AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1084580


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1084580 MtrunA17_Chr5g0399261 80.427 281 23 4 1 268 5 266 3.52e-155 432
Msa1084580 MtrunA17_Chr4g0056091 41.883 308 128 11 1 265 1 300 1.09e-53 176
Msa1084580 MtrunA17_Chr7g0231181 30.172 348 148 12 1 265 1 336 4.06e-31 118
Msa1084580 MtrunA17_Chr4g0012691 28.076 317 138 11 1 245 2 300 4.79e-20 88.6
Msa1084580 MtrunA17_Chr4g0018761 27.027 259 140 11 6 246 9 236 2.79e-16 76.3
Msa1084580 MtrunA17_Chr3g0079061 26.502 283 151 12 6 250 8 271 4.75e-14 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1084580 AT3G60580.1 30.744 309 136 11 1 265 1 275 1.87e-27 107
Msa1084580 AT1G02030.1 29.688 320 107 16 2 268 3 257 4.43e-24 98.2
Msa1084580 AT2G45120.1 32.234 273 149 9 1 245 1 265 2.41e-22 94.4
Msa1084580 AT4G16610.1 34.444 180 99 5 3 177 4 169 4.31e-17 77.8

Find 41 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGTACTACTACTGTTTGT+TGG 0.284162 7_2:+84969777 None:intergenic
GTTATAGCAGCTTCTTCTTC+AGG 0.287165 7_2:+84969483 None:intergenic
AGAAGATGAAAATGAGAGTA+TGG 0.289041 7_2:+84969817 None:intergenic
GTGAGATTGTGTTTGTGGTT+GGG 0.304906 7_2:+84969859 None:intergenic
TTTGGTTCTTATCAAGCATT+AGG 0.305236 7_2:-84969234 Msa1084580:CDS
TGATGCTATCAAGAGATAAA+TGG 0.312199 7_2:-84969455 Msa1084580:CDS
TGAGATTGTGTTTGTGGTTG+GGG 0.323538 7_2:+84969860 None:intergenic
AAAAGTGAAGTAACAGGTTC+TGG 0.326984 7_2:+84969516 None:intergenic
GGTGAGATTGTGTTTGTGGT+TGG 0.402930 7_2:+84969858 None:intergenic
TGTTGTTGAGAAAGAAAACT+TGG 0.417388 7_2:+84969683 None:intergenic
GTGTGGTGAGATTGTGTTTG+TGG 0.419011 7_2:+84969854 None:intergenic
TCTTCTTCCAAGATGGATAG+AGG 0.427918 7_2:+84969193 None:intergenic
AATCTCACCTCTATCCATCT+TGG 0.444489 7_2:-84969200 Msa1084580:CDS
TTCATCAATGGTAAAGCATT+GGG 0.449808 7_2:-84969932 Msa1084580:CDS
TTATAGCAGCTTCTTCTTCA+GGG 0.455323 7_2:+84969484 None:intergenic
ATTATAAATGTGACAAATGT+GGG 0.460652 7_2:-84969386 Msa1084580:CDS
GAAGAAGAACAAGAAGTTTG+TGG 0.463316 7_2:-84969411 Msa1084580:CDS
AAGAAGAACAAGAAGTTTGT+GGG 0.463576 7_2:-84969410 Msa1084580:CDS
ATTCATCAATGGTAAAGCAT+TGG 0.467655 7_2:-84969933 Msa1084580:CDS
TGCTCAAGAACATTCATCAA+TGG 0.467969 7_2:-84969944 Msa1084580:CDS
TGGAAGAGGAAGAGGGAGGG+TGG 0.478080 7_2:+84969886 None:intergenic
GAGAGTATGGTAGAAGAAGT+AGG 0.483653 7_2:+84969830 None:intergenic
CTTTAGAAGTTCACAAGCAA+TGG 0.490495 7_2:-84969355 Msa1084580:CDS
GGTTTGGAAGAGGAAGAGGG+AGG 0.491265 7_2:+84969882 None:intergenic
TTGAGTTGGGTTCTTTGACT+CGG 0.515544 7_2:+84969629 None:intergenic
AAGTTGAAAAGTGAAGTAAC+AGG 0.534456 7_2:+84969510 None:intergenic
GTTGTTGAGAAAGAAAACTT+GGG 0.543214 7_2:+84969684 None:intergenic
GGATCATCTTCTTATGATGA+AGG 0.547481 7_2:+84969132 None:intergenic
TGGTAGAAGAAGTAGGAGTG+TGG 0.559870 7_2:+84969837 None:intergenic
AATTATAAATGTGACAAATG+TGG 0.560495 7_2:-84969387 Msa1084580:CDS
GTTTGGAAGAGGAAGAGGGA+GGG 0.560895 7_2:+84969883 None:intergenic
AGCATTGGGTGGACACATGA+AGG 0.563543 7_2:-84969918 Msa1084580:CDS
GAGATTGTGTTTGTGGTTGG+GGG 0.564499 7_2:+84969861 None:intergenic
TATAGCAGCTTCTTCTTCAG+GGG 0.571162 7_2:+84969485 None:intergenic
CCTTAGGACAAAACACACAT+TGG 0.573593 7_2:+84969259 None:intergenic
ATCTCTTGATAGCATCATGA+GGG 0.581541 7_2:+84969461 None:intergenic
GGTTCTTATCAAGCATTAGG+TGG 0.596035 7_2:-84969231 Msa1084580:CDS
ATCAATGGTAAAGCATTGGG+TGG 0.611558 7_2:-84969929 Msa1084580:CDS
TATCTCTTGATAGCATCATG+AGG 0.628708 7_2:+84969460 None:intergenic
GTAGTTAGTGCCAAATGGAG+AGG 0.644078 7_2:-84969982 None:intergenic
TCATCTTCTTATGATGAAGG+TGG 0.658652 7_2:+84969135 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAAAGTTTGAAACTTTTTT+GGG + chr7_2:84969404-84969423 None:intergenic 20.0%
!! AATTATAAATGTGACAAATG+TGG - chr7_2:84969724-84969743 Msa1084580:CDS 20.0%
!! ATTATAAATGTGACAAATGT+GGG - chr7_2:84969725-84969744 Msa1084580:CDS 20.0%
!!! ATTGGAATATTTTATGATCA+CGG + chr7_2:84969837-84969856 None:intergenic 20.0%
!!! TGAAAGTTTGAAACTTTTTT+GGG + chr7_2:84969404-84969423 None:intergenic 20.0%
!! AATTATAAATGTGACAAATG+TGG - chr7_2:84969724-84969743 Msa1084580:CDS 20.0%
!! ATTATAAATGTGACAAATGT+GGG - chr7_2:84969725-84969744 Msa1084580:CDS 20.0%
!!! ATTGGAATATTTTATGATCA+CGG + chr7_2:84969837-84969856 None:intergenic 20.0%
!!! CTGAAAGTTTGAAACTTTTT+TGG + chr7_2:84969405-84969424 None:intergenic 25.0%
!!! CTGAAAGTTTGAAACTTTTT+TGG + chr7_2:84969405-84969424 None:intergenic 25.0%
ATTCATCAATGGTAAAGCAT+TGG - chr7_2:84969178-84969197 Msa1084580:CDS 30.0%
! TTCATCAATGGTAAAGCATT+GGG - chr7_2:84969179-84969198 Msa1084580:CDS 30.0%
AGAAGATGAAAATGAGAGTA+TGG + chr7_2:84969297-84969316 None:intergenic 30.0%
TTTGTACTACTACTGTTTGT+TGG + chr7_2:84969337-84969356 None:intergenic 30.0%
ATGAAAAGAGTCCAATGTAT+AGG - chr7_2:84969366-84969385 Msa1084580:CDS 30.0%
! TTTTCTCTCAACCTATACAT+TGG + chr7_2:84969380-84969399 None:intergenic 30.0%
GTTGTTGAGAAAGAAAACTT+GGG + chr7_2:84969430-84969449 None:intergenic 30.0%
TGTTGTTGAGAAAGAAAACT+TGG + chr7_2:84969431-84969450 None:intergenic 30.0%
!!! TGAGTTTTCGTTTTTGAGTT+GGG + chr7_2:84969498-84969517 None:intergenic 30.0%
!! TTGTTCTGAATTTTGGACAA+AGG + chr7_2:84969521-84969540 None:intergenic 30.0%
!! GCTTCTTTTGTTCTGAATTT+TGG + chr7_2:84969528-84969547 None:intergenic 30.0%
AAGTTGAAAAGTGAAGTAAC+AGG + chr7_2:84969604-84969623 None:intergenic 30.0%
TGATGCTATCAAGAGATAAA+TGG - chr7_2:84969656-84969675 Msa1084580:CDS 30.0%
AAGAAGAACAAGAAGTTTGT+GGG - chr7_2:84969701-84969720 Msa1084580:CDS 30.0%
TGATAAGAACCAAAAACCTT+AGG + chr7_2:84969871-84969890 None:intergenic 30.0%
!! TTTGGTTCTTATCAAGCATT+AGG - chr7_2:84969877-84969896 Msa1084580:CDS 30.0%
ATTCATCAATGGTAAAGCAT+TGG - chr7_2:84969178-84969197 Msa1084580:CDS 30.0%
! TTCATCAATGGTAAAGCATT+GGG - chr7_2:84969179-84969198 Msa1084580:CDS 30.0%
AGAAGATGAAAATGAGAGTA+TGG + chr7_2:84969297-84969316 None:intergenic 30.0%
TTTGTACTACTACTGTTTGT+TGG + chr7_2:84969337-84969356 None:intergenic 30.0%
ATGAAAAGAGTCCAATGTAT+AGG - chr7_2:84969366-84969385 Msa1084580:CDS 30.0%
! TTTTCTCTCAACCTATACAT+TGG + chr7_2:84969380-84969399 None:intergenic 30.0%
GTTGTTGAGAAAGAAAACTT+GGG + chr7_2:84969430-84969449 None:intergenic 30.0%
TGTTGTTGAGAAAGAAAACT+TGG + chr7_2:84969431-84969450 None:intergenic 30.0%
!!! TGAGTTTTCGTTTTTGAGTT+GGG + chr7_2:84969498-84969517 None:intergenic 30.0%
!! TTGTTCTGAATTTTGGACAA+AGG + chr7_2:84969521-84969540 None:intergenic 30.0%
!! GCTTCTTTTGTTCTGAATTT+TGG + chr7_2:84969528-84969547 None:intergenic 30.0%
AAGTTGAAAAGTGAAGTAAC+AGG + chr7_2:84969604-84969623 None:intergenic 30.0%
TGATGCTATCAAGAGATAAA+TGG - chr7_2:84969656-84969675 Msa1084580:CDS 30.0%
AAGAAGAACAAGAAGTTTGT+GGG - chr7_2:84969701-84969720 Msa1084580:CDS 30.0%
TGATAAGAACCAAAAACCTT+AGG + chr7_2:84969871-84969890 None:intergenic 30.0%
!! TTTGGTTCTTATCAAGCATT+AGG - chr7_2:84969877-84969896 Msa1084580:CDS 30.0%
TGCTCAAGAACATTCATCAA+TGG - chr7_2:84969167-84969186 Msa1084580:CDS 35.0%
!!! GTGAGTTTTCGTTTTTGAGT+TGG + chr7_2:84969499-84969518 None:intergenic 35.0%
AAAAGTGAAGTAACAGGTTC+TGG + chr7_2:84969598-84969617 None:intergenic 35.0%
TTATAGCAGCTTCTTCTTCA+GGG + chr7_2:84969630-84969649 None:intergenic 35.0%
! ATCTCTTGATAGCATCATGA+GGG + chr7_2:84969653-84969672 None:intergenic 35.0%
! TATCTCTTGATAGCATCATG+AGG + chr7_2:84969654-84969673 None:intergenic 35.0%
GAAGAAGAACAAGAAGTTTG+TGG - chr7_2:84969700-84969719 Msa1084580:CDS 35.0%
! CTTTAGAAGTTCACAAGCAA+TGG - chr7_2:84969756-84969775 Msa1084580:intron 35.0%
! GTGTTTTGTCCTAAGGTTTT+TGG - chr7_2:84969859-84969878 Msa1084580:CDS 35.0%
TTCTTCTTCTTCTTCCAAGA+TGG + chr7_2:84969928-84969947 None:intergenic 35.0%
TGCTCAAGAACATTCATCAA+TGG - chr7_2:84969167-84969186 Msa1084580:CDS 35.0%
!!! GTGAGTTTTCGTTTTTGAGT+TGG + chr7_2:84969499-84969518 None:intergenic 35.0%
AAAAGTGAAGTAACAGGTTC+TGG + chr7_2:84969598-84969617 None:intergenic 35.0%
TTATAGCAGCTTCTTCTTCA+GGG + chr7_2:84969630-84969649 None:intergenic 35.0%
! ATCTCTTGATAGCATCATGA+GGG + chr7_2:84969653-84969672 None:intergenic 35.0%
! TATCTCTTGATAGCATCATG+AGG + chr7_2:84969654-84969673 None:intergenic 35.0%
GAAGAAGAACAAGAAGTTTG+TGG - chr7_2:84969700-84969719 Msa1084580:CDS 35.0%
! CTTTAGAAGTTCACAAGCAA+TGG - chr7_2:84969756-84969775 Msa1084580:intron 35.0%
! GTGTTTTGTCCTAAGGTTTT+TGG - chr7_2:84969859-84969878 Msa1084580:CDS 35.0%
TTCTTCTTCTTCTTCCAAGA+TGG + chr7_2:84969928-84969947 None:intergenic 35.0%
!! ATCAATGGTAAAGCATTGGG+TGG - chr7_2:84969182-84969201 Msa1084580:CDS 40.0%
TGAGATTGTGTTTGTGGTTG+GGG + chr7_2:84969254-84969273 None:intergenic 40.0%
GTGAGATTGTGTTTGTGGTT+GGG + chr7_2:84969255-84969274 None:intergenic 40.0%
! GAGAGTATGGTAGAAGAAGT+AGG + chr7_2:84969284-84969303 None:intergenic 40.0%
!! TTGAGTTGGGTTCTTTGACT+CGG + chr7_2:84969485-84969504 None:intergenic 40.0%
TATAGCAGCTTCTTCTTCAG+GGG + chr7_2:84969629-84969648 None:intergenic 40.0%
GTTATAGCAGCTTCTTCTTC+AGG + chr7_2:84969631-84969650 None:intergenic 40.0%
CCTTAGGACAAAACACACAT+TGG + chr7_2:84969855-84969874 None:intergenic 40.0%
! CCAATGTGTGTTTTGTCCTA+AGG - chr7_2:84969852-84969871 Msa1084580:CDS 40.0%
GGTTCTTATCAAGCATTAGG+TGG - chr7_2:84969880-84969899 Msa1084580:CDS 40.0%
AATCTCACCTCTATCCATCT+TGG - chr7_2:84969911-84969930 Msa1084580:CDS 40.0%
TCTTCTTCCAAGATGGATAG+AGG + chr7_2:84969921-84969940 None:intergenic 40.0%
!! ATCAATGGTAAAGCATTGGG+TGG - chr7_2:84969182-84969201 Msa1084580:CDS 40.0%
TGAGATTGTGTTTGTGGTTG+GGG + chr7_2:84969254-84969273 None:intergenic 40.0%
GTGAGATTGTGTTTGTGGTT+GGG + chr7_2:84969255-84969274 None:intergenic 40.0%
! GAGAGTATGGTAGAAGAAGT+AGG + chr7_2:84969284-84969303 None:intergenic 40.0%
!! TTGAGTTGGGTTCTTTGACT+CGG + chr7_2:84969485-84969504 None:intergenic 40.0%
TATAGCAGCTTCTTCTTCAG+GGG + chr7_2:84969629-84969648 None:intergenic 40.0%
GTTATAGCAGCTTCTTCTTC+AGG + chr7_2:84969631-84969650 None:intergenic 40.0%
CCTTAGGACAAAACACACAT+TGG + chr7_2:84969855-84969874 None:intergenic 40.0%
! CCAATGTGTGTTTTGTCCTA+AGG - chr7_2:84969852-84969871 Msa1084580:CDS 40.0%
GGTTCTTATCAAGCATTAGG+TGG - chr7_2:84969880-84969899 Msa1084580:CDS 40.0%
AATCTCACCTCTATCCATCT+TGG - chr7_2:84969911-84969930 Msa1084580:CDS 40.0%
TCTTCTTCCAAGATGGATAG+AGG + chr7_2:84969921-84969940 None:intergenic 40.0%
GAGATTGTGTTTGTGGTTGG+GGG + chr7_2:84969253-84969272 None:intergenic 45.0%
GGTGAGATTGTGTTTGTGGT+TGG + chr7_2:84969256-84969275 None:intergenic 45.0%
GTGTGGTGAGATTGTGTTTG+TGG + chr7_2:84969260-84969279 None:intergenic 45.0%
TGGTAGAAGAAGTAGGAGTG+TGG + chr7_2:84969277-84969296 None:intergenic 45.0%
GAGATTGTGTTTGTGGTTGG+GGG + chr7_2:84969253-84969272 None:intergenic 45.0%
GGTGAGATTGTGTTTGTGGT+TGG + chr7_2:84969256-84969275 None:intergenic 45.0%
GTGTGGTGAGATTGTGTTTG+TGG + chr7_2:84969260-84969279 None:intergenic 45.0%
TGGTAGAAGAAGTAGGAGTG+TGG + chr7_2:84969277-84969296 None:intergenic 45.0%
! AGCATTGGGTGGACACATGA+AGG - chr7_2:84969193-84969212 Msa1084580:CDS 50.0%
GTTTGGAAGAGGAAGAGGGA+GGG + chr7_2:84969231-84969250 None:intergenic 50.0%
TGTGTTTGTGGTTGGGGGTT+TGG + chr7_2:84969248-84969267 None:intergenic 50.0%
! AGCATTGGGTGGACACATGA+AGG - chr7_2:84969193-84969212 Msa1084580:CDS 50.0%
GTTTGGAAGAGGAAGAGGGA+GGG + chr7_2:84969231-84969250 None:intergenic 50.0%
TGTGTTTGTGGTTGGGGGTT+TGG + chr7_2:84969248-84969267 None:intergenic 50.0%
GGTTTGGAAGAGGAAGAGGG+AGG + chr7_2:84969232-84969251 None:intergenic 55.0%
GGGGGTTTGGAAGAGGAAGA+GGG + chr7_2:84969235-84969254 None:intergenic 55.0%
TGGGGGTTTGGAAGAGGAAG+AGG + chr7_2:84969236-84969255 None:intergenic 55.0%
TGTGGTTGGGGGTTTGGAAG+AGG + chr7_2:84969242-84969261 None:intergenic 55.0%
GGTTTGGAAGAGGAAGAGGG+AGG + chr7_2:84969232-84969251 None:intergenic 55.0%
GGGGGTTTGGAAGAGGAAGA+GGG + chr7_2:84969235-84969254 None:intergenic 55.0%
TGGGGGTTTGGAAGAGGAAG+AGG + chr7_2:84969236-84969255 None:intergenic 55.0%
TGTGGTTGGGGGTTTGGAAG+AGG + chr7_2:84969242-84969261 None:intergenic 55.0%
TGGAAGAGGAAGAGGGAGGG+TGG + chr7_2:84969228-84969247 None:intergenic 60.0%
TGGAAGAGGAAGAGGGAGGG+TGG + chr7_2:84969228-84969247 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 84969143 84969990 84969143 ID=Msa1084580;Name=Msa1084580
chr7_2 mRNA 84969143 84969990 84969143 ID=Msa1084580-mRNA-1;Parent=Msa1084580;Name=Msa1084580-mRNA-1;_AED=0.03;_eAED=0.17;_QI=0|0|0|1|1|1|2|0|268
chr7_2 exon 84969787 84969990 84969787 ID=Msa1084580-mRNA-1:exon:22884;Parent=Msa1084580-mRNA-1
chr7_2 exon 84969143 84969745 84969143 ID=Msa1084580-mRNA-1:exon:22883;Parent=Msa1084580-mRNA-1
chr7_2 CDS 84969787 84969990 84969787 ID=Msa1084580-mRNA-1:cds;Parent=Msa1084580-mRNA-1
chr7_2 CDS 84969143 84969745 84969143 ID=Msa1084580-mRNA-1:cds;Parent=Msa1084580-mRNA-1
Gene Sequence

>Msa1084580

ATGGAGAGGTACAAATGCAAGCTTTGCTCAAGAACATTCATCAATGGTAAAGCATTGGGTGGACACATGAAGGCTCATTTTGCCACCCTCCCTCTTCCTCTTCCAAACCCCCAACCACAAACACAATCTCACCACACTCCTACTTCTTCTACCATACTCTCATTTTCATCTTCTTCTGAAAATGAACAAGACCAACAAACAGTAGTTGAGAGAAAATCCCAAAAAAGTTTCAAACTTTCAGATCCCAAGTTTTCTTTCTCAACAACAGAGACTATTGTTCATGACAGAGAGAGTGAAACCGAGTCAAAGAACCCAACTCAAAAACGAAAACTCACCTTTGTCCAAAATTCAGAACAAAAGAAGCTTAAACAAAGTTTGAAAGATTCACATTCACAACTAACAGAAACTGAACCAGAACCTGTTACTTCACTTTTCAACTTTTCCCCTGAAGAAGAAGCTGCTATAACCCTCATGATGCTATCAAGAGATAAATGGAAGATCAATGTTGCTGTCAAAGAAGAAGAACAAGAAGTTTGTGGGAATTATAAATGTGACAAATGTGGGAATAATAACTTTAGAAGTTCACAAGCAATGGAAAGTCACAAAAGTATTTGTCTTCAAAATGAAACAAATCTTGCTTCAACAAGTAGCCGTGATCATAAAATATTCCAATGTGTGTTTTGTCCTAAGGTTTTTGGTTCTTATCAAGCATTAGGTGGTCACAAAAAATCTCACCTCTATCCATCTTGGAAGAAGAAGAAGAAGAAGCTATGTTTTTTCGATCTCAACTTGCCACCTTCATCATAA

Protein sequence

>Msa1084580

MERYKCKLCSRTFINGKALGGHMKAHFATLPLPLPNPQPQTQSHHTPTSSTILSFSSSSENEQDQQTVVERKSQKSFKLSDPKFSFSTTETIVHDRESETESKNPTQKRKLTFVQNSEQKKLKQSLKDSHSQLTETEPEPVTSLFNFSPEEEAAITLMMLSRDKWKINVAVKEEEQEVCGNYKCDKCGNNNFRSSQAMESHKSICLQNETNLASTSSRDHKIFQCVFCPKVFGSYQALGGHKKSHLYPSWKKKKKKLCFFDLNLPPSS*