AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003996

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003996.t1 MTR_4g064873 93.258 178 7 2 1 178 1 173 1.78e-117 330
MS.gene003996.t1 MTR_7g063220 37.107 159 57 5 20 178 23 138 3.83e-20 82.0
MS.gene003996.t1 MTR_1g075430 60.317 63 21 2 10 69 8 69 3.00e-16 73.2
MS.gene003996.t1 MTR_1g044225 44.304 79 43 1 13 90 18 96 2.00e-14 67.8
MS.gene003996.t1 MTR_3g068095 65.909 44 13 1 21 64 55 96 2.79e-13 66.2
MS.gene003996.t1 MTR_1g070250 70.732 41 11 1 21 60 38 78 3.94e-13 64.7
MS.gene003996.t1 MTR_4g021270 74.286 35 9 0 21 55 59 93 4.25e-13 66.2
MS.gene003996.t1 MTR_2g076060 30.460 174 85 6 21 162 50 219 4.52e-13 65.1
MS.gene003996.t1 MTR_5g014400 32.768 177 79 6 21 165 80 248 4.85e-13 65.5
MS.gene003996.t1 MTR_5g080660 72.973 37 10 0 21 57 47 83 7.08e-13 64.7
MS.gene003996.t1 MTR_1g070265 66.667 33 11 0 21 53 35 67 1.95e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003996.t1 AT3G53820 35.220 159 63 7 21 174 19 142 1.98e-17 75.1
MS.gene003996.t1 AT3G09290 80.000 35 7 0 21 55 33 67 1.24e-15 71.2
MS.gene003996.t1 AT5G06070 72.222 36 10 0 21 56 53 88 2.40e-13 65.9
MS.gene003996.t1 AT5G43540 55.357 56 17 2 23 70 35 90 8.68e-13 62.8
MS.gene003996.t1 AT2G37740 59.091 44 18 0 11 54 27 70 1.61e-12 64.7
MS.gene003996.t1 AT3G23130 68.571 35 11 0 21 55 45 79 2.56e-12 62.8
MS.gene003996.t1 AT4G17810 32.414 145 83 4 21 165 44 173 5.91e-12 61.2
MS.gene003996.t1 AT2G42410 56.098 41 18 0 21 61 73 113 2.47e-11 60.8
MS.gene003996.t1 AT2G42410 56.098 41 18 0 21 61 47 87 2.48e-11 60.5
MS.gene003996.t1 AT2G42410 56.098 41 18 0 21 61 47 87 2.48e-11 60.5
MS.gene003996.t1 AT4G17810 64.103 39 13 1 21 58 44 82 2.73e-11 60.1

Find 33 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTCAATTACCATCTAATT+TGG 0.170331 4.3:+39251853 MS.gene003996:CDS
CTGGTACCCGTTGGCTTTGA+TGG 0.228413 4.3:-39252172 None:intergenic
AATTAGATGGTAATTGAGTT+TGG 0.335367 4.3:-39251850 None:intergenic
TTAGACCTTGAACTAAGATT+AGG 0.355982 4.3:+39252133 MS.gene003996:CDS
ACAATATTAGTATTCAAGTT+TGG 0.372182 4.3:-39251911 None:intergenic
TAGACCTTGAACTAAGATTA+GGG 0.384535 4.3:+39252134 MS.gene003996:CDS
AATTACACTCATAAGATCTA+AGG 0.395050 4.3:-39251727 None:intergenic
CCCTTTGAACTTGACCTTGT+GGG 0.399837 4.3:-39252054 None:intergenic
GCTTTGCTTTGTCTTTCCTA+TGG 0.427666 4.3:-39251802 None:intergenic
GGAAATTATTACTACACAAA+AGG 0.438306 4.3:+39252075 MS.gene003996:CDS
GAGTCTGATCAACATGATAA+AGG 0.445854 4.3:+39251674 MS.gene003996:CDS
GAACTTCCCTCCAAATTAGA+TGG 0.446674 4.3:-39251863 None:intergenic
ATTTGTGTTTCATTTCTAGT+TGG 0.455559 4.3:-39252025 None:intergenic
TTCTCTAATGCACAAGCTCT+TGG 0.469634 4.3:+39251764 MS.gene003996:CDS
AGAATTTCATCACCTCTAGA+AGG 0.475968 4.3:-39251959 None:intergenic
TCCCACAAGGTCAAGTTCAA+AGG 0.482764 4.3:+39252053 MS.gene003996:CDS
TCAATTACCATCTAATTTGG+AGG 0.483513 4.3:+39251856 MS.gene003996:CDS
CACCTCTAGAAGGAGCTTGT+TGG 0.486575 4.3:-39251949 None:intergenic
CCCACAAGGTCAAGTTCAAA+GGG 0.499228 4.3:+39252054 MS.gene003996:CDS
TTTGATGGATCATGTGGCTC+AGG 0.503162 4.3:-39252157 None:intergenic
CAGGCCCTAATCTTAGTTCA+AGG 0.522982 4.3:-39252138 None:intergenic
CATGATCCATCAAAGCCAAC+GGG 0.534522 4.3:+39252166 MS.gene003996:CDS
TCTAATGCACAAGCTCTTGG+TGG 0.538110 4.3:+39251767 MS.gene003996:CDS
TCCCTTTGAACTTGACCTTG+TGG 0.538332 4.3:-39252055 None:intergenic
TCCGATGAAGAATCTTGAGC+AGG 0.539565 4.3:-39252109 None:intergenic
ACCTGCTCAAGATTCTTCAT+CGG 0.568940 4.3:+39252108 MS.gene003996:CDS
CAATTACCATCTAATTTGGA+GGG 0.604261 4.3:+39251857 MS.gene003996:CDS
GTGGACACATGAATATCCAT+AGG 0.606044 4.3:+39251786 MS.gene003996:CDS
CACCAACAAGCTCCTTCTAG+AGG 0.609713 4.3:+39251947 MS.gene003996:CDS
ACATGATCCATCAAAGCCAA+CGG 0.613032 4.3:+39252165 MS.gene003996:CDS
GTTGGCTTTGATGGATCATG+TGG 0.637580 4.3:-39252163 None:intergenic
TCTGATCAACATGATAAAGG+TGG 0.671643 4.3:+39251677 MS.gene003996:CDS
ACACAAATTAATATCCCACA+AGG 0.716304 4.3:+39252040 MS.gene003996:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACAATATTAGTATTCAAGTT+TGG - chr4.3:39251914-39251933 None:intergenic 20.0%
! AACTCAATTACCATCTAATT+TGG + chr4.3:39251853-39251872 MS.gene003996:CDS 25.0%
! AATTACACTCATAAGATCTA+AGG - chr4.3:39251730-39251749 None:intergenic 25.0%
! AATTAGATGGTAATTGAGTT+TGG - chr4.3:39251853-39251872 None:intergenic 25.0%
! GGAAATTATTACTACACAAA+AGG + chr4.3:39252075-39252094 MS.gene003996:CDS 25.0%
!!! ATTTGTGTTTCATTTCTAGT+TGG - chr4.3:39252028-39252047 None:intergenic 25.0%
ACACAAATTAATATCCCACA+AGG + chr4.3:39252040-39252059 MS.gene003996:CDS 30.0%
CAATTACCATCTAATTTGGA+GGG + chr4.3:39251857-39251876 MS.gene003996:CDS 30.0%
TAGACCTTGAACTAAGATTA+GGG + chr4.3:39252134-39252153 MS.gene003996:CDS 30.0%
TCAATTACCATCTAATTTGG+AGG + chr4.3:39251856-39251875 MS.gene003996:CDS 30.0%
TTAGACCTTGAACTAAGATT+AGG + chr4.3:39252133-39252152 MS.gene003996:CDS 30.0%
AGAATTTCATCACCTCTAGA+AGG - chr4.3:39251962-39251981 None:intergenic 35.0%
GAGTCTGATCAACATGATAA+AGG + chr4.3:39251674-39251693 MS.gene003996:CDS 35.0%
TCTGATCAACATGATAAAGG+TGG + chr4.3:39251677-39251696 MS.gene003996:CDS 35.0%
! GAGTGTAATTTTTGCAAGAG+AGG + chr4.3:39251740-39251759 MS.gene003996:CDS 35.0%
ACATGATCCATCAAAGCCAA+CGG + chr4.3:39252165-39252184 MS.gene003996:CDS 40.0%
ACCTGCTCAAGATTCTTCAT+CGG + chr4.3:39252108-39252127 MS.gene003996:CDS 40.0%
GAACTTCCCTCCAAATTAGA+TGG - chr4.3:39251866-39251885 None:intergenic 40.0%
GCTTTGCTTTGTCTTTCCTA+TGG - chr4.3:39251805-39251824 None:intergenic 40.0%
GTGGACACATGAATATCCAT+AGG + chr4.3:39251786-39251805 MS.gene003996:CDS 40.0%
TTCTCTAATGCACAAGCTCT+TGG + chr4.3:39251764-39251783 MS.gene003996:CDS 40.0%
!! AAGAATTTTCTGGTACCCGT+TGG - chr4.3:39252184-39252203 None:intergenic 40.0%
!! GTTGGTGATTCAGCAAAAAG+TGG - chr4.3:39252010-39252029 None:intergenic 40.0%
CAGGCCCTAATCTTAGTTCA+AGG - chr4.3:39252141-39252160 None:intergenic 45.0%
CATGATCCATCAAAGCCAAC+GGG + chr4.3:39252166-39252185 MS.gene003996:CDS 45.0%
CCCACAAGGTCAAGTTCAAA+GGG + chr4.3:39252054-39252073 MS.gene003996:CDS 45.0%
CCCTTTGAACTTGACCTTGT+GGG - chr4.3:39252057-39252076 None:intergenic 45.0%
TCCCACAAGGTCAAGTTCAA+AGG + chr4.3:39252053-39252072 MS.gene003996:CDS 45.0%
TCCCTTTGAACTTGACCTTG+TGG - chr4.3:39252058-39252077 None:intergenic 45.0%
TCCGATGAAGAATCTTGAGC+AGG - chr4.3:39252112-39252131 None:intergenic 45.0%
TCTAATGCACAAGCTCTTGG+TGG + chr4.3:39251767-39251786 MS.gene003996:CDS 45.0%
! TTTGATGGATCATGTGGCTC+AGG - chr4.3:39252160-39252179 None:intergenic 45.0%
!! GTTGGCTTTGATGGATCATG+TGG - chr4.3:39252166-39252185 None:intergenic 45.0%
CACCAACAAGCTCCTTCTAG+AGG + chr4.3:39251947-39251966 MS.gene003996:CDS 50.0%
! CACCTCTAGAAGGAGCTTGT+TGG - chr4.3:39251952-39251971 None:intergenic 50.0%
!! CTGGTACCCGTTGGCTTTGA+TGG - chr4.3:39252175-39252194 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 39251671 39252207 39251671 ID=MS.gene003996
chr4.3 mRNA 39251671 39252207 39251671 ID=MS.gene003996.t1;Parent=MS.gene003996
chr4.3 exon 39251671 39252207 39251671 ID=MS.gene003996.t1.exon1;Parent=MS.gene003996.t1
chr4.3 CDS 39251671 39252207 39251671 ID=cds.MS.gene003996.t1;Parent=MS.gene003996.t1
Gene Sequence

>MS.gene003996

ATGGAGTCTGATCAACATGATAAAGGTGGTGATGATCAAGATGCAAAACAAGTGAACCTTAGATCTTATGAGTGTAATTTTTGCAAGAGAGGATTCTCTAATGCACAAGCTCTTGGTGGACACATGAATATCCATAGGAAAGACAAAGCAAAGCTCAAACAACAATCTTCAACAAATTACCAAACTCAATTACCATCTAATTTGGAGGGAAGTTCTAGTGAAGAGATCAACAAATTATTACCAAACTTGAATACTAATATTGTGTCTCAACAAGATCACCAACAAGCTCCTTCTAGAGGTGATGAAATTCTTGTAACTCAAGTGAGAACACAACTTCCACTTTTTGCTGAATCACCAACTAGAAATGAAACACAAATTAATATCCCACAAGGTCAAGTTCAAAGGGAAATTATTACTACACAAAAGGCTTTGTTATTACCTGCTCAAGATTCTTCATCGGAGTTAGACCTTGAACTAAGATTAGGGCCTGAGCCACATGATCCATCAAAGCCAACGGGTACCAGAAAATTCTTTTAA
Protein sequence

>MS.gene003996.t1

MESDQHDKGGDDQDAKQVNLRSYECNFCKRGFSNAQALGGHMNIHRKDKAKLKQQSSTNYQTQLPSNLEGSSSEEINKLLPNLNTNIVSQQDHQQAPSRGDEILVTQVRTQLPLFAESPTRNETQINIPQGQVQREIITTQKALLLPAQDSSSELDLELRLGPEPHDPSKPTGTRKFF