AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0391230

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0391230 MtrunA17_Chr8g0373341 55.396 139 24 2 33 133 125 263 1.09e-40 137
Msa0391230 MtrunA17_Chr8g0373361 70.370 54 16 0 33 86 153 206 8.65e-19 80.9
Msa0391230 MtrunA17_Chr8g0373001 70.370 54 13 1 36 86 151 204 1.14e-17 77.8
Msa0391230 MtrunA17_Chr5g0404321 66.667 57 16 1 33 86 150 206 2.02e-17 77.0
Msa0391230 MtrunA17_Chr2g0286441 52.239 67 29 1 23 86 124 190 3.41e-15 70.9
Msa0391230 MtrunA17_Chr1g0156151 64.815 54 16 1 36 86 153 206 8.79e-15 68.2
Msa0391230 MtrunA17_Chr1g0155301 58.333 60 22 1 30 86 163 222 5.60e-14 67.4
Msa0391230 MtrunA17_Chr1g0196071 45.455 77 39 1 23 96 135 211 8.89e-14 66.6
Msa0391230 MtrunA17_Chr1g0201891 38.318 107 44 4 13 104 136 235 3.08e-12 62.4
Msa0391230 MtrunA17_Chr2g0278511 43.023 86 39 3 13 95 137 215 7.55e-12 61.2
Msa0391230 MtrunA17_Chr2g0315641 41.975 81 39 2 14 86 113 193 1.53e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0391230 AT1G47270.2 50.000 74 34 1 30 100 161 234 8.03e-18 78.6
Msa0391230 AT1G47270.1 50.000 74 34 1 30 100 162 235 8.80e-18 78.6
Msa0391230 AT1G47270.3 50.000 74 34 1 30 100 137 210 8.76e-17 75.5
Msa0391230 AT2G47900.3 51.471 68 30 1 23 87 139 206 1.16e-14 69.7
Msa0391230 AT2G47900.2 55.172 58 23 1 33 87 148 205 8.61e-14 67.0
Msa0391230 AT2G47900.1 55.172 58 23 1 33 87 148 205 8.61e-14 67.0
Msa0391230 AT1G53320.1 47.761 67 32 1 23 86 129 195 2.65e-12 62.8
Msa0391230 AT1G76900.2 44.872 78 33 3 13 87 140 210 1.89e-11 60.5
Msa0391230 AT1G76900.1 44.872 78 33 3 13 87 140 210 1.89e-11 60.5
Msa0391230 AT1G76900.3 44.872 78 33 3 13 87 140 210 1.89e-11 60.5
Msa0391230 AT2G18280.2 57.692 52 19 1 37 85 147 198 2.58e-11 60.1
Msa0391230 AT2G18280.1 57.692 52 19 1 37 85 147 198 2.58e-11 60.1
Msa0391230 AT3G06380.2 36.458 96 50 2 20 104 24 119 8.16e-11 58.2

Find 22 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTACATTCCTGATGTATT+TGG 0.157633 3_2:+2729376 None:intergenic
ATATTCACTGTGTTTGAAAA+AGG 0.209880 3_2:-2729435 None:intergenic
GCACAGTTTACACTTGAAAA+TGG 0.250030 3_2:-2730051 None:intergenic
TGGTTGGGGCCCTGACTTCA+TGG 0.311483 3_2:+2730027 Msa0391230:CDS
TAGCTGCGAAAATGATAAAA+AGG 0.366386 3_2:+2729684 Msa0391230:CDS
ATTGTATGGCAGTTAATAAT+AGG 0.397969 3_2:+2729648 Msa0391230:intron
TGAAAATGGCCCATGAAGTC+AGG 0.412357 3_2:-2730037 None:intergenic
GGAAGAGCATCACAATGGTT+GGG 0.430305 3_2:+2730012 Msa0391230:CDS
GGTTGGGGCCCTGACTTCAT+GGG 0.474980 3_2:+2730028 Msa0391230:CDS
GGGAAGAGCATCACAATGGT+TGG 0.483765 3_2:+2730011 Msa0391230:CDS
AATGAGCCTTGGCTCAGTGC+TGG 0.521850 3_2:-2729953 None:intergenic
AGTCAAGGATATGACGAAGT+TGG 0.525647 3_2:-2729708 None:intergenic
TAAAGGTCTCAAATGAGCCT+TGG 0.532815 3_2:-2729964 None:intergenic
AACTTCGTCATATCCTTGAC+TGG 0.547745 3_2:+2729710 Msa0391230:CDS
AAAGTTTCATCAAATACAGA+AGG 0.566100 3_2:-2729920 None:intergenic
GAAGAGCATCACAATGGTTG+GGG 0.571615 3_2:+2730013 Msa0391230:CDS
CCTTGGCTCAGTGCTGGTGA+AGG 0.581909 3_2:-2729947 None:intergenic
CCTTCACCAGCACTGAGCCA+AGG 0.586880 3_2:+2729947 Msa0391230:CDS
GAAAATGGCCCATGAAGTCA+GGG 0.604079 3_2:-2730036 None:intergenic
ACAAATATGTTTGTAAACTG+AGG 0.610066 3_2:+2729756 Msa0391230:CDS
ACTGTCGTATAGAGTGAACT+TGG 0.646011 3_2:-2729894 None:intergenic
AGATGGGAAGAGCATCACAA+TGG 0.704024 3_2:+2730007 Msa0391230:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATTTGATTTATATACATA+CGG + chr3_2:2729851-2729870 Msa0391230:intron 15.0%
! TATTCACTGTGTTTGAAAAA+GGG - chr3_2:2729437-2729456 None:intergenic 25.0%
! ATATTCACTGTGTTTGAAAA+AGG - chr3_2:2729438-2729457 None:intergenic 25.0%
! ATTGTATGGCAGTTAATAAT+AGG + chr3_2:2729648-2729667 Msa0391230:intron 25.0%
! ACAAATATGTTTGTAAACTG+AGG + chr3_2:2729756-2729775 Msa0391230:CDS 25.0%
!!! CATTTTTTTTAGCCTTCTAT+AGG + chr3_2:2729800-2729819 Msa0391230:intron 25.0%
! TCAAATTGCGAGTATTATAA+GGG - chr3_2:2729839-2729858 None:intergenic 25.0%
! ATCAAATTGCGAGTATTATA+AGG - chr3_2:2729840-2729859 None:intergenic 25.0%
! AAAGTTTCATCAAATACAGA+AGG - chr3_2:2729923-2729942 None:intergenic 25.0%
!!! AGTCTTGTTTTTCAGTATAA+AGG - chr3_2:2729984-2730003 None:intergenic 25.0%
!! TTGGTTTGGTTGTAATTGTA+TGG + chr3_2:2729634-2729653 Msa0391230:intron 30.0%
TAGCTGCGAAAATGATAAAA+AGG + chr3_2:2729684-2729703 Msa0391230:CDS 30.0%
AAATTGCGAGTATTATAAGG+GGG - chr3_2:2729837-2729856 None:intergenic 30.0%
CAAATTGCGAGTATTATAAG+GGG - chr3_2:2729838-2729857 None:intergenic 30.0%
TTGATTTATATACATACGGC+AGG + chr3_2:2729855-2729874 Msa0391230:intron 30.0%
TGAAAAACAAGACTCTTAGA+TGG + chr3_2:2729990-2730009 Msa0391230:CDS 30.0%
GAAAAACAAGACTCTTAGAT+GGG + chr3_2:2729991-2730010 Msa0391230:CDS 30.0%
ACTTACTTGCTCTACGTTTA+TGG + chr3_2:2729528-2729547 Msa0391230:intron 35.0%
!! CGTATTTAAGCAGCTTGTTT+TGG + chr3_2:2729615-2729634 Msa0391230:intron 35.0%
!!! TTAAGCAGCTTGTTTTGGTT+TGG + chr3_2:2729620-2729639 Msa0391230:intron 35.0%
AGAAAAATCATCTCCAGTCA+AGG - chr3_2:2729726-2729745 None:intergenic 35.0%
! ATACGGCAGGTCAAATTTTT+GGG + chr3_2:2729868-2729887 Msa0391230:intron 35.0%
CACTGTGTTTGAAAAAGGGA+TGG - chr3_2:2729433-2729452 None:intergenic 40.0%
AGTCAAGGATATGACGAAGT+TGG - chr3_2:2729711-2729730 None:intergenic 40.0%
AACTTCGTCATATCCTTGAC+TGG + chr3_2:2729710-2729729 Msa0391230:CDS 40.0%
GTGGAAGAAAAGCCTATAGA+AGG - chr3_2:2729815-2729834 None:intergenic 40.0%
! CATACGGCAGGTCAAATTTT+TGG + chr3_2:2729867-2729886 Msa0391230:intron 40.0%
! TACGGCAGGTCAAATTTTTG+GGG + chr3_2:2729869-2729888 Msa0391230:intron 40.0%
ACTGTCGTATAGAGTGAACT+TGG - chr3_2:2729897-2729916 None:intergenic 40.0%
TAAAGGTCTCAAATGAGCCT+TGG - chr3_2:2729967-2729986 None:intergenic 40.0%
TTGCGAGTATTATAAGGGGG+TGG - chr3_2:2729834-2729853 None:intergenic 45.0%
!! AGATGGGAAGAGCATCACAA+TGG + chr3_2:2730007-2730026 Msa0391230:CDS 45.0%
!! GGAAGAGCATCACAATGGTT+GGG + chr3_2:2730012-2730031 Msa0391230:CDS 45.0%
!! GAAGAGCATCACAATGGTTG+GGG + chr3_2:2730013-2730032 Msa0391230:CDS 45.0%
GAAAATGGCCCATGAAGTCA+GGG - chr3_2:2730039-2730058 None:intergenic 45.0%
TGAAAATGGCCCATGAAGTC+AGG - chr3_2:2730040-2730059 None:intergenic 45.0%
!! GGGAAGAGCATCACAATGGT+TGG + chr3_2:2730011-2730030 Msa0391230:CDS 50.0%
AATGAGCCTTGGCTCAGTGC+TGG - chr3_2:2729956-2729975 None:intergenic 55.0%
!! CCTTGGCTCAGTGCTGGTGA+AGG - chr3_2:2729950-2729969 None:intergenic 60.0%
! CCTTCACCAGCACTGAGCCA+AGG + chr3_2:2729947-2729966 Msa0391230:CDS 60.0%
TGGTTGGGGCCCTGACTTCA+TGG + chr3_2:2730027-2730046 Msa0391230:CDS 60.0%
GGTTGGGGCCCTGACTTCAT+GGG + chr3_2:2730028-2730047 Msa0391230:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 2729389 2730066 2729389 ID=Msa0391230;Name=Msa0391230
chr3_2 mRNA 2729389 2730066 2729389 ID=Msa0391230-mRNA-1;Parent=Msa0391230;Name=Msa0391230-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|0|0|1|0.5|0.66|3|0|133
chr3_2 exon 2729389 2729482 2729389 ID=Msa0391230-mRNA-1:exon:822;Parent=Msa0391230-mRNA-1
chr3_2 exon 2729660 2729777 2729660 ID=Msa0391230-mRNA-1:exon:823;Parent=Msa0391230-mRNA-1
chr3_2 exon 2729877 2730066 2729877 ID=Msa0391230-mRNA-1:exon:824;Parent=Msa0391230-mRNA-1
chr3_2 CDS 2729389 2729482 2729389 ID=Msa0391230-mRNA-1:cds;Parent=Msa0391230-mRNA-1
chr3_2 CDS 2729660 2729777 2729660 ID=Msa0391230-mRNA-1:cds;Parent=Msa0391230-mRNA-1
chr3_2 CDS 2729877 2730066 2729877 ID=Msa0391230-mRNA-1:cds;Parent=Msa0391230-mRNA-1
Gene Sequence

>Msa0391230

ATGTATTTGGAGCAATGTAAGTATTTCATTGCAGAAACATACCATCCCTTTTTCAAACACAGTGAATATCTATTTTCAAATTTCTCATCTTTAATTAATAATAGGAGTAAGTTGTTATTAGCTGCGAAAATGATAAAAAGGTCCAACTTCGTCATATCCTTGACTGGAGATGATTTTTCTCTAGCAAGTAACAAATATGTTTGTAAACTGAGGTCAAATTTTTGGGGCACCAAGTTCACTCTATACGACAGTCAACCTTCTGTATTTGATGAAACTTTTTCTCCTTCACCAGCACTGAGCCAAGGCTCATTTGAGACCTTTATACTGAAAAACAAGACTCTTAGATGGGAAGAGCATCACAATGGTTGGGGCCCTGACTTCATGGGCCATTTTCAAGTGTAA
Protein sequence

>Msa0391230

MYLEQCKYFIAETYHPFFKHSEYLFSNFSSLINNRSKLLLAAKMIKRSNFVISLTGDDFSLASNKYVCKLRSNFWGTKFTLYDSQPSVFDETFSPSPALSQGSFETFILKNKTLRWEEHHNGWGPDFMGHFQV*