0%
CTTCTGCAACACTACTCTAG+CGG - chr2_4:47802450-47802469 Msa0331780:CDS 45.0%
! AGAGGTGTGTACTACTGTAC+AGG + chr2_4:47803666-47803685 None:intergenic 45.0%
GAGACTTGAGAGAGAAAGAG+AGG + chr2_4:47803684-47803703 None:intergenic 45.0%
GAAAGCAGGAAGGAAGTTGT+AGG - chr2_4:47804431-47804450 Msa0331780:five_prime_UTR 45.0%
! CTAGGTTGCTCATGGACTAA+AGG + chr2_4:47804497-47804516 None:intergenic 45.0%
!! TAAAATTAATTATTATAAGT+GGG + chr2_4:47802058-47802077 None:intergenic 5.0%
!! AAAAAATAATTATATATATG+AGG - chr2_4:47802724-47802743 Msa0331780:intron 5.0%
!! TAAATAAATCAATTTAAAAA+GGG + chr2_4:47802892-47802911 None:intergenic 5.0%
!! TTAAATAAATCAATTTAAAA+AGG + chr2_4:47802893-47802912 None:intergenic 5.0%
!!! ATAAATAAATATGTTAATTT+TGG + chr2_4:47802955-47802974 None:intergenic 5.0%
TAGGATGGGACTAGACTGGT+CGG + chr2_4:47802107-47802126 None:intergenic 50.0%
TGGTTAGGATGGGACTAGAC+TGG + chr2_4:47802111-47802130 None:intergenic 50.0%
TAGGGCTAGACTCACAGAGA+AGG - chr2_4:47802829-47802848 Msa0331780:intron 50.0%
TGAGGGTGATCTTGTTGAGG+AGG + chr2_4:47804169-47804188 None:intergenic 50.0%
TCCTCAACAAGATCACCCTC+AGG - chr2_4:47804168-47804187 Msa0331780:CDS 50.0%
ACCTGAGGGTGATCTTGTTG+AGG + chr2_4:47804172-47804191 None:intergenic 50.0%
!! GAGGAGTTCTAGGTTGCTCA+TGG + chr2_4:47804505-47804524 None:intergenic 50.0%
CGACGAATTGGAGGAGTTCT+AGG + chr2_4:47804515-47804534 None:intergenic 50.0%
TGAGACTCACGACGAATTGG+AGG + chr2_4:47804524-47804543 None:intergenic 50.0%
GAGTGAGACTCACGACGAAT+TGG + chr2_4:47804527-47804546 None:intergenic 50.0%
! AGGATGGGACTAGACTGGTC+GGG + chr2_4:47802106-47802125 None:intergenic 55.0%
! GGATGGGACTAGACTGGTCG+GGG + chr2_4:47802105-47802124 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 47802050 47804580 47802050 ID=Msa0331780;Name=Msa0331780
chr2_4 mRNA 47802050 47804580 47802050 ID=Msa0331780-mRNA-1;Parent=Msa0331780;Name=Msa0331780-mRNA-1;_AED=0.04;_eAED=0.04;_QI=341|1|0.66|1|1|1|3|0|129
chr2_4 exon 47802050 47802229 47802050 ID=Msa0331780-mRNA-1:exon:14408;Parent=Msa0331780-mRNA-1
chr2_4 exon 47802441 47802569 47802441 ID=Msa0331780-mRNA-1:exon:14407;Parent=Msa0331780-mRNA-1
chr2_4 exon 47804159 47804580 47804159 ID=Msa0331780-mRNA-1:exon:14406;Parent=Msa0331780-mRNA-1
chr2_4 five_prime_UTR 47804240 47804580 47804240 ID=Msa0331780-mRNA-1:five_prime_utr;Parent=Msa0331780-mRNA-1
chr2_4 CDS 47804159 47804239 47804159 ID=Msa0331780-mRNA-1:cds;Parent=Msa0331780-mRNA-1
chr2_4 CDS 47802441 47802569 47802441 ID=Msa0331780-mRNA-1:cds;Parent=Msa0331780-mRNA-1
chr2_4 CDS 47802050 47802229 47802050 ID=Msa0331780-mRNA-1:cds;Parent=Msa0331780-mRNA-1
Gene Sequence

>Msa0331780

ATGTCAATGGATATGAATATGATGGCAACAAATGAACGTGTTTGTTATGTTCACTGCAACTTCTGCAACACTACTCTAGCGGTTAGTGTTCCATGCAGTAGTTTGCTGACTATAGTGACAGTTAGATGTGGTCATTGTGCTAATTTGCTTTCTGTTAACATGGGAGCAGCATCACTTCAATCTTTTCCTCCTCAACAAGATCACCCTCAGAAACAGCAGCTTATAAACTGTCATCAAGAAGAAAGCAGGAAGGAAGTTGTAGGATCATCATCATCTTCTTCTTCAAAATGCAAAGCATTTCAGCCTTTAGTCCATGAGCAACCTAGAACTCCTCCAATTCGTCGTGAGTCTCACTCTCACACACACACACTTTATAATTTTTCCTCCTAA

Protein sequence

>Msa0331780

MSMDMNMMATNERVCYVHCNFCNTTLAVSVPCSSLLTIVTVRCGHCANLLSVNMGAASLQSFPPQQDHPQKQQLINCHQEESRKEVVGSSSSSSSKCKAFQPLVHEQPRTPPIRRESHSHTHTLYNFSS*