AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0210150

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0210150 MtrunA17_Chr5g0394621 84.483 174 26 1 1 173 1 174 1.36e-101 290
Msa0210150 MtrunA17_Chr5g0394631 68.966 174 53 1 1 173 1 174 5.05e-75 230
Msa0210150 MtrunA17_Chr5g0394631 68.263 167 42 6 1 162 214 374 5.04e-62 196
Msa0210150 MtrunA17_Chr1g0204951 59.394 165 62 3 1 162 1 163 7.81e-61 187
Msa0210150 MtrunA17_Chr1g0204971 59.477 153 58 2 1 151 1 151 1.11e-57 179
Msa0210150 MtrunA17_Chr7g0273661 35.294 136 85 1 16 151 3 135 4.24e-27 100
Msa0210150 MtrunA17_Chr7g0223351 33.824 136 85 2 20 155 7 137 3.84e-20 82.4
Msa0210150 MtrunA17_Chr7g0223361 32.026 153 99 3 17 168 4 152 5.82e-20 82.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0210150 AT2G32030.1 46.000 150 66 4 3 151 14 149 4.51e-39 132
Msa0210150 AT2G32020.1 47.794 136 64 2 21 155 19 148 3.14e-36 124
Msa0210150 AT3G22560.1 33.333 150 94 3 20 166 6 152 2.26e-20 83.6

Find 42 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCAAGGTCAGAAAGATTA+AGG 0.227074 2_1:+50074134 None:intergenic
CTCTTCTTTGTCACGTGGTT+TGG 0.270188 2_1:+50074189 None:intergenic
ATGTTCTAGGCTCTAAATAT+TGG 0.292142 2_1:-50073895 Msa0210150:CDS
GCAGAACTTGGCTATGTTCT+AGG 0.302641 2_1:-50073908 Msa0210150:CDS
TAAGGGGTCGGAGTGTGATT+TGG 0.307480 2_1:+50074152 None:intergenic
TGTTCTAGGCTCTAAATATT+GGG 0.316974 2_1:-50073894 Msa0210150:CDS
AAGGGGTCGGAGTGTGATTT+GGG 0.320072 2_1:+50074153 None:intergenic
ATATAGCTTCAAAGTTTCTA+TGG 0.332117 2_1:-50074018 Msa0210150:CDS
TCCATCAATGATCGTGCAAT+TGG 0.335248 2_1:-50073983 Msa0210150:CDS
CCCAATTGCACGATCATTGA+TGG 0.338330 2_1:+50073982 None:intergenic
AATGTTGGGTCTCAGAGTTT+TGG 0.354229 2_1:-50073773 Msa0210150:CDS
GCTCTAAATATTGGGGTAAA+GGG 0.356917 2_1:-50073886 Msa0210150:CDS
GGCTCTAAATATTGGGGTAA+AGG 0.422886 2_1:-50073887 Msa0210150:CDS
AGTTGCCAAGTTCTGCTCTT+GGG 0.428431 2_1:-50074083 Msa0210150:CDS
GTTGATGCCATCATCCTTGC+TGG 0.429573 2_1:+50074051 None:intergenic
CACTTGTTTCACAACACACT+TGG 0.439429 2_1:+50073859 None:intergenic
ATTCTGTGAGTTGTCTTACT+TGG 0.446468 2_1:-50073825 Msa0210150:CDS
AAGTTGCCAAGTTCTGCTCT+TGG 0.477212 2_1:-50074084 Msa0210150:CDS
AGGAAATATTTGTTCATGAA+AGG 0.477898 2_1:-50073718 Msa0210150:CDS
CCATCAATGATCGTGCAATT+GGG 0.483539 2_1:-50073982 Msa0210150:CDS
GTTCACTTGGTGATAAATCA+AGG 0.487497 2_1:-50073940 Msa0210150:CDS
GTGAGTTGTCTTACTTGGAA+AGG 0.487957 2_1:-50073820 Msa0210150:CDS
GCTTGAAGCTTTAGTTGATG+TGG 0.488968 2_1:-50073798 Msa0210150:CDS
TCTCTATCCTCAAGTTCACT+TGG 0.489247 2_1:-50073953 Msa0210150:CDS
TTCTGACCTTGATGATCTCA+TGG 0.490514 2_1:-50074125 Msa0210150:CDS
ATCAAGGTCAGAAAGATTAA+GGG 0.492658 2_1:+50074135 None:intergenic
TAGTTGATGTGGAAAATGTT+GGG 0.494202 2_1:-50073787 Msa0210150:CDS
TTAGTTGATGTGGAAAATGT+TGG 0.523001 2_1:-50073788 Msa0210150:CDS
AGGAACGAATGTGCAGAACT+TGG 0.523520 2_1:-50073920 Msa0210150:CDS
ACCTTGATGATCTCATGGTA+TGG 0.538119 2_1:-50074120 Msa0210150:CDS
TGTTGTGAAACAAGTGGTTA+AGG 0.541729 2_1:-50073852 Msa0210150:CDS
TTTATCACCAAGTGAACTTG+AGG 0.557862 2_1:+50073946 None:intergenic
CTCTACACCAGCAAGGATGA+TGG 0.559987 2_1:-50074058 Msa0210150:CDS
CTCTAAATATTGGGGTAAAG+GGG 0.564900 2_1:-50073885 Msa0210150:CDS
GAGTTCCCAAGAGCAGAACT+TGG 0.571214 2_1:+50074078 None:intergenic
ATTCTCTCTTCTTTGTCACG+TGG 0.580393 2_1:+50074184 None:intergenic
GGTCAGAAAGATTAAGGGGT+CGG 0.585362 2_1:+50074140 None:intergenic
GTTCTAGGCTCTAAATATTG+GGG 0.619040 2_1:-50073893 Msa0210150:CDS
TCCATACCATGAGATCATCA+AGG 0.632686 2_1:+50074119 None:intergenic
TCAAGGTCAGAAAGATTAAG+GGG 0.633672 2_1:+50074136 None:intergenic
TTGGGAACTCTACACCAGCA+AGG 0.679749 2_1:-50074065 Msa0210150:CDS
CAAGTGTGTTGTGAAACAAG+TGG 0.740021 2_1:-50073858 Msa0210150:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATAGCTTCAAAGTTTCTA+TGG - chr2_1:50073902-50073921 Msa0210150:CDS 25.0%
! AGGAAATATTTGTTCATGAA+AGG - chr2_1:50074202-50074221 Msa0210150:CDS 25.0%
ATCAAGGTCAGAAAGATTAA+GGG + chr2_1:50073788-50073807 None:intergenic 30.0%
!! ATGTTCTAGGCTCTAAATAT+TGG - chr2_1:50074025-50074044 Msa0210150:CDS 30.0%
!! TGTTCTAGGCTCTAAATATT+GGG - chr2_1:50074026-50074045 Msa0210150:CDS 30.0%
! TTAGTTGATGTGGAAAATGT+TGG - chr2_1:50074132-50074151 Msa0210150:CDS 30.0%
! TAGTTGATGTGGAAAATGTT+GGG - chr2_1:50074133-50074152 Msa0210150:CDS 30.0%
! AAAGTTGGTTTCCAAAAAGA+GGG - chr2_1:50074172-50074191 Msa0210150:CDS 30.0%
TCAAGGTCAGAAAGATTAAG+GGG + chr2_1:50073787-50073806 None:intergenic 35.0%
CATCAAGGTCAGAAAGATTA+AGG + chr2_1:50073789-50073808 None:intergenic 35.0%
TTTATCACCAAGTGAACTTG+AGG + chr2_1:50073977-50073996 None:intergenic 35.0%
! GTTCACTTGGTGATAAATCA+AGG - chr2_1:50073980-50073999 Msa0210150:CDS 35.0%
!! GTTCTAGGCTCTAAATATTG+GGG - chr2_1:50074027-50074046 Msa0210150:CDS 35.0%
! GCTCTAAATATTGGGGTAAA+GGG - chr2_1:50074034-50074053 Msa0210150:CDS 35.0%
CTCTAAATATTGGGGTAAAG+GGG - chr2_1:50074035-50074054 Msa0210150:CDS 35.0%
TGTTGTGAAACAAGTGGTTA+AGG - chr2_1:50074068-50074087 Msa0210150:CDS 35.0%
ATTCTGTGAGTTGTCTTACT+TGG - chr2_1:50074095-50074114 Msa0210150:CDS 35.0%
! GAAAGTTGGTTTCCAAAAAG+AGG - chr2_1:50074171-50074190 Msa0210150:CDS 35.0%
ATTCTCTCTTCTTTGTCACG+TGG + chr2_1:50073739-50073758 None:intergenic 40.0%
! TTCTGACCTTGATGATCTCA+TGG - chr2_1:50073795-50073814 Msa0210150:CDS 40.0%
! ACCTTGATGATCTCATGGTA+TGG - chr2_1:50073800-50073819 Msa0210150:CDS 40.0%
TCCATACCATGAGATCATCA+AGG + chr2_1:50073804-50073823 None:intergenic 40.0%
TCCATCAATGATCGTGCAAT+TGG - chr2_1:50073937-50073956 Msa0210150:CDS 40.0%
CCATCAATGATCGTGCAATT+GGG - chr2_1:50073938-50073957 Msa0210150:CDS 40.0%
TCTCTATCCTCAAGTTCACT+TGG - chr2_1:50073967-50073986 Msa0210150:CDS 40.0%
!! GGCTCTAAATATTGGGGTAA+AGG - chr2_1:50074033-50074052 Msa0210150:CDS 40.0%
CACTTGTTTCACAACACACT+TGG + chr2_1:50074064-50074083 None:intergenic 40.0%
CAAGTGTGTTGTGAAACAAG+TGG - chr2_1:50074062-50074081 Msa0210150:CDS 40.0%
GTGAGTTGTCTTACTTGGAA+AGG - chr2_1:50074100-50074119 Msa0210150:CDS 40.0%
! GCTTGAAGCTTTAGTTGATG+TGG - chr2_1:50074122-50074141 Msa0210150:CDS 40.0%
! AATGTTGGGTCTCAGAGTTT+TGG - chr2_1:50074147-50074166 Msa0210150:CDS 40.0%
!!! CTCAGAGTTTTGGAGAAAGT+TGG - chr2_1:50074157-50074176 Msa0210150:CDS 40.0%
CTCTTCTTTGTCACGTGGTT+TGG + chr2_1:50073734-50073753 None:intergenic 45.0%
GGTCAGAAAGATTAAGGGGT+CGG + chr2_1:50073783-50073802 None:intergenic 45.0%
AAGTTGCCAAGTTCTGCTCT+TGG - chr2_1:50073836-50073855 Msa0210150:CDS 45.0%
AGTTGCCAAGTTCTGCTCTT+GGG - chr2_1:50073837-50073856 Msa0210150:CDS 45.0%
CCCAATTGCACGATCATTGA+TGG + chr2_1:50073941-50073960 None:intergenic 45.0%
AGGAACGAATGTGCAGAACT+TGG - chr2_1:50074000-50074019 Msa0210150:CDS 45.0%
GCAGAACTTGGCTATGTTCT+AGG - chr2_1:50074012-50074031 Msa0210150:CDS 45.0%
TCCAAAAAGAGGGAGTTCTG+AGG - chr2_1:50074182-50074201 Msa0210150:CDS 45.0%
! TCCTCAGAACTCCCTCTTTT+TGG + chr2_1:50074186-50074205 None:intergenic 45.0%
AAGGGGTCGGAGTGTGATTT+GGG + chr2_1:50073770-50073789 None:intergenic 50.0%
TAAGGGGTCGGAGTGTGATT+TGG + chr2_1:50073771-50073790 None:intergenic 50.0%
GAGTTCCCAAGAGCAGAACT+TGG + chr2_1:50073845-50073864 None:intergenic 50.0%
TTGGGAACTCTACACCAGCA+AGG - chr2_1:50073855-50073874 Msa0210150:CDS 50.0%
CTCTACACCAGCAAGGATGA+TGG - chr2_1:50073862-50073881 Msa0210150:CDS 50.0%
GTTGATGCCATCATCCTTGC+TGG + chr2_1:50073872-50073891 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 50073709 50074233 50073709 ID=Msa0210150;Name=Msa0210150
chr2_1 mRNA 50073709 50074233 50073709 ID=Msa0210150-mRNA-1;Parent=Msa0210150;Name=Msa0210150-mRNA-1;_AED=0.26;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|174
chr2_1 exon 50073709 50074233 50073709 ID=Msa0210150-mRNA-1:exon:13836;Parent=Msa0210150-mRNA-1
chr2_1 CDS 50073709 50074233 50073709 ID=Msa0210150-mRNA-1:cds;Parent=Msa0210150-mRNA-1
Gene Sequence

>Msa0210150

ATGGAGATAACTTCTATTTCTTCCAAACCACGTGACAAAGAAGAGAGAATTGATCTAACCCAAATCACACTCCGACCCCTTAATCTTTCTGACCTTGATGATCTCATGGTATGGACAACTGATGAAAAAGTTGCCAAGTTCTGCTCTTGGGAACTCTACACCAGCAAGGATGATGGCATCAACTTCATTGAAAATATAGCTTCAAAGTTTCTATGGTGCAAAGCAATATCCATCAATGATCGTGCAATTGGGTGTGTTTCTCTATCCTCAAGTTCACTTGGTGATAAATCAAGGAACGAATGTGCAGAACTTGGCTATGTTCTAGGCTCTAAATATTGGGGTAAAGGGGTTGCCAAGTGTGTTGTGAAACAAGTGGTTAAGGCTGCATTCTGTGAGTTGTCTTACTTGGAAAGGCTTGAAGCTTTAGTTGATGTGGAAAATGTTGGGTCTCAGAGTTTTGGAGAAAGTTGGTTTCCAAAAAGAGGGAGTTCTGAGGAAATATTTGTTCATGAAAGGAAAAAGTAG
Protein sequence

>Msa0210150

MEITSISSKPRDKEERIDLTQITLRPLNLSDLDDLMVWTTDEKVAKFCSWELYTSKDDGINFIENIASKFLWCKAISINDRAIGCVSLSSSSLGDKSRNECAELGYVLGSKYWGKGVAKCVVKQVVKAAFCELSYLERLEALVDVENVGSQSFGESWFPKRGSSEEIFVHERKK*