AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06027


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06027.t1 MTR_8g099085 99.522 209 1 0 14 222 135 343 2.00e-148 417
MS.gene06027.t1 MTR_1g099420 73.148 216 58 0 7 222 127 342 5.61e-116 334
MS.gene06027.t1 MTR_8g467540 29.469 207 127 4 25 218 120 320 1.15e-17 80.5
MS.gene06027.t1 MTR_8g467540 29.469 207 127 4 25 218 120 320 1.15e-17 80.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06027.t1 AT5G60750 79.524 210 42 1 14 222 138 347 8.00e-116 334
MS.gene06027.t1 AT1G14270 45.882 85 46 0 134 218 124 208 1.51e-18 81.3
MS.gene06027.t1 AT1G14270 45.882 85 46 0 134 218 124 208 1.51e-18 81.3
MS.gene06027.t1 AT1G14270 45.882 85 46 0 134 218 144 228 2.58e-18 80.9
MS.gene06027.t1 AT1G14270 45.882 85 46 0 134 218 250 334 1.09e-17 80.9
MS.gene06027.t1 AT2G20725 41.573 89 48 1 130 218 215 299 3.29e-13 67.8

Find 63 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCAGTGACAAGGCTAAAT+AGG 0.223638 4.1:-5064696 None:intergenic
CAATGTTGTTGCATAGTCTT+TGG 0.238859 4.1:+5065199 MS.gene06027:CDS
ACACCACACAGGCATGTATT+TGG 0.285573 4.1:-5065052 None:intergenic
AAGGATTCTTTGACATTTAG+AGG 0.293855 4.1:+5064667 MS.gene06027:CDS
ATGCTGCCACTTATATTTCT+TGG 0.297795 4.1:+5065129 MS.gene06027:CDS
CCTTGCTGAAGCCAGTTATA+TGG 0.298053 4.1:-5064648 None:intergenic
AGTTTAGCCTGGAAGGAAAA+TGG 0.299581 4.1:+5064797 MS.gene06027:CDS
GCCTGTGTGGTGTGCAATAC+TGG 0.349411 4.1:+5065062 MS.gene06027:CDS
TGCTGCCACTTATATTTCTT+GGG 0.375579 4.1:+5065130 MS.gene06027:CDS
TCATGTTTCCTCTTGTCAAT+CGG 0.417015 4.1:+5064845 MS.gene06027:CDS
ATCAGTGACAAGGCTAAATA+GGG 0.430586 4.1:-5064695 None:intergenic
AGACTATGCAACAACATTGA+TGG 0.439339 4.1:-5065195 None:intergenic
TCCGTCCCCTTCCACCCGAC+TGG 0.444389 4.1:+5064770 MS.gene06027:CDS
GCCACTTATATTTCTTGGGA+TGG 0.450363 4.1:+5065134 MS.gene06027:CDS
CTTGCTGAAGCCAGTTATAT+GGG 0.459032 4.1:-5064647 None:intergenic
TTCTTTGACATTTAGAGGGC+AGG 0.461094 4.1:+5064672 MS.gene06027:CDS
TATATTTCTTGGGATGGTGA+TGG 0.475959 4.1:+5065140 MS.gene06027:CDS
TCGATGGCAGGATGGGTAGT+AGG 0.477125 4.1:-5064888 None:intergenic
TGATTGTTCAACACTTGAAA+GGG 0.482634 4.1:-5064920 None:intergenic
TTGATTGTTCAACACTTGAA+AGG 0.487389 4.1:-5064921 None:intergenic
CGACTGGTTCAAGTTTAGCC+TGG 0.494889 4.1:+5064786 MS.gene06027:CDS
ATATTTCTTGGGATGGTGAT+GGG 0.495092 4.1:+5065141 MS.gene06027:CDS
ATCGGTCTGCGCTCCTGTGT+GGG 0.497992 4.1:+5064990 MS.gene06027:CDS
CTTGAACCAGTCGGGTGGAA+GGG 0.500064 4.1:-5064776 None:intergenic
ACCTGTGTCGATGGCAGGAT+GGG 0.500774 4.1:-5064895 None:intergenic
TTGAACCAGTCGGGTGGAAG+GGG 0.510746 4.1:-5064775 None:intergenic
CCAGTTATATGGGCTGCAAA+AGG 0.512015 4.1:-5064637 None:intergenic
TATCGGTCTGCGCTCCTGTG+TGG 0.516259 4.1:+5064989 MS.gene06027:CDS
GACCTGTGTCGATGGCAGGA+TGG 0.530416 4.1:-5064896 None:intergenic
GATGTAACTGAAGGACTAGC+TGG 0.531776 4.1:+5064715 MS.gene06027:CDS
ACTTGAACCAGTCGGGTGGA+AGG 0.533549 4.1:-5064777 None:intergenic
AGGCTAAACTTGAACCAGTC+GGG 0.535684 4.1:-5064784 None:intergenic
GTTGTATGCAATTGTAGTAT+CGG 0.544728 4.1:+5064972 MS.gene06027:CDS
GGGTGACCTGTGTCGATGGC+AGG 0.545730 4.1:-5064900 None:intergenic
AATATGGTCGTTGCACTCCA+TGG 0.550589 4.1:-5064372 None:intergenic
TGGTTCAAGTTTAGCCTGGA+AGG 0.555909 4.1:+5064790 MS.gene06027:CDS
ACCATCCCAAGAAATATAAG+TGG 0.557728 4.1:-5065135 None:intergenic
TTGAACAATCAATAAAAGCA+AGG 0.561023 4.1:+5064932 MS.gene06027:CDS
GCATGTATTTGGTAAGTGAC+GGG 0.563519 4.1:-5065041 None:intergenic
ACCAGTCGGGTGGAAGGGGA+CGG 0.564379 4.1:-5064771 None:intergenic
GGCATGTATTTGGTAAGTGA+CGG 0.567093 4.1:-5065042 None:intergenic
CAGGCTAAACTTGAACCAGT+CGG 0.579922 4.1:-5064785 None:intergenic
AGGATTCTTTGACATTTAGA+GGG 0.596115 4.1:+5064668 MS.gene06027:CDS
GTGTGATATTTACACGGTCA+AGG 0.600158 4.1:+5065163 MS.gene06027:CDS
TTGTTGCATAGTCTTTGGAA+TGG 0.609310 4.1:+5065204 MS.gene06027:CDS
TGAGAGAGCCGATTGACAAG+AGG 0.610131 4.1:-5064853 None:intergenic
GCAGGATGGGTAGTAGGTCA+AGG 0.610496 4.1:-5064882 None:intergenic
GCATACAACAACATTGCCAC+AGG 0.610600 4.1:-5064958 None:intergenic
TGAACAATCAATAAAAGCAA+GGG 0.613230 4.1:+5064933 MS.gene06027:CDS
GGTCTGCGCTCCTGTGTGGG+AGG 0.621158 4.1:+5064993 MS.gene06027:CDS
GTAATCGATGGGTTGTACCA+TGG 0.622454 4.1:+5064355 None:intergenic
CCATATAACTGGCTTCAGCA+AGG 0.626497 4.1:+5064648 MS.gene06027:CDS
CTTGTCACTGATGTAACTGA+AGG 0.627885 4.1:+5064706 MS.gene06027:CDS
ACCCATCCTGCCATCGACAC+AGG 0.628035 4.1:+5064894 MS.gene06027:CDS
ACCAGTATTGCACACCACAC+AGG 0.628546 4.1:-5065063 None:intergenic
CTAAACTTGAACCAGTCGGG+TGG 0.632925 4.1:-5064781 None:intergenic
AATAAAAGCAAGGGATCCTG+TGG 0.652461 4.1:+5064942 MS.gene06027:CDS
GAAAGGGTGACCTGTGTCGA+TGG 0.653532 4.1:-5064904 None:intergenic
CTTCAGTTACATCAGTGACA+AGG 0.657659 4.1:-5064705 None:intergenic
AAAACTATTTCCTCCCACAC+AGG 0.659992 4.1:-5065003 None:intergenic
TTACCAAATACATGCCTGTG+TGG 0.698661 4.1:+5065049 MS.gene06027:CDS
TGATGGGTGTGATATTTACA+CGG 0.748257 4.1:+5065157 MS.gene06027:CDS
GTGACGGGAGTAGAAAACCG+CGG 0.770907 4.1:-5065026 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGAAACACTTACTTTTAATA+TGG - chr4.1:5064391-5064410 None:intergenic 20.0%
! TGAACAATCAATAAAAGCAA+GGG + chr4.1:5064933-5064952 MS.gene06027:CDS 25.0%
! TTGAACAATCAATAAAAGCA+AGG + chr4.1:5064932-5064951 MS.gene06027:CDS 25.0%
AAGGATTCTTTGACATTTAG+AGG + chr4.1:5064667-5064686 MS.gene06027:CDS 30.0%
AGGATTCTTTGACATTTAGA+GGG + chr4.1:5064668-5064687 MS.gene06027:CDS 30.0%
ATTCCTCGCAGTTAAAATTT+AGG + chr4.1:5064461-5064480 MS.gene06027:intron 30.0%
GTTGTATGCAATTGTAGTAT+CGG + chr4.1:5064972-5064991 MS.gene06027:CDS 30.0%
TGATTGTTCAACACTTGAAA+GGG - chr4.1:5064923-5064942 None:intergenic 30.0%
TTCCTCGCAGTTAAAATTTA+GGG + chr4.1:5064462-5064481 MS.gene06027:intron 30.0%
TTGATTGTTCAACACTTGAA+AGG - chr4.1:5064924-5064943 None:intergenic 30.0%
! GTTAAAATTTAGGGTACATG+TGG + chr4.1:5064471-5064490 MS.gene06027:intron 30.0%
!! TTGCACATTTTAACATACAG+AGG + chr4.1:5065106-5065125 MS.gene06027:CDS 30.0%
!!! CATTTTGGTTTATAGGATCT+TGG + chr4.1:5064608-5064627 MS.gene06027:intron 30.0%
ACCATCCCAAGAAATATAAG+TGG - chr4.1:5065138-5065157 None:intergenic 35.0%
AGACTATGCAACAACATTGA+TGG - chr4.1:5065198-5065217 None:intergenic 35.0%
ATATTTCTTGGGATGGTGAT+GGG + chr4.1:5065141-5065160 MS.gene06027:CDS 35.0%
ATCAGTGACAAGGCTAAATA+GGG - chr4.1:5064698-5064717 None:intergenic 35.0%
CAATGTTGTTGCATAGTCTT+TGG + chr4.1:5065199-5065218 MS.gene06027:CDS 35.0%
GATTTCAACTCTGCTCAATT+GGG - chr4.1:5064513-5064532 None:intergenic 35.0%
TATATTTCTTGGGATGGTGA+TGG + chr4.1:5065140-5065159 MS.gene06027:CDS 35.0%
TCATGTTTCCTCTTGTCAAT+CGG + chr4.1:5064845-5064864 MS.gene06027:CDS 35.0%
! ATGCTGCCACTTATATTTCT+TGG + chr4.1:5065129-5065148 MS.gene06027:CDS 35.0%
! TGATGGGTGTGATATTTACA+CGG + chr4.1:5065157-5065176 MS.gene06027:CDS 35.0%
! TGCTGCCACTTATATTTCTT+GGG + chr4.1:5065130-5065149 MS.gene06027:CDS 35.0%
! TTGTTGCATAGTCTTTGGAA+TGG + chr4.1:5065204-5065223 MS.gene06027:CDS 35.0%
!! ATGGCATTTTGATGTTGTCA+TGG + chr4.1:5064816-5064835 MS.gene06027:CDS 35.0%
!! TGGCATTTTGATGTTGTCAT+GGG + chr4.1:5064817-5064836 MS.gene06027:CDS 35.0%
!!! ACATCGGCATTTTGGTTTAT+AGG + chr4.1:5064601-5064620 MS.gene06027:intron 35.0%
!!! TACCCTAAATTTTAACTGCG+AGG - chr4.1:5064467-5064486 None:intergenic 35.0%
AAAACTATTTCCTCCCACAC+AGG - chr4.1:5065006-5065025 None:intergenic 40.0%
AACAATAAACGCTCAACCTG+AGG + chr4.1:5064536-5064555 MS.gene06027:intron 40.0%
AATAAAAGCAAGGGATCCTG+TGG + chr4.1:5064942-5064961 MS.gene06027:CDS 40.0%
AGGTTGAGCGTTTATTGTTC+AGG - chr4.1:5064535-5064554 None:intergenic 40.0%
AGTTTAGCCTGGAAGGAAAA+TGG + chr4.1:5064797-5064816 MS.gene06027:CDS 40.0%
CATCAGTGACAAGGCTAAAT+AGG - chr4.1:5064699-5064718 None:intergenic 40.0%
CTTCAGTTACATCAGTGACA+AGG - chr4.1:5064708-5064727 None:intergenic 40.0%
CTTGCTGAAGCCAGTTATAT+GGG - chr4.1:5064650-5064669 None:intergenic 40.0%
CTTGTCACTGATGTAACTGA+AGG + chr4.1:5064706-5064725 MS.gene06027:CDS 40.0%
GCATGTATTTGGTAAGTGAC+GGG - chr4.1:5065044-5065063 None:intergenic 40.0%
GCCACTTATATTTCTTGGGA+TGG + chr4.1:5065134-5065153 MS.gene06027:CDS 40.0%
GGATTTCAACTCTGCTCAAT+TGG - chr4.1:5064514-5064533 None:intergenic 40.0%
GGCATGTATTTGGTAAGTGA+CGG - chr4.1:5065045-5065064 None:intergenic 40.0%
GGTTATGCTTCTTTGGACAT+CGG + chr4.1:5064585-5064604 MS.gene06027:intron 40.0%
GTGTGATATTTACACGGTCA+AGG + chr4.1:5065163-5065182 MS.gene06027:CDS 40.0%
TTACCAAATACATGCCTGTG+TGG + chr4.1:5065049-5065068 MS.gene06027:CDS 40.0%
TTCTTTGACATTTAGAGGGC+AGG + chr4.1:5064672-5064691 MS.gene06027:CDS 40.0%
! TTCTTTGGACATCGGCATTT+TGG + chr4.1:5064593-5064612 MS.gene06027:intron 40.0%
!!! CAAAATGCCATTTTCCTTCC+AGG - chr4.1:5064807-5064826 None:intergenic 40.0%
AATATGGTCGTTGCACTCCA+TGG - chr4.1:5064375-5064394 None:intergenic 45.0%
ACACCACACAGGCATGTATT+TGG - chr4.1:5065055-5065074 None:intergenic 45.0%
AGGCTAAACTTGAACCAGTC+GGG - chr4.1:5064787-5064806 None:intergenic 45.0%
ATTCGTGCAATCTTTGACGC+AGG + chr4.1:5064564-5064583 MS.gene06027:intron 45.0%
ATTGCACGAATTACAGCCTC+AGG - chr4.1:5064555-5064574 None:intergenic 45.0%
CAGGCTAAACTTGAACCAGT+CGG - chr4.1:5064788-5064807 None:intergenic 45.0%
CCTTGCTGAAGCCAGTTATA+TGG - chr4.1:5064651-5064670 None:intergenic 45.0%
GCATACAACAACATTGCCAC+AGG - chr4.1:5064961-5064980 None:intergenic 45.0%
TAGGGTACATGTGGCAATCA+TGG + chr4.1:5064480-5064499 MS.gene06027:intron 45.0%
TGACGCAGGTTATGCTTCTT+TGG + chr4.1:5064578-5064597 MS.gene06027:intron 45.0%
! CCAGTTATATGGGCTGCAAA+AGG - chr4.1:5064640-5064659 None:intergenic 45.0%
! CCATATAACTGGCTTCAGCA+AGG + chr4.1:5064648-5064667 MS.gene06027:CDS 45.0%
! CCTTTTGCAGCCCATATAAC+TGG + chr4.1:5064637-5064656 MS.gene06027:CDS 45.0%
! GATGTAACTGAAGGACTAGC+TGG + chr4.1:5064715-5064734 MS.gene06027:CDS 45.0%
! TGGGAGGAAATAGTTTTCCG+CGG + chr4.1:5065009-5065028 MS.gene06027:CDS 45.0%
! TGGTTCAAGTTTAGCCTGGA+AGG + chr4.1:5064790-5064809 MS.gene06027:CDS 45.0%
ACCAGTATTGCACACCACAC+AGG - chr4.1:5065066-5065085 None:intergenic 50.0%
CTAAACTTGAACCAGTCGGG+TGG - chr4.1:5064784-5064803 None:intergenic 50.0%
TGAGAGAGCCGATTGACAAG+AGG - chr4.1:5064856-5064875 None:intergenic 50.0%
! CGACTGGTTCAAGTTTAGCC+TGG + chr4.1:5064786-5064805 MS.gene06027:CDS 50.0%
ACTTGAACCAGTCGGGTGGA+AGG - chr4.1:5064780-5064799 None:intergenic 55.0%
CTTGAACCAGTCGGGTGGAA+GGG - chr4.1:5064779-5064798 None:intergenic 55.0%
GAAAGGGTGACCTGTGTCGA+TGG - chr4.1:5064907-5064926 None:intergenic 55.0%
GCAGGATGGGTAGTAGGTCA+AGG - chr4.1:5064885-5064904 None:intergenic 55.0%
GCCTGTGTGGTGTGCAATAC+TGG + chr4.1:5065062-5065081 MS.gene06027:CDS 55.0%
TCGATGGCAGGATGGGTAGT+AGG - chr4.1:5064891-5064910 None:intergenic 55.0%
TTGAACCAGTCGGGTGGAAG+GGG - chr4.1:5064778-5064797 None:intergenic 55.0%
! ACCTGTGTCGATGGCAGGAT+GGG - chr4.1:5064898-5064917 None:intergenic 55.0%
! GTGACGGGAGTAGAAAACCG+CGG - chr4.1:5065029-5065048 None:intergenic 55.0%
ACCCATCCTGCCATCGACAC+AGG + chr4.1:5064894-5064913 MS.gene06027:CDS 60.0%
ATCGGTCTGCGCTCCTGTGT+GGG + chr4.1:5064990-5065009 MS.gene06027:CDS 60.0%
TATCGGTCTGCGCTCCTGTG+TGG + chr4.1:5064989-5065008 MS.gene06027:CDS 60.0%
! GACCTGTGTCGATGGCAGGA+TGG - chr4.1:5064899-5064918 None:intergenic 60.0%
ACCAGTCGGGTGGAAGGGGA+CGG - chr4.1:5064774-5064793 None:intergenic 65.0%
! GGGTGACCTGTGTCGATGGC+AGG - chr4.1:5064903-5064922 None:intergenic 65.0%
GGTCTGCGCTCCTGTGTGGG+AGG + chr4.1:5064993-5065012 MS.gene06027:CDS 70.0%
TCCGTCCCCTTCCACCCGAC+TGG + chr4.1:5064770-5064789 MS.gene06027:CDS 70.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 5064362 5065254 5064362 ID=MS.gene06027
chr4.1 mRNA 5064362 5065254 5064362 ID=MS.gene06027.t1;Parent=MS.gene06027
chr4.1 exon 5064362 5064398 5064362 ID=MS.gene06027.t1.exon1;Parent=MS.gene06027.t1
chr4.1 CDS 5064362 5064398 5064362 ID=cds.MS.gene06027.t1;Parent=MS.gene06027.t1
chr4.1 exon 5064623 5065254 5064623 ID=MS.gene06027.t1.exon2;Parent=MS.gene06027.t1
chr4.1 CDS 5064623 5065254 5064623 ID=cds.MS.gene06027.t1;Parent=MS.gene06027.t1
Gene Sequence

>MS.gene06027

ATGGGTTGTACCATGGAGTGCAACGACCATATTAAAAGTAAGTGTTTCTCTAAAGTTTCATCAAAGTATAATTATGAAAAGTTTCGCTTTTGTTTATCAATTCCTCGCAGTTAAAATTTAGGGTACATGTGGCAATCATGGAATGTATCCCAATTGAGCAGAGTTGAAATCCTGAACAATAAACGCTCAACCTGAGGCTGTAATTCGTGCAATCTTTGACGCAGGTTATGCTTCTTTGGACATCGGCATTTTGGTTTATAGGATCTTGGATGATTCCTTTTGCAGCCCATATAACTGGCTTCAGCAAGGATTCTTTGACATTTAGAGGGCAGGCCCTATTTAGCCTTGTCACTGATGTAACTGAAGGACTAGCTGGAATTGCAATTCTTGTTCGTTGTCTTTCACGATTCCGTCCCCTTCCACCCGACTGGTTCAAGTTTAGCCTGGAAGGAAAATGGCATTTTGATGTTGTCATGGGTTGTCTCATGTTTCCTCTTGTCAATCGGCTCTCTCAGTTCAACCTTGACCTACTACCCATCCTGCCATCGACACAGGTCACCCTTTCAAGTGTTGAACAATCAATAAAAGCAAGGGATCCTGTGGCAATGTTGTTGTATGCAATTGTAGTATCGGTCTGCGCTCCTGTGTGGGAGGAAATAGTTTTCCGCGGTTTTCTACTCCCGTCACTTACCAAATACATGCCTGTGTGGTGTGCAATACTGGTAAGTTCAGTTGCGTTTGCGCTTGCACATTTTAACATACAGAGGATGCTGCCACTTATATTTCTTGGGATGGTGATGGGTGTGATATTTACACGGTCAAGGAATTTATTGCCATCAATGTTGTTGCATAGTCTTTGGAATGGCTTTGTCTTTTTAGATTTGATGAAATAG

Protein sequence

>MS.gene06027.t1

MGCTMECNDHIKRSWMIPFAAHITGFSKDSLTFRGQALFSLVTDVTEGLAGIAILVRCLSRFRPLPPDWFKFSLEGKWHFDVVMGCLMFPLVNRLSQFNLDLLPILPSTQVTLSSVEQSIKARDPVAMLLYAIVVSVCAPVWEEIVFRGFLLPSLTKYMPVWCAILVSSVAFALAHFNIQRMLPLIFLGMVMGVIFTRSRNLLPSMLLHSLWNGFVFLDLMK