AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1190380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1190380 MtrunA17_Chr8g0359161 96.569 204 7 0 1 204 1 204 1.03e-147 408
Msa1190380 MtrunA17_Chr8g0359111 66.832 202 67 0 3 204 1 202 1.50e-103 296
Msa1190380 MtrunA17_Chr1g0173431 68.317 202 61 2 5 204 1 201 4.63e-98 283
Msa1190380 MtrunA17_Chr4g0022761 67.327 202 60 2 5 204 1 198 1.82e-94 273
Msa1190380 MtrunA17_Chr3g0082651 66.667 204 63 3 5 204 1 203 4.02e-94 273
Msa1190380 MtrunA17_Chr3g0082661 67.157 204 62 3 5 204 1 203 5.00e-94 273
Msa1190380 MtrunA17_Chr3g0082681 66.667 204 63 3 5 204 1 203 8.74e-94 272
Msa1190380 MtrunA17_Chr3g0082641 65.686 204 67 2 3 204 1 203 1.70e-93 271
Msa1190380 MtrunA17_Chr3g0082671 65.686 204 67 2 3 204 1 203 6.48e-93 270
Msa1190380 MtrunA17_Chr4g0022751 63.366 202 72 1 5 204 1 202 2.05e-90 263
Msa1190380 MtrunA17_Chr7g0269461 63.054 203 72 3 3 204 1 201 5.23e-89 260
Msa1190380 MtrunA17_Chr2g0314441 55.789 190 71 3 16 201 15 195 2.58e-71 215
Msa1190380 MtrunA17_Chr2g0314431 45.274 201 84 7 5 193 1 187 8.02e-45 147
Msa1190380 MtrunA17_Chr6g0482041 33.511 188 104 8 29 202 30 210 2.39e-17 77.0
Msa1190380 MtrunA17_Chr6g0481911 28.351 194 123 9 9 193 4 190 8.08e-14 67.4
Msa1190380 MtrunA17_Chr6g0467771 29.775 178 113 6 29 201 31 201 5.75e-12 62.8
Msa1190380 MtrunA17_Chr6g0481941 28.571 203 124 10 1 193 1 192 5.00e-11 59.7
Msa1190380 MtrunA17_Chr6g0467761 29.545 176 117 6 29 201 32 203 6.84e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1190380 AT1G17860.1 30.481 187 115 6 20 203 20 194 1.60e-15 72.0
Msa1190380 AT1G73260.1 31.548 168 106 7 41 203 41 204 5.81e-14 68.2

Find 54 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCATATGGTAACTTCTTT+AGG 0.202488 8_1:-33266652 Msa1190380:CDS
CCTCCTTTGTTTGTGATAAC+TGG 0.265337 8_1:+33266938 None:intergenic
ATCACGACTTCGACGATGTT+AGG 0.298935 8_1:-33266808 Msa1190380:CDS
CGACTGTGTCGAAGACAAAC+TGG 0.334067 8_1:+33266999 None:intergenic
TATTCCTCGTCGCCTTCAAC+TGG 0.432772 8_1:+33266971 None:intergenic
AGTGCTACTAATGGATCATA+TGG 0.432987 8_1:-33266665 Msa1190380:CDS
GGAAGAGATAGTGCTACTAA+TGG 0.447916 8_1:-33266674 Msa1190380:CDS
GGTCTTGAGAACACTGGCTT+AGG 0.457139 8_1:-33266869 Msa1190380:CDS
TTCTCAAGACCAACATGTAA+AGG 0.464201 8_1:+33266881 None:intergenic
TCACGACTTCGACGATGTTA+GGG 0.467925 8_1:-33266807 Msa1190380:CDS
TTCATTTCTGCTGATCATAG+TGG 0.471060 8_1:+33266910 None:intergenic
ATACATGAGCAAGAATTATG+AGG 0.476793 8_1:+33267050 None:intergenic
CAATCAACAGAATGGAGATT+GGG 0.482818 8_1:-33266737 Msa1190380:CDS
AGGGAGGGGACCACCATCAA+GGG 0.484944 8_1:+33266505 None:intergenic
GAGGGAGGGGACCACCATCA+AGG 0.485248 8_1:+33266504 None:intergenic
GGAAGAAGGTTGATTATCAC+TGG 0.495698 8_1:-33266695 Msa1190380:CDS
TTCTGGAAAACAAGAGGGAG+GGG 0.496214 8_1:+33266491 None:intergenic
GTACACAACTTGATGAAGCT+TGG 0.498312 8_1:+33266759 None:intergenic
AAGTCGTGATGGGGAGCAAA+AGG 0.500088 8_1:+33266821 None:intergenic
TCTCAAGACCAACATGTAAA+GGG 0.503765 8_1:+33266882 None:intergenic
ACAATCAACAGAATGGAGAT+TGG 0.508137 8_1:-33266738 Msa1190380:CDS
AACATCGTCGAAGTCGTGAT+GGG 0.515072 8_1:+33266811 None:intergenic
ATTGTAGAGACCCCACTTGA+AGG 0.515965 8_1:-33266629 Msa1190380:CDS
CACTGGCTTAGGACACGGTC+TGG 0.532480 8_1:-33266858 Msa1190380:CDS
CAACTAGGACATACCTCTGT+AGG 0.534967 8_1:+33266584 None:intergenic
GAATCATGCCCTTTACATGT+TGG 0.540282 8_1:-33266890 Msa1190380:CDS
GTTGTGTACAATCAACAGAA+TGG 0.542722 8_1:-33266745 Msa1190380:CDS
TAACATCGTCGAAGTCGTGA+TGG 0.545399 8_1:+33266810 None:intergenic
GACTGTGTCGAAGACAAACT+GGG 0.554983 8_1:+33267000 None:intergenic
ATTCTTTCTGGAAAACAAGA+GGG 0.555637 8_1:+33266486 None:intergenic
CTTTGTTTGTGATAACTGGA+CGG 0.556090 8_1:+33266942 None:intergenic
GTTGATATGCTGAATGAGAA+TGG 0.566614 8_1:-33266542 Msa1190380:CDS
AAGATACTAAGAGTGGAAGA+AGG 0.571477 8_1:-33266709 Msa1190380:CDS
CCACATTCAAATCTACAACT+AGG 0.573570 8_1:+33266569 None:intergenic
TTTCTGGAAAACAAGAGGGA+GGG 0.581340 8_1:+33266490 None:intergenic
TATTCTTTCTGGAAAACAAG+AGG 0.582397 8_1:+33266485 None:intergenic
CAGTTTGTCTTCGACACAGT+CGG 0.584758 8_1:-33266998 Msa1190380:CDS
TACATGAGCAAGAATTATGA+GGG 0.589317 8_1:+33267051 None:intergenic
TATTATACATACCTTCAAGT+GGG 0.589842 8_1:+33266618 None:intergenic
AAACTGGGCTATTGTTGTTG+TGG 0.592731 8_1:+33267015 None:intergenic
CGTCCAGTTATCACAAACAA+AGG 0.595247 8_1:-33266941 Msa1190380:CDS
ACAGTCGGAGAACCAGTTGA+AGG 0.605474 8_1:-33266983 Msa1190380:CDS
CATGTTGGTCTTGAGAACAC+TGG 0.606261 8_1:-33266875 Msa1190380:CDS
AGTAGATAATCTCATTGACA+TGG 0.610571 8_1:+33267078 None:intergenic
ACATCGTCGAAGTCGTGATG+GGG 0.622395 8_1:+33266812 None:intergenic
GAGAACACTGGCTTAGGACA+CGG 0.624273 8_1:-33266863 Msa1190380:CDS
CTTTCTGGAAAACAAGAGGG+AGG 0.626753 8_1:+33266489 None:intergenic
ATATTATACATACCTTCAAG+TGG 0.635907 8_1:+33266617 None:intergenic
CCTAGTTGTAGATTTGAATG+TGG 0.636625 8_1:-33266569 Msa1190380:CDS
TATACAGTGGTGTCCTACAG+AGG 0.674639 8_1:-33266597 Msa1190380:CDS
ATTATACATACCTTCAAGTG+GGG 0.680213 8_1:+33266619 None:intergenic
AGAACCAGTTGAAGGCGACG+AGG 0.683558 8_1:-33266975 Msa1190380:CDS
CCAGTTATCACAAACAAAGG+AGG 0.688592 8_1:-33266938 Msa1190380:CDS
AAGGTATGTATAATATACAG+TGG 0.689864 8_1:-33266610 Msa1190380:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TATTATACATACCTTCAAGT+GGG + chr8_1:33266945-33266964 None:intergenic 25.0%
! ATATTATACATACCTTCAAG+TGG + chr8_1:33266946-33266965 None:intergenic 25.0%
! AAGGTATGTATAATATACAG+TGG - chr8_1:33266950-33266969 Msa1190380:CDS 25.0%
TACATGAGCAAGAATTATGA+GGG + chr8_1:33266512-33266531 None:intergenic 30.0%
ATACATGAGCAAGAATTATG+AGG + chr8_1:33266513-33266532 None:intergenic 30.0%
GATCATATGGTAACTTCTTT+AGG - chr8_1:33266908-33266927 Msa1190380:CDS 30.0%
ATTATACATACCTTCAAGTG+GGG + chr8_1:33266944-33266963 None:intergenic 30.0%
! ATTCTTTCTGGAAAACAAGA+GGG + chr8_1:33267077-33267096 None:intergenic 30.0%
! TATTCTTTCTGGAAAACAAG+AGG + chr8_1:33267078-33267097 None:intergenic 30.0%
! CTTTGTTTGTGATAACTGGA+CGG + chr8_1:33266621-33266640 None:intergenic 35.0%
TTCATTTCTGCTGATCATAG+TGG + chr8_1:33266653-33266672 None:intergenic 35.0%
TCTCAAGACCAACATGTAAA+GGG + chr8_1:33266681-33266700 None:intergenic 35.0%
TTCTCAAGACCAACATGTAA+AGG + chr8_1:33266682-33266701 None:intergenic 35.0%
GTTGTGTACAATCAACAGAA+TGG - chr8_1:33266815-33266834 Msa1190380:CDS 35.0%
ACAATCAACAGAATGGAGAT+TGG - chr8_1:33266822-33266841 Msa1190380:CDS 35.0%
CAATCAACAGAATGGAGATT+GGG - chr8_1:33266823-33266842 Msa1190380:CDS 35.0%
GGTGAAAAAGATACTAAGAG+TGG - chr8_1:33266844-33266863 Msa1190380:CDS 35.0%
AAGATACTAAGAGTGGAAGA+AGG - chr8_1:33266851-33266870 Msa1190380:CDS 35.0%
! AGTGCTACTAATGGATCATA+TGG - chr8_1:33266895-33266914 Msa1190380:CDS 35.0%
CCACATTCAAATCTACAACT+AGG + chr8_1:33266994-33267013 None:intergenic 35.0%
CCTAGTTGTAGATTTGAATG+TGG - chr8_1:33266991-33267010 Msa1190380:CDS 35.0%
GTTGATATGCTGAATGAGAA+TGG - chr8_1:33267018-33267037 Msa1190380:CDS 35.0%
! TGAGAATGGTAAGATTTTGC+TGG - chr8_1:33267032-33267051 Msa1190380:CDS 35.0%
! AAACTGGGCTATTGTTGTTG+TGG + chr8_1:33266548-33266567 None:intergenic 40.0%
CGTCCAGTTATCACAAACAA+AGG - chr8_1:33266619-33266638 Msa1190380:CDS 40.0%
! CCTCCTTTGTTTGTGATAAC+TGG + chr8_1:33266625-33266644 None:intergenic 40.0%
CCAGTTATCACAAACAAAGG+AGG - chr8_1:33266622-33266641 Msa1190380:CDS 40.0%
GAATCATGCCCTTTACATGT+TGG - chr8_1:33266670-33266689 Msa1190380:CDS 40.0%
GTACACAACTTGATGAAGCT+TGG + chr8_1:33266804-33266823 None:intergenic 40.0%
! GGAAGAAGGTTGATTATCAC+TGG - chr8_1:33266865-33266884 Msa1190380:CDS 40.0%
! GGAAGAGATAGTGCTACTAA+TGG - chr8_1:33266886-33266905 Msa1190380:CDS 40.0%
! TTTCTGGAAAACAAGAGGGA+GGG + chr8_1:33267073-33267092 None:intergenic 40.0%
GACTGTGTCGAAGACAAACT+GGG + chr8_1:33266563-33266582 None:intergenic 45.0%
CAGTTTGTCTTCGACACAGT+CGG - chr8_1:33266562-33266581 Msa1190380:CDS 45.0%
!! CATGTTGGTCTTGAGAACAC+TGG - chr8_1:33266685-33266704 Msa1190380:CDS 45.0%
AACATCGTCGAAGTCGTGAT+GGG + chr8_1:33266752-33266771 None:intergenic 45.0%
TAACATCGTCGAAGTCGTGA+TGG + chr8_1:33266753-33266772 None:intergenic 45.0%
ATCACGACTTCGACGATGTT+AGG - chr8_1:33266752-33266771 Msa1190380:CDS 45.0%
TCACGACTTCGACGATGTTA+GGG - chr8_1:33266753-33266772 Msa1190380:CDS 45.0%
ATTGTAGAGACCCCACTTGA+AGG - chr8_1:33266931-33266950 Msa1190380:CDS 45.0%
TATACAGTGGTGTCCTACAG+AGG - chr8_1:33266963-33266982 Msa1190380:CDS 45.0%
CAACTAGGACATACCTCTGT+AGG + chr8_1:33266979-33266998 None:intergenic 45.0%
! AAGATTTTGCTGGCCCTTGA+TGG - chr8_1:33267042-33267061 Msa1190380:CDS 45.0%
! TTCTGGAAAACAAGAGGGAG+GGG + chr8_1:33267072-33267091 None:intergenic 45.0%
! CTTTCTGGAAAACAAGAGGG+AGG + chr8_1:33267074-33267093 None:intergenic 45.0%
CGACTGTGTCGAAGACAAAC+TGG + chr8_1:33266564-33266583 None:intergenic 50.0%
ACAGTCGGAGAACCAGTTGA+AGG - chr8_1:33266577-33266596 Msa1190380:CDS 50.0%
TATTCCTCGTCGCCTTCAAC+TGG + chr8_1:33266592-33266611 None:intergenic 50.0%
!! GGTCTTGAGAACACTGGCTT+AGG - chr8_1:33266691-33266710 Msa1190380:CDS 50.0%
!! GAGAACACTGGCTTAGGACA+CGG - chr8_1:33266697-33266716 Msa1190380:CDS 50.0%
! AAGTCGTGATGGGGAGCAAA+AGG + chr8_1:33266742-33266761 None:intergenic 50.0%
ACATCGTCGAAGTCGTGATG+GGG + chr8_1:33266751-33266770 None:intergenic 50.0%
! ATTTTGCTGGCCCTTGATGG+TGG - chr8_1:33267045-33267064 Msa1190380:CDS 50.0%
AGAACCAGTTGAAGGCGACG+AGG - chr8_1:33266585-33266604 Msa1190380:CDS 55.0%
!! CACTGGCTTAGGACACGGTC+TGG - chr8_1:33266702-33266721 Msa1190380:CDS 60.0%
AGGGAGGGGACCACCATCAA+GGG + chr8_1:33267058-33267077 None:intergenic 60.0%
GAGGGAGGGGACCACCATCA+AGG + chr8_1:33267059-33267078 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 33266484 33267098 33266484 ID=Msa1190380;Name=Msa1190380
chr8_1 mRNA 33266484 33267098 33266484 ID=Msa1190380-mRNA-1;Parent=Msa1190380;Name=Msa1190380-mRNA-1;_AED=0.19;_eAED=0.19;_QI=0|-1|0|1|-1|1|1|0|204
chr8_1 exon 33266484 33267098 33266484 ID=Msa1190380-mRNA-1:exon:11220;Parent=Msa1190380-mRNA-1
chr8_1 CDS 33266484 33267098 33266484 ID=Msa1190380-mRNA-1:cds;Parent=Msa1190380-mRNA-1
Gene Sequence

>Msa1190380

ATGTCAATGAGATTATCTACTAGAACCCTCATAATTCTTGCTCATGTATGTCTCTTTATAACCACAACAACAATAGCCCAGTTTGTCTTCGACACAGTCGGAGAACCAGTTGAAGGCGACGAGGAATATTTTATCCGTCCAGTTATCACAAACAAAGGAGGACGTTCCACTATGATCAGCAGAAATGAATCATGCCCTTTACATGTTGGTCTTGAGAACACTGGCTTAGGACACGGTCTGGTTGTGAAATTCACACCTTTTGCTCCCCATCACGACTTCGACGATGTTAGGGTTAACAGAGACTTAAGAATAACATTCCAAGCTTCATCAAGTTGTGTACAATCAACAGAATGGAGATTGGGTGAAAAAGATACTAAGAGTGGAAGAAGGTTGATTATCACTGGAAGAGATAGTGCTACTAATGGATCATATGGTAACTTCTTTAGGATTGTAGAGACCCCACTTGAAGGTATGTATAATATACAGTGGTGTCCTACAGAGGTATGTCCTAGTTGTAGATTTGAATGTGGAACTGTTGATATGCTGAATGAGAATGGTAAGATTTTGCTGGCCCTTGATGGTGGTCCCCTCCCTCTTGTTTTCCAGAAAGAATAA
Protein sequence

>Msa1190380

MSMRLSTRTLIILAHVCLFITTTTIAQFVFDTVGEPVEGDEEYFIRPVITNKGGRSTMISRNESCPLHVGLENTGLGHGLVVKFTPFAPHHDFDDVRVNRDLRITFQASSSCVQSTEWRLGEKDTKSGRRLIITGRDSATNGSYGNFFRIVETPLEGMYNIQWCPTEVCPSCRFECGTVDMLNENGKILLALDGGPLPLVFQKE*