AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062861

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062861.t1 MTR_1g043450 98.058 103 2 0 1 103 50 152 4.60e-68 201
MS.gene062861.t1 MTR_1g074040 71.845 103 29 0 1 103 49 151 9.30e-52 159
MS.gene062861.t1 MTR_1g073950 69.903 103 31 0 1 103 50 152 4.83e-50 155
MS.gene062861.t1 MTR_4g021340 54.808 104 45 1 1 102 51 154 6.09e-34 114
MS.gene062861.t1 MTR_4g058950 39.604 101 60 1 2 102 85 184 2.97e-19 78.2
MS.gene062861.t1 MTR_4g113590 63.043 46 17 0 1 46 9 54 1.31e-14 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062861.t1 AT3G23200 67.647 102 33 0 1 102 23 124 4.73e-46 144
MS.gene062861.t1 AT3G23200 67.647 102 33 0 1 102 50 151 6.12e-46 145
MS.gene062861.t1 AT3G53850 52.885 104 47 1 1 102 50 153 8.89e-34 114
MS.gene062861.t1 AT3G53850 52.885 104 47 1 1 102 50 153 8.89e-34 114
MS.gene062861.t1 AT3G53850 52.885 104 47 1 1 102 37 140 9.51e-34 114
MS.gene062861.t1 AT5G02060 50.000 102 49 1 1 100 50 151 3.03e-25 92.8
MS.gene062861.t1 AT2G28370 44.000 100 55 1 3 102 80 178 7.28e-21 82.4
MS.gene062861.t1 AT2G37200 42.045 88 49 2 14 101 93 178 5.57e-19 77.4
MS.gene062861.t1 AT2G37200 42.045 88 49 2 14 101 122 207 1.03e-18 77.4

Find 20 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATTAACCAAAGCATTATT+AGG 0.170267 1.1:+27410990 None:intergenic
GATATGGGACATTGCCATTT+TGG 0.170837 1.1:-27411085 MS.gene062861:CDS
GCCTCTTTGTTGTTGGTGAT+TGG 0.275327 1.1:-27411539 MS.gene062861:CDS
CAATGGCTTTACAAATCATT+TGG 0.304130 1.1:-27411635 MS.gene062861:CDS
TTTGACACTCCTCTCCAAAA+TGG 0.331427 1.1:+27411071 None:intergenic
CCTCTTTGTTGTTGGTGATT+GGG 0.376698 1.1:-27411538 MS.gene062861:intron
GCTGCAGCTTCTGCCTCAGC+TGG 0.388706 1.1:-27411130 MS.gene062861:CDS
TATTAACCAAAGCATTATTA+GGG 0.389148 1.1:+27410991 None:intergenic
TTGATTAGCCTCTTTGTTGT+TGG 0.412424 1.1:-27411546 MS.gene062861:CDS
TATCATCCCTAATAATGCTT+TGG 0.418492 1.1:-27410997 MS.gene062861:CDS
TTCGTTGGATGCTTATGCTT+TGG 0.430874 1.1:-27411598 MS.gene062861:CDS
ATGCTTTGGTTAATAGCAGC+AGG 0.438809 1.1:-27410983 MS.gene062861:CDS
AGGCAAAAGCAACAGAAATC+TGG 0.443728 1.1:+27411044 None:intergenic
ACAAAGAGGCTAATCAATAC+AGG 0.449483 1.1:+27411552 None:intergenic
AATGGCAATGTCCCATATCA+TGG 0.478377 1.1:+27411089 None:intergenic
CCCAATCACCAACAACAAAG+AGG 0.590501 1.1:+27411538 None:intergenic
CAAAGAGGCTAATCAATACA+GGG 0.608265 1.1:+27411553 None:intergenic
AATTGAGATCCAGCTCATGA+AGG 0.614269 1.1:+27411024 None:intergenic
TGCTTTGGTTAATAGCAGCA+GGG 0.625504 1.1:-27410982 MS.gene062861:CDS
CAAAACTGTAAGTCCAGCTG+AGG 0.661899 1.1:+27411117 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGTTATAAGTTGTTTTCAT+AGG + chr1.1:27411326-27411345 None:intergenic 20.0%
!!! TATTAACCAAAGCATTATTA+GGG + chr1.1:27411624-27411643 None:intergenic 20.0%
! AAACAGTTTCACAAATTCTA+AGG + chr1.1:27411227-27411246 None:intergenic 25.0%
! TTGCTTCAAACAAATTAGTT+AGG + chr1.1:27411128-27411147 None:intergenic 25.0%
!! CTATTAACCAAAGCATTATT+AGG + chr1.1:27411625-27411644 None:intergenic 25.0%
!! TAGAATTTGTGAAACTGTTT+TGG - chr1.1:27411227-27411246 MS.gene062861:intron 25.0%
!!! TAACAAATGCTTGTTTTGAT+TGG - chr1.1:27411179-27411198 MS.gene062861:intron 25.0%
ATCCAAACAAGACTTAAGTT+TGG - chr1.1:27411425-27411444 MS.gene062861:intron 30.0%
TATCATCCCTAATAATGCTT+TGG - chr1.1:27411615-27411634 MS.gene062861:CDS 30.0%
TTATGCTTTGGTGAAAAAGA+AGG - chr1.1:27411026-27411045 MS.gene062861:CDS 30.0%
! GTTTTGTACTTCCATGATAT+GGG - chr1.1:27411512-27411531 MS.gene062861:intron 30.0%
!! AACCAAACTTAAGTCTTGTT+TGG + chr1.1:27411430-27411449 None:intergenic 30.0%
!! AGGTAATTTTGAAGAGCTTA+TGG + chr1.1:27411306-27411325 None:intergenic 30.0%
!! AGTTTTGTACTTCCATGATA+TGG - chr1.1:27411511-27411530 MS.gene062861:intron 30.0%
ACAAAGAGGCTAATCAATAC+AGG + chr1.1:27411063-27411082 None:intergenic 35.0%
CAAAGAGGCTAATCAATACA+GGG + chr1.1:27411062-27411081 None:intergenic 35.0%
!! TTCACAAATTCTAAGGCAAG+TGG + chr1.1:27411220-27411239 None:intergenic 35.0%
!! TTGATTAGCCTCTTTGTTGT+TGG - chr1.1:27411066-27411085 MS.gene062861:CDS 35.0%
AATGGCAATGTCCCATATCA+TGG + chr1.1:27411526-27411545 None:intergenic 40.0%
AATTGAGATCCAGCTCATGA+AGG + chr1.1:27411591-27411610 None:intergenic 40.0%
AGGCAAAAGCAACAGAAATC+TGG + chr1.1:27411571-27411590 None:intergenic 40.0%
ATGCTTTGGTTAATAGCAGC+AGG - chr1.1:27411629-27411648 MS.gene062861:CDS 40.0%
TGCTTTGGTTAATAGCAGCA+GGG - chr1.1:27411630-27411649 MS.gene062861:CDS 40.0%
TTCGTTGGATGCTTATGCTT+TGG - chr1.1:27411014-27411033 MS.gene062861:CDS 40.0%
TTTGACACTCCTCTCCAAAA+TGG + chr1.1:27411544-27411563 None:intergenic 40.0%
! GATATTGTTGCTGTTACCTG+TGG + chr1.1:27411458-27411477 None:intergenic 40.0%
!! CCTCTTTGTTGTTGGTGATT+GGG - chr1.1:27411074-27411093 MS.gene062861:CDS 40.0%
!! GATATGGGACATTGCCATTT+TGG - chr1.1:27411527-27411546 MS.gene062861:intron 40.0%
!! TAAGTTTGGTTCTTGACCAC+AGG - chr1.1:27411439-27411458 MS.gene062861:intron 40.0%
CAAAACTGTAAGTCCAGCTG+AGG + chr1.1:27411498-27411517 None:intergenic 45.0%
CCCAATCACCAACAACAAAG+AGG + chr1.1:27411077-27411096 None:intergenic 45.0%
!! GAGTTTTGTGCTTGCTTCGT+TGG - chr1.1:27410999-27411018 MS.gene062861:CDS 45.0%
!! GCCTCTTTGTTGTTGGTGAT+TGG - chr1.1:27411073-27411092 MS.gene062861:CDS 45.0%
!! TTGCTTTTGCCTTCATGAGC+TGG - chr1.1:27411579-27411598 MS.gene062861:CDS 45.0%
!!! GGGACATTGCCATTTTGGAG+AGG - chr1.1:27411532-27411551 MS.gene062861:intron 50.0%
GCTGCAGCTTCTGCCTCAGC+TGG - chr1.1:27411482-27411501 MS.gene062861:intron 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 27410979 27411655 27410979 ID=MS.gene062861
chr1.1 mRNA 27410979 27411655 27410979 ID=MS.gene062861.t1;Parent=MS.gene062861
chr1.1 exon 27411539 27411655 27411539 ID=MS.gene062861.t1.exon1;Parent=MS.gene062861.t1
chr1.1 CDS 27411539 27411655 27411539 ID=cds.MS.gene062861.t1;Parent=MS.gene062861.t1
chr1.1 exon 27410979 27411173 27410979 ID=MS.gene062861.t1.exon2;Parent=MS.gene062861.t1
chr1.1 CDS 27410979 27411173 27410979 ID=cds.MS.gene062861.t1;Parent=MS.gene062861.t1
Gene Sequence

>MS.gene062861

ATGGCTTTACAAATCATTTGGAGTTTTGTGCTTGCTTCGTTGGATGCTTATGCTTTGGTGAAAAAGAAGGTTCTGCTTAACCCTGTATTGATTAGCCTCTTTGTTGTTGGTGATTGGGTTAGTCTCTTGAGTAAATCTATACTTTTCCTAACTAATTTGTTTGAAGCAATAAGACATGTTGATTATGATGCTTATCGTTTTAACAAATGCTTGTTTTGATTGGTTTATTTGAGCTTCTCCACTTGCCTTAGAATTTGTGAAACTGTTTTGGAGAGATTATTGAAACAACTTATGACATGTACATAAGCTGTTTTTAGCTTATTTCCATAAGCTCTTCAAAATTACCTATGAAAACAACTTATAACTTATATGAAAATAGTTTATAGTTATACATAAGCACTTTATATCATACTTGCTTGTGCTATAAGCACTTAATTAAGTTGTTTATCCAAACAAGACTTAAGTTTGGTTCTTGACCACAGGTAACAGCAACAATATCTCTAGCTGCAGCTTCTGCCTCAGCTGGACTTACAGTTTTGTACTTCCATGATATGGGACATTGCCATTTTGGAGAGGAGTGTCAAAAGTACCAGATTTCTGTTGCTTTTGCCTTCATGAGCTGGATCTCAATTTCAATATCATCCCTAATAATGCTTTGGTTAATAGCAGCAGGGTAG
Protein sequence

>MS.gene062861.t1

MALQIIWSFVLASLDAYALVKKKVLLNPVLISLFVVGDWVTATISLAAASASAGLTVLYFHDMGHCHFGEECQKYQISVAFAFMSWISISISSLIMLWLIAAG