AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25097

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25097.t1 MTR_8g021250 100.000 103 0 0 1 103 1 103 1.62e-72 212
MS.gene25097.t1 MTR_8g021250 100.000 103 0 0 1 103 1 103 4.16e-72 211
MS.gene25097.t1 MTR_2g042700 79.439 107 22 0 1 107 1 107 8.43e-60 180
MS.gene25097.t1 MTR_2g042700 81.553 103 19 0 1 103 1 103 8.50e-60 179
MS.gene25097.t1 MTR_4g084910 38.356 73 44 1 14 85 7 79 1.63e-12 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25097.t1 AT3G14080 86.408 103 14 0 1 103 1 103 2.50e-63 189
MS.gene25097.t1 AT3G14080 86.408 103 14 0 1 103 1 103 2.50e-63 189
MS.gene25097.t1 AT1G19120 80.374 107 21 0 1 107 1 107 5.39e-61 183
MS.gene25097.t1 AT3G14080 90.123 81 8 0 1 81 1 81 5.68e-50 154
MS.gene25097.t1 AT3G14080 82.418 91 14 1 15 103 3 93 1.35e-48 151
MS.gene25097.t1 AT1G65700 38.667 75 45 1 12 85 4 78 4.34e-12 58.5
MS.gene25097.t1 AT1G65700 38.667 75 45 1 12 85 4 78 4.34e-12 58.5

Find 31 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATTAATATACGACAATAAT+AGG 0.265043 8.4:+72397806 None:intergenic
GGGGAAAATGTTGTTCTAAT+TGG 0.311566 8.4:-72398100 MS.gene25097:CDS
GTAGAAAGGTAGAGATCCTC+AGG 0.460456 8.4:+72399063 None:intergenic
GCAGCTAACGCTGTTCTTGA+GGG 0.491345 8.4:-72398190 MS.gene25097:intron
GTGTTCCTACAGAAGAAATC+AGG 0.501365 8.4:-72397949 MS.gene25097:CDS
TTCTTGAGGGTGCCTGTGAG+AGG 0.503890 8.4:-72398177 MS.gene25097:CDS
GTAGGAACACGCGTCATATG+TGG 0.510896 8.4:+72397962 None:intergenic
TGCAGCTAACGCTGTTCTTG+AGG 0.511473 8.4:-72398191 MS.gene25097:intron
TATGTCTTGGGCTGCTCCTG+AGG 0.516307 8.4:-72399079 MS.gene25097:CDS
AACTAGCAAGTGAAGTAGAA+AGG 0.522695 8.4:+72399049 None:intergenic
CTATATTGTGACATCCCTCT+AGG 0.524354 8.4:-72398139 MS.gene25097:CDS
ACGAGATGGTAGAAAGCTCA+TGG 0.524959 8.4:-72398314 MS.gene25097:CDS
TAGGAACACGCGTCATATGT+GGG 0.543008 8.4:+72397963 None:intergenic
GCCTGTGAGAGGGTAATTGT+TGG 0.562739 8.4:-72398166 MS.gene25097:CDS
CTAGGTCTTTATGTAATCCG+TGG 0.570170 8.4:-72398121 MS.gene25097:CDS
TGTTGTTCTAATTGGTGAGA+TGG 0.571580 8.4:-72398092 MS.gene25097:intron
CTTCTTATATTGCTACGAGA+TGG 0.573728 8.4:-72398328 MS.gene25097:CDS
CGAGATGGTAGAAAGCTCAT+GGG 0.590247 8.4:-72398313 MS.gene25097:CDS
TAGGTCTTTATGTAATCCGT+GGG 0.590765 8.4:-72398120 MS.gene25097:CDS
TCTTGAGGGTGCCTGTGAGA+GGG 0.598880 8.4:-72398176 MS.gene25097:CDS
TCTACATGAAACAGATTCGT+AGG 0.606867 8.4:-72397723 MS.gene25097:intron
ACCCTCCTGATTTCTTCTGT+AGG 0.607048 8.4:+72397944 None:intergenic
ACCAACAATTACCCTCTCAC+AGG 0.608128 8.4:+72398165 None:intergenic
AGGAACACGCGTCATATGTG+GGG 0.634207 8.4:+72397964 None:intergenic
TTCCTACAGAAGAAATCAGG+AGG 0.637433 8.4:-72397946 MS.gene25097:CDS
GGATTACATAAAGACCTAGA+GGG 0.677541 8.4:+72398125 None:intergenic
GGAACACGCGTCATATGTGG+GGG 0.684221 8.4:+72397965 None:intergenic
CGGATTACATAAAGACCTAG+AGG 0.700189 8.4:+72398124 None:intergenic
TCCTACAGAAGAAATCAGGA+GGG 0.714873 8.4:-72397945 MS.gene25097:intron
GAGATGGTAGAAAGCTCATG+GGG 0.721011 8.4:-72398312 MS.gene25097:CDS
AGGTCTTTATGTAATCCGTG+GGG 0.758020 8.4:-72398119 MS.gene25097:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAGACAAAAATAAAAACA+TGG + chr8.4:72397811-72397830 None:intergenic 15.0%
!! TATTAATATACGACAATAAT+AGG + chr8.4:72398992-72399011 None:intergenic 15.0%
!!! ATCATAAAGAAGTTTAATTT+AGG + chr8.4:72398884-72398903 None:intergenic 15.0%
!! TATTAATGGTAATTAAGCTT+GGG - chr8.4:72398368-72398387 MS.gene25097:intron 20.0%
!! TTATTAATGGTAATTAAGCT+TGG - chr8.4:72398367-72398386 MS.gene25097:intron 20.0%
!!! AGAAATAGTTTTAAATGCAA+AGG + chr8.4:72398748-72398767 None:intergenic 20.0%
!!! GAAATAGTTTTAAATGCAAA+GGG + chr8.4:72398747-72398766 None:intergenic 20.0%
! AAGAAACATATGGATATGTT+TGG - chr8.4:72398075-72398094 MS.gene25097:intron 25.0%
! ATAAATAAGTCAATCCAAAC+AGG + chr8.4:72397952-72397971 None:intergenic 25.0%
! ATAATTAAAAAAGACCCGTT+TGG - chr8.4:72397882-72397901 MS.gene25097:intron 25.0%
! GCTTAATTACCATTAATAAC+TGG + chr8.4:72398366-72398385 None:intergenic 25.0%
! TCAGTAATAGAACATAAGAT+TGG + chr8.4:72398430-72398449 None:intergenic 25.0%
! TGATGAAAACCAGTTATTAA+TGG - chr8.4:72398354-72398373 MS.gene25097:intron 25.0%
!! ATTTTTATTGTGACCTTGAT+TGG - chr8.4:72397829-72397848 MS.gene25097:CDS 25.0%
AAGTTCAAATTCTCCAATCA+AGG + chr8.4:72397845-72397864 None:intergenic 30.0%
AATAAGTTCGTGTTACCAAA+CGG + chr8.4:72397900-72397919 None:intergenic 30.0%
ACATCCTGAAAATTGAAAGA+CGG + chr8.4:72398794-72398813 None:intergenic 30.0%
CATTGTTTGTAAAGAGATGT+AGG + chr8.4:72399020-72399039 None:intergenic 30.0%
CTACATCTCTTTACAAACAA+TGG - chr8.4:72399018-72399037 MS.gene25097:intron 30.0%
TACCTATCAACTTAAGCTTT+GGG - chr8.4:72398154-72398173 MS.gene25097:CDS 30.0%
TATCCATATGTTTCTTGTCA+AGG + chr8.4:72398071-72398090 None:intergenic 30.0%
TGAACTTATAGCTTATAAGC+TGG - chr8.4:72397858-72397877 MS.gene25097:intron 30.0%
TTTCTTGTCAAGGTAGTTTA+CGG + chr8.4:72398061-72398080 None:intergenic 30.0%
! CATTGTATTGCTTTAAGTGA+GGG + chr8.4:72398940-72398959 None:intergenic 30.0%
AACTAGCAAGTGAAGTAGAA+AGG + chr8.4:72397749-72397768 None:intergenic 35.0%
AAGTAGCTTATTGACCTGTT+TGG - chr8.4:72397935-72397954 MS.gene25097:intron 35.0%
ACCTATCAACTTAAGCTTTG+GGG - chr8.4:72398155-72398174 MS.gene25097:CDS 35.0%
ATAAGTTCGTGTTACCAAAC+GGG + chr8.4:72397899-72397918 None:intergenic 35.0%
CTACCTATCAACTTAAGCTT+TGG - chr8.4:72398153-72398172 MS.gene25097:CDS 35.0%
CTACCTTGACAAGAAACATA+TGG - chr8.4:72398065-72398084 MS.gene25097:intron 35.0%
CTTCTTATATTGCTACGAGA+TGG - chr8.4:72398467-72398486 MS.gene25097:intron 35.0%
GGATTACATAAAGACCTAGA+GGG + chr8.4:72398673-72398692 None:intergenic 35.0%
GGGGAAAATGTTGTTCTAAT+TGG - chr8.4:72398695-72398714 MS.gene25097:intron 35.0%
GTAAAGATTTGACATGCGTT+AGG - chr8.4:72398551-72398570 MS.gene25097:intron 35.0%
GTTAGCTGCATGTTATTGAT+AGG + chr8.4:72398594-72398613 None:intergenic 35.0%
TAGGTCTTTATGTAATCCGT+GGG - chr8.4:72398675-72398694 MS.gene25097:intron 35.0%
TCTACATGAAACAGATTCGT+AGG - chr8.4:72399072-72399091 MS.gene25097:CDS 35.0%
TGTTGTTCTAATTGGTGAGA+TGG - chr8.4:72398703-72398722 MS.gene25097:intron 35.0%
TTCTTGTCAAGGTAGTTTAC+GGG + chr8.4:72398060-72398079 None:intergenic 35.0%
! ACAACCGTCTTTCAATTTTC+AGG - chr8.4:72398787-72398806 MS.gene25097:intron 35.0%
! CTTCGCTCTTTTGATCAATT+TGG - chr8.4:72398509-72398528 MS.gene25097:intron 35.0%
! GCATTGTATTGCTTTAAGTG+AGG + chr8.4:72398941-72398960 None:intergenic 35.0%
! TTAGAACAACATTTTCCCCA+CGG + chr8.4:72398694-72398713 None:intergenic 35.0%
!! GTCTTTCAATTTTCAGGATG+TGG - chr8.4:72398793-72398812 MS.gene25097:intron 35.0%
AGGTCTTTATGTAATCCGTG+GGG - chr8.4:72398676-72398695 MS.gene25097:intron 40.0%
ATCTTGCACACAAGTCTTTC+TGG - chr8.4:72398297-72398316 MS.gene25097:CDS 40.0%
ATGATCTAACTCCTGAGAGA+TGG - chr8.4:72398110-72398129 MS.gene25097:CDS 40.0%
CGGATTACATAAAGACCTAG+AGG + chr8.4:72398674-72398693 None:intergenic 40.0%
CTAGGTCTTTATGTAATCCG+TGG - chr8.4:72398674-72398693 MS.gene25097:intron 40.0%
CTATATTGTGACATCCCTCT+AGG - chr8.4:72398656-72398675 MS.gene25097:intron 40.0%
GTGTTCCTACAGAAGAAATC+AGG - chr8.4:72398846-72398865 MS.gene25097:intron 40.0%
TCCTACAGAAGAAATCAGGA+GGG - chr8.4:72398850-72398869 MS.gene25097:intron 40.0%
TTCCTACAGAAGAAATCAGG+AGG - chr8.4:72398849-72398868 MS.gene25097:intron 40.0%
TTTAAGTGAGGGCAAGAACA+AGG + chr8.4:72398929-72398948 None:intergenic 40.0%
! GTTGATAGGTAGCACATGAA+TGG + chr8.4:72398145-72398164 None:intergenic 40.0%
!! ACCCCAAAGCTTAAGTTGAT+AGG + chr8.4:72398159-72398178 None:intergenic 40.0%
!! CAATTTTCAGGATGTGGAGA+GGG - chr8.4:72398799-72398818 MS.gene25097:intron 40.0%
!! TCAATTTTCAGGATGTGGAG+AGG - chr8.4:72398798-72398817 MS.gene25097:intron 40.0%
ACCAACAATTACCCTCTCAC+AGG + chr8.4:72398633-72398652 None:intergenic 45.0%
ACCCTCCTGATTTCTTCTGT+AGG + chr8.4:72398854-72398873 None:intergenic 45.0%
ACGAGATGGTAGAAAGCTCA+TGG - chr8.4:72398481-72398500 MS.gene25097:intron 45.0%
CGAGATGGTAGAAAGCTCAT+GGG - chr8.4:72398482-72398501 MS.gene25097:intron 45.0%
GAGATGGTAGAAAGCTCATG+GGG - chr8.4:72398483-72398502 MS.gene25097:intron 45.0%
GGTTACAAAAGCCATCTCTC+AGG + chr8.4:72398124-72398143 None:intergenic 45.0%
GTAGAAAGGTAGAGATCCTC+AGG + chr8.4:72397735-72397754 None:intergenic 45.0%
TAGGAACACGCGTCATATGT+GGG + chr8.4:72398835-72398854 None:intergenic 45.0%
AGGAACACGCGTCATATGTG+GGG + chr8.4:72398834-72398853 None:intergenic 50.0%
GCAGCTAACGCTGTTCTTGA+GGG - chr8.4:72398605-72398624 MS.gene25097:intron 50.0%
GCCTGTGAGAGGGTAATTGT+TGG - chr8.4:72398629-72398648 MS.gene25097:intron 50.0%
GTAGGAACACGCGTCATATG+TGG + chr8.4:72398836-72398855 None:intergenic 50.0%
TGCAGCTAACGCTGTTCTTG+AGG - chr8.4:72398604-72398623 MS.gene25097:intron 50.0%
!! TTTTCAGGATGTGGAGAGGG+AGG - chr8.4:72398802-72398821 MS.gene25097:intron 50.0%
GGAACACGCGTCATATGTGG+GGG + chr8.4:72398833-72398852 None:intergenic 55.0%
!! TCTTGAGGGTGCCTGTGAGA+GGG - chr8.4:72398619-72398638 MS.gene25097:intron 55.0%
!! TTCTTGAGGGTGCCTGTGAG+AGG - chr8.4:72398618-72398637 MS.gene25097:intron 55.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 72397717 72399100 72397717 ID=MS.gene25097
chr8.4 mRNA 72397717 72399100 72397717 ID=MS.gene25097.t1;Parent=MS.gene25097
chr8.4 exon 72399040 72399100 72399040 ID=MS.gene25097.t1.exon1;Parent=MS.gene25097.t1
chr8.4 CDS 72399040 72399100 72399040 ID=cds.MS.gene25097.t1;Parent=MS.gene25097.t1
chr8.4 exon 72398287 72398355 72398287 ID=MS.gene25097.t1.exon2;Parent=MS.gene25097.t1
chr8.4 CDS 72398287 72398355 72398287 ID=cds.MS.gene25097.t1;Parent=MS.gene25097.t1
chr8.4 exon 72398093 72398208 72398093 ID=MS.gene25097.t1.exon3;Parent=MS.gene25097.t1
chr8.4 CDS 72398093 72398208 72398093 ID=cds.MS.gene25097.t1;Parent=MS.gene25097.t1
chr8.4 exon 72397946 72398008 72397946 ID=MS.gene25097.t1.exon4;Parent=MS.gene25097.t1
chr8.4 CDS 72397946 72398008 72397946 ID=cds.MS.gene25097.t1;Parent=MS.gene25097.t1
chr8.4 exon 72397817 72397867 72397817 ID=MS.gene25097.t1.exon5;Parent=MS.gene25097.t1
chr8.4 CDS 72397817 72397867 72397817 ID=cds.MS.gene25097.t1;Parent=MS.gene25097.t1
chr8.4 exon 72397717 72397731 72397717 ID=MS.gene25097.t1.exon6;Parent=MS.gene25097.t1
chr8.4 CDS 72397717 72397731 72397717 ID=cds.MS.gene25097.t1;Parent=MS.gene25097.t1
Gene Sequence

>MS.gene25097

ATGTCTTGGGCTGCTCCTGAGGATCTCTACCTTTCTACTTCACTTGCTAGTTATCTTGACAGTAACAATCTCTCTCTCTTTCTTTCTCTCTCCATGTTTTTATTTTTGTCTAATTTTTATTGTGACCTTGATTGGAGAATTTGAACTTATAGCTTATAAGCTGGTATAATTAAAAAAGACCCGTTTGGTAACACGAACTTATTTTCATGAGTTAATTCAAGTAGCTTATTGACCTGTTTGGATTGACTTATTTATTTATTAGCTTATGCAAAACAGTTTATGCAAATAAATAAGCTTTTATGTATTATTCATAAGTTCTCACTAACAAAAATTGTTTTTTCCCGTAAACTACCTTGACAAGAAACATATGGATATGTTTGGTATGATATAATTATGATCTAACTCCTGAGAGATGGCTTTTGTAACCATTCATGTGCTACCTATCAACTTAAGCTTTGGGGTAGTTCATTCGCGACAATATTTTTTTTTTTTGAGCTGAAGATGCAAATGTCATTGCTTTTGAATTGTAATTTGTTTGAAAGAATAGTCTTAACTCTTGACGTTACATTGCTTTTGACATATCTTGCACACAAGTCTTTCTGGAAAAGAGAAAAATTGTACATATATTGTTCAAATGTGATGAAAACCAGTTATTAATGGTAATTAAGCTTGGGTTTACAATTGATGTGAAACTGATTTTATATTTCGTACCAATCTTATGTTCTATTACTGATCTTTTCTGTAGAGAAACTTCTTATATTGCTACGAGATGGTAGAAAGCTCATGGGGACACTTCGCTCTTTTGATCAATTTGGTAACAACTTCTCAAATTACGTAAAGATTTGACATGCGTTAGGTTGAGTTTCTAATATTTCCTATCAATAACATGCAGCTAACGCTGTTCTTGAGGGTGCCTGTGAGAGGGTAATTGTTGGTGATCTATATTGTGACATCCCTCTAGGTCTTTATGTAATCCGTGGGGAAAATGTTGTTCTAATTGGTGAGATGGTATGATTGCTAACTATTTCCCTTTGCATTTAAAACTATTTCTACTTTTTAATCTCAGTTTTACAACCGTCTTTCAATTTTCAGGATGTGGAGAGGGAGGAACTTCCCCCACATATGACGCGTGTTCCTACAGAAGAAATCAGGAGGGTAAATACTCCTAAATTAAACTTCTTTATGATATTCTTTGTCTATTTTCTGTCGCCTTGTTCTTGCCCTCACTTAAAGCAATACAATGCTGTGACGTCGTCATTCATTGCAGAAGTGCCTATTATTGTCGTATATTAATATTTTTCCTACATCTCTTTACAAACAATGGTTATTTTGAAGTTGTAAAGCACTTCTGAACTTCTACATGAAACAGATTCGTAGGACTTGA
Protein sequence

>MS.gene25097.t1

MSWAAPEDLYLSTSLASYLDKKLLILLRDGRKLMGTLRSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEMDVEREELPPHMTRVPTEEIRRQYNAVTSSFIAEVPIIVIRRT