AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene75835

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75835.t1 MTR_2g049530 71.751 177 17 2 1 146 1 175 2.63e-86 252
MS.gene75835.t1 MTR_2g049630 55.294 170 43 2 1 139 1 168 1.70e-56 182
MS.gene75835.t1 MTR_2g049610 48.421 190 59 3 5 159 3 188 1.62e-52 168
MS.gene75835.t1 MTR_4g107170 36.486 222 83 8 5 184 3 208 1.84e-33 120
MS.gene75835.t1 MTR_4g045977 35.217 230 97 8 1 185 1 223 7.63e-31 115
MS.gene75835.t1 MTR_6g005440 34.641 153 68 3 5 125 3 155 4.90e-21 88.6
MS.gene75835.t1 MTR_6g005450 33.333 153 70 2 5 125 3 155 2.26e-19 84.3
MS.gene75835.t1 MTR_1g115290 33.333 153 61 4 40 161 2 144 6.55e-19 79.7
MS.gene75835.t1 MTR_1g114730 31.429 175 81 3 5 140 3 177 8.52e-19 82.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATAAAAGTTGATTCTTATA+TGG 0.256581 2.1:-42679426 None:intergenic
CACAATCTCTTTGTGCACTT+TGG 0.360623 2.1:-42679096 None:intergenic
TTTATCACAAGCATCAATCT+TGG 0.387641 2.1:-42679201 None:intergenic
AAAGGATCATCAGAGCTATA+TGG 0.400445 2.1:-42679353 None:intergenic
AGTTTATGATATTAGTGAAA+TGG 0.403158 2.1:+42679322 MS.gene75835:CDS
CAATCATAGAAGCAAGAGAT+TGG 0.430450 2.1:+42678842 MS.gene75835:CDS
CCATGTTTCATTAACATGGA+TGG 0.445316 2.1:+42679143 MS.gene75835:CDS
TCAAGGGTATACTGCCTTTG+AGG 0.461147 2.1:-42679284 None:intergenic
GGATCCATGTTTCATTAACA+TGG 0.484124 2.1:+42679139 MS.gene75835:CDS
GGCATTTACAATAGCAGTGA+AGG 0.489452 2.1:-42679180 None:intergenic
CATGTTTCATTAACATGGAT+GGG 0.492136 2.1:+42679144 MS.gene75835:CDS
CTTGCTTCAAATGATCATCA+AGG 0.510589 2.1:-42679301 None:intergenic
ATATCATCAAGTGGCTTCAA+AGG 0.513800 2.1:-42679371 None:intergenic
CCATCCATGTTAATGAAACA+TGG 0.517489 2.1:-42679143 None:intergenic
ATGAAACATGGATCCCAAGT+TGG 0.522632 2.1:-42679131 None:intergenic
TGAAGAACAAGTATCCAACT+TGG 0.543614 2.1:+42679117 MS.gene75835:CDS
GATGGTGATGGTGATGGTGA+TGG 0.551622 2.1:+42678924 MS.gene75835:CDS
GCTTGCTTGATTGTATATGA+TGG 0.565053 2.1:+42678906 MS.gene75835:CDS
GTATATGATGGTGATGGTGA+TGG 0.573214 2.1:+42678918 MS.gene75835:CDS
CCTTGCATGACACTCCTCAA+AGG 0.584844 2.1:+42679270 MS.gene75835:CDS
TGATATTATTAATGAGACTG+TGG 0.596644 2.1:+42679388 MS.gene75835:CDS
TTGCTTCAAATGATCATCAA+GGG 0.599459 2.1:-42679300 None:intergenic
ACATTCAAGATGAAAGAGCT+CGG 0.609572 2.1:+42678808 MS.gene75835:CDS
AGGCACTAGTTTGATCACCT+TGG 0.609845 2.1:-42679250 None:intergenic
TTGATTGTATATGATGGTGA+TGG 0.617734 2.1:+42678912 MS.gene75835:CDS
GTAGAAATGGGTCGTCGACG+TGG 0.619828 2.1:+42678768 None:intergenic
GAAGAACAAGTATCCAACTT+GGG 0.633303 2.1:+42679118 MS.gene75835:CDS
CCTTTGAGGAGTGTCATGCA+AGG 0.640393 2.1:-42679270 None:intergenic
TCATTAATAATATCATCAAG+TGG 0.648809 2.1:-42679380 None:intergenic
ATGCTGAAAACTATGCACCA+AGG 0.728933 2.1:+42679233 MS.gene75835:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTTTATGATATTAGTGAAA+TGG + chr2.1:42679322-42679341 MS.gene75835:CDS 20.0%
!! TCATTAATAATATCATCAAG+TGG - chr2.1:42679383-42679402 None:intergenic 20.0%
! TGATATTATTAATGAGACTG+TGG + chr2.1:42679388-42679407 MS.gene75835:CDS 25.0%
!! TCTGAATTTTCTAACAAGTT+TGG + chr2.1:42678876-42678895 MS.gene75835:CDS 25.0%
ATATGAGCAACAAAAGATTG+AGG + chr2.1:42679001-42679020 MS.gene75835:intron 30.0%
CAAAAGATTCGACAATTGTA+CGG + chr2.1:42678964-42678983 MS.gene75835:intron 30.0%
CATGTTTCATTAACATGGAT+GGG + chr2.1:42679144-42679163 MS.gene75835:CDS 30.0%
TATGAGCAACAAAAGATTGA+GGG + chr2.1:42679002-42679021 MS.gene75835:intron 30.0%
TTGCTCATATTATTCAAGCA+TGG - chr2.1:42678991-42679010 None:intergenic 30.0%
TTGCTTCAAATGATCATCAA+GGG - chr2.1:42679303-42679322 None:intergenic 30.0%
TTTATCACAAGCATCAATCT+TGG - chr2.1:42679204-42679223 None:intergenic 30.0%
! GAATCTTTTGACATAGTCAT+TGG - chr2.1:42678954-42678973 None:intergenic 30.0%
! TTGATTGTATATGATGGTGA+TGG + chr2.1:42678912-42678931 MS.gene75835:CDS 30.0%
AAAGGATCATCAGAGCTATA+TGG - chr2.1:42679356-42679375 None:intergenic 35.0%
ACATTCAAGATGAAAGAGCT+CGG + chr2.1:42678808-42678827 MS.gene75835:CDS 35.0%
ATATCATCAAGTGGCTTCAA+AGG - chr2.1:42679374-42679393 None:intergenic 35.0%
CAATCATAGAAGCAAGAGAT+TGG + chr2.1:42678842-42678861 MS.gene75835:CDS 35.0%
CCATCCATGTTAATGAAACA+TGG - chr2.1:42679146-42679165 None:intergenic 35.0%
CCATGTTTCATTAACATGGA+TGG + chr2.1:42679143-42679162 MS.gene75835:CDS 35.0%
CTTGCTTCAAATGATCATCA+AGG - chr2.1:42679304-42679323 None:intergenic 35.0%
GAAGAACAAGTATCCAACTT+GGG + chr2.1:42679118-42679137 MS.gene75835:CDS 35.0%
GCTTGCTTGATTGTATATGA+TGG + chr2.1:42678906-42678925 MS.gene75835:CDS 35.0%
GGATCCATGTTTCATTAACA+TGG + chr2.1:42679139-42679158 MS.gene75835:CDS 35.0%
TGAAGAACAAGTATCCAACT+TGG + chr2.1:42679117-42679136 MS.gene75835:CDS 35.0%
ATGAAACATGGATCCCAAGT+TGG - chr2.1:42679134-42679153 None:intergenic 40.0%
ATGCTGAAAACTATGCACCA+AGG + chr2.1:42679233-42679252 MS.gene75835:CDS 40.0%
CACAATCTCTTTGTGCACTT+TGG - chr2.1:42679099-42679118 None:intergenic 40.0%
GGCATTTACAATAGCAGTGA+AGG - chr2.1:42679183-42679202 None:intergenic 40.0%
!! GTATATGATGGTGATGGTGA+TGG + chr2.1:42678918-42678937 MS.gene75835:CDS 40.0%
! AGGCACTAGTTTGATCACCT+TGG - chr2.1:42679253-42679272 None:intergenic 45.0%
! TCAAGGGTATACTGCCTTTG+AGG - chr2.1:42679287-42679306 None:intergenic 45.0%
CCTTGCATGACACTCCTCAA+AGG + chr2.1:42679270-42679289 MS.gene75835:CDS 50.0%
!! CCTTTGAGGAGTGTCATGCA+AGG - chr2.1:42679273-42679292 None:intergenic 50.0%
!! GATGGTGATGGTGATGGTGA+TGG + chr2.1:42678924-42678943 MS.gene75835:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 42678774 42679433 42678774 ID=MS.gene75835
chr2.1 mRNA 42678774 42679433 42678774 ID=MS.gene75835.t1;Parent=MS.gene75835
chr2.1 exon 42678774 42678980 42678774 ID=MS.gene75835.t1.exon1;Parent=MS.gene75835.t1
chr2.1 CDS 42678774 42678980 42678774 ID=cds.MS.gene75835.t1;Parent=MS.gene75835.t1
chr2.1 exon 42679074 42679433 42679074 ID=MS.gene75835.t1.exon2;Parent=MS.gene75835.t1
chr2.1 CDS 42679074 42679433 42679074 ID=cds.MS.gene75835.t1;Parent=MS.gene75835.t1
Gene Sequence

>MS.gene75835

ATGGGTCGTCGACGTGGAAAATTAACTTTGAAACACATTCAAGATGAAAGAGCTCGGAAATTAGCTTTCAATCATAGAAGCAAGAGATTGGCAAAAAGAGTTTCTGAATTTTCTAACAAGTTTGGAGTTGAAGCTTGCTTGATTGTATATGATGGTGATGGTGATGGTGATGGTAGACCAATGACTATGTCAAAAGATTCGACAATTGTACGGTCCATGCTTGAATAATATGAGCAACAAAAGATTGAGGGTACAACTACAAAGATCTTTGATGTGAAAGACTATTTTGCAAATAAGAAGAATAAGATTGAAGCTGAGATTTCCAAAGTGCACAAAGAGATTGTGAAGAACAAGTATCCAACTTGGGATCCATGTTTCATTAACATGGATGGGAAGCAACTCAAAGCCTTCACTGCTATTGTAAATGCCAAGATTGATGCTTGTGATAAAAAAATTAGCATGCTGAAAACTATGCACCAAGGTGATCAAACTAGTGCCTTGCATGACACTCCTCAAAGGCAGTATACCCTTGATGATCATTTGAAGCAAGTTTATGATATTAGTGAAATGGTTCAAATGCCATATAGCTCTGATGATCCTTTGAAGCCACTTGATGATATTATTAATGAGACTGTGGATTTCACTAATCATGCCATATAA
Protein sequence

>MS.gene75835.t1

MGRRRGKLTLKHIQDERARKLAFNHRSKRLAKRVSEFSNKFGVEACLIVYDGDGDGDGRPMTMSKDSTINKIEAEISKVHKEIVKNKYPTWDPCFINMDGKQLKAFTAIVNAKIDACDKKISMLKTMHQGDQTSALHDTPQRQYTLDDHLKQVYDISEMVQMPYSSDDPLKPLDDIINETVDFTNHAI