AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene017672

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene017672.t1 MTR_7g022250 78.243 239 44 3 1 231 1 239 7.15e-138 386
MS.gene017672.t1 MTR_7g028890 79.060 234 32 2 1 231 1 220 6.85e-132 370
MS.gene017672.t1 MTR_7g028915 75.214 234 33 2 1 231 1 212 2.28e-124 351
MS.gene017672.t1 MTR_7g022270 59.896 192 39 4 22 211 6 161 1.20e-73 221
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene017672.t1 AT1G66140 29.121 182 99 4 77 231 82 260 5.92e-11 61.2

Find 41 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGTGTGGATATCATTATTA+TGG 0.231665 7.2:+19833385 MS.gene017672:CDS
CTCCTTCCCCTTGTTGCACA+TGG 0.338672 7.2:-19832966 None:intergenic
TATATAATAATCAAAGCTTA+AGG 0.354043 7.2:-19833651 None:intergenic
TCCAAGCATTGTTAAAAGCT+TGG 0.375606 7.2:-19833303 None:intergenic
CACCATCTCTCCATTCCATA+TGG 0.384400 7.2:+19833363 MS.gene017672:CDS
CTTAAGGGTCAAATCAATCT+TGG 0.396784 7.2:-19833635 None:intergenic
AATGATATCCACACCCCATA+TGG 0.402297 7.2:-19833378 None:intergenic
AATTACTCAAATGGTGATCA+AGG 0.411277 7.2:+19833328 MS.gene017672:CDS
AACAATATGATTCAGCATGC+AGG 0.425567 7.2:+19833412 MS.gene017672:CDS
ATGTTGAAACTCAGAATTCA+AGG 0.446337 7.2:+19833071 MS.gene017672:CDS
GCTTGGATAAATTACTCAAA+TGG 0.450589 7.2:+19833319 MS.gene017672:CDS
AGTAGCCAATTTGAAGATGA+TGG 0.452167 7.2:+19833006 MS.gene017672:CDS
AATATGTCTGAGATTGAAGT+TGG 0.464395 7.2:+19833538 MS.gene017672:CDS
TCATCTGCTTCATCTATCTC+TGG 0.464587 7.2:-19833484 None:intergenic
ACCATCTCTCCATTCCATAT+GGG 0.464694 7.2:+19833364 MS.gene017672:CDS
TCACAGGAAAAGTATTCAAA+AGG 0.468253 7.2:+19833180 MS.gene017672:CDS
TTCACTAGTCCACAGGCATT+AGG 0.474635 7.2:+19833232 MS.gene017672:CDS
TGAAGTTGGTTCAGTTTCAA+AGG 0.476665 7.2:+19833552 MS.gene017672:CDS
TTGGATTCATTGTTGATCAC+AGG 0.479894 7.2:+19833164 MS.gene017672:CDS
TGTTAGTGATGAAGTTGATC+AGG 0.482731 7.2:+19833582 MS.gene017672:CDS
CAAGAGAAAGGCAATTGTGC+TGG 0.501297 7.2:+19833039 MS.gene017672:CDS
CTTTGATGCCATGTGCAACA+AGG 0.514941 7.2:+19832958 None:intergenic
ATATAATAATCAAAGCTTAA+GGG 0.520066 7.2:-19833650 None:intergenic
GAAGTTGGTTCAGTTTCAAA+GGG 0.529917 7.2:+19833553 MS.gene017672:CDS
TCTCCATTCCATATGGGGTG+TGG 0.536840 7.2:+19833370 MS.gene017672:CDS
GGAAAATCAGAACAAGAGAA+AGG 0.539450 7.2:+19833027 MS.gene017672:CDS
ACAATATGATTCAGCATGCA+GGG 0.561522 7.2:+19833413 MS.gene017672:CDS
CCCCATATGGAATGGAGAGA+TGG 0.561790 7.2:-19833365 None:intergenic
TGCCATGTGCAACAAGGGGA+AGG 0.572549 7.2:+19832964 None:intergenic
CAGAAAGTTCACTAGTCCAC+AGG 0.575345 7.2:+19833225 MS.gene017672:CDS
TTTGATGCCATGTGCAACAA+GGG 0.577704 7.2:+19832959 None:intergenic
GTGCAACAAGGGGAAGGAGA+AGG 0.585340 7.2:+19832970 MS.gene017672:CDS
GTTGGTTCAGTTTCAAAGGG+AGG 0.593873 7.2:+19833556 MS.gene017672:CDS
TATCCACACCCCATATGGAA+TGG 0.594771 7.2:-19833373 None:intergenic
CCATCTCTCCATTCCATATG+GGG 0.598148 7.2:+19833365 MS.gene017672:CDS
ATTACTCAAATGGTGATCAA+GGG 0.605537 7.2:+19833329 MS.gene017672:CDS
GGAAGACAAAGAGACTCAAG+AGG 0.634668 7.2:+19833603 MS.gene017672:CDS
TGATGACCACCTAATGCCTG+TGG 0.637178 7.2:-19833241 None:intergenic
TTGATGCCATGTGCAACAAG+GGG 0.659240 7.2:+19832960 None:intergenic
ACTAGTCCACAGGCATTAGG+TGG 0.661075 7.2:+19833235 MS.gene017672:CDS
AGACAAAGAGACTCAAGAGG+AGG 0.673262 7.2:+19833606 MS.gene017672:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGAATCCAAAAAGAAGAAA+TGG - chr7.2:19833154-19833173 None:intergenic 25.0%
!! ATTTCTCCATTTCTTCTTTT+TGG + chr7.2:19833145-19833164 MS.gene017672:CDS 25.0%
!! ATTTTCCATCATCTTCAAAT+TGG - chr7.2:19833014-19833033 None:intergenic 25.0%
!! TTCTTCAACAACATCTTTTT+GGG - chr7.2:19833101-19833120 None:intergenic 25.0%
AATTACTCAAATGGTGATCA+AGG + chr7.2:19833328-19833347 MS.gene017672:CDS 30.0%
ATGTTGAAACTCAGAATTCA+AGG + chr7.2:19833071-19833090 MS.gene017672:CDS 30.0%
ATTACTCAAATGGTGATCAA+GGG + chr7.2:19833329-19833348 MS.gene017672:CDS 30.0%
GCTTGGATAAATTACTCAAA+TGG + chr7.2:19833319-19833338 MS.gene017672:CDS 30.0%
TAGAGAGAAGTCTCAAAAAA+AGG + chr7.2:19833278-19833297 MS.gene017672:CDS 30.0%
! AATATGTCTGAGATTGAAGT+TGG + chr7.2:19833538-19833557 MS.gene017672:CDS 30.0%
! CTTCTTCAACAACATCTTTT+TGG - chr7.2:19833102-19833121 None:intergenic 30.0%
! TCTTCAACAACATCTTTTTG+GGG - chr7.2:19833100-19833119 None:intergenic 30.0%
! TTTTATGCAGGGAATTTGTA+TGG + chr7.2:19833445-19833464 MS.gene017672:CDS 30.0%
!! TCACAGGAAAAGTATTCAAA+AGG + chr7.2:19833180-19833199 MS.gene017672:CDS 30.0%
AACAATATGATTCAGCATGC+AGG + chr7.2:19833412-19833431 MS.gene017672:CDS 35.0%
ACAATATGATTCAGCATGCA+GGG + chr7.2:19833413-19833432 MS.gene017672:CDS 35.0%
AGTAGCCAATTTGAAGATGA+TGG + chr7.2:19833006-19833025 MS.gene017672:CDS 35.0%
CTTAAGGGTCAAATCAATCT+TGG - chr7.2:19833638-19833657 None:intergenic 35.0%
GGAAAATCAGAACAAGAGAA+AGG + chr7.2:19833027-19833046 MS.gene017672:CDS 35.0%
GGGTGTGGATATCATTATTA+TGG + chr7.2:19833385-19833404 MS.gene017672:CDS 35.0%
TTGGATTCATTGTTGATCAC+AGG + chr7.2:19833164-19833183 MS.gene017672:CDS 35.0%
! GAAGTTGGTTCAGTTTCAAA+GGG + chr7.2:19833553-19833572 MS.gene017672:CDS 35.0%
! GGTCTACAAACTTTTATGCA+GGG + chr7.2:19833434-19833453 MS.gene017672:CDS 35.0%
! TCCAAGCATTGTTAAAAGCT+TGG - chr7.2:19833306-19833325 None:intergenic 35.0%
! TCCAAGCTTTTAACAATGCT+TGG + chr7.2:19833302-19833321 MS.gene017672:CDS 35.0%
! TGAAGTTGGTTCAGTTTCAA+AGG + chr7.2:19833552-19833571 MS.gene017672:CDS 35.0%
! TGTTAGTGATGAAGTTGATC+AGG + chr7.2:19833582-19833601 MS.gene017672:CDS 35.0%
AATGATATCCACACCCCATA+TGG - chr7.2:19833381-19833400 None:intergenic 40.0%
ACCATCTCTCCATTCCATAT+GGG + chr7.2:19833364-19833383 MS.gene017672:CDS 40.0%
TCATCTGCTTCATCTATCTC+TGG - chr7.2:19833487-19833506 None:intergenic 40.0%
! GGGTCTACAAACTTTTATGC+AGG + chr7.2:19833433-19833452 MS.gene017672:CDS 40.0%
AGACAAAGAGACTCAAGAGG+AGG + chr7.2:19833606-19833625 MS.gene017672:CDS 45.0%
CAAGAGAAAGGCAATTGTGC+TGG + chr7.2:19833039-19833058 MS.gene017672:CDS 45.0%
CACCATCTCTCCATTCCATA+TGG + chr7.2:19833363-19833382 MS.gene017672:CDS 45.0%
CAGAAAGTTCACTAGTCCAC+AGG + chr7.2:19833225-19833244 MS.gene017672:CDS 45.0%
CCATCTCTCCATTCCATATG+GGG + chr7.2:19833365-19833384 MS.gene017672:CDS 45.0%
GGAAGACAAAGAGACTCAAG+AGG + chr7.2:19833603-19833622 MS.gene017672:CDS 45.0%
TATCCACACCCCATATGGAA+TGG - chr7.2:19833376-19833395 None:intergenic 45.0%
TTCACTAGTCCACAGGCATT+AGG + chr7.2:19833232-19833251 MS.gene017672:CDS 45.0%
! GTTGGTTCAGTTTCAAAGGG+AGG + chr7.2:19833556-19833575 MS.gene017672:CDS 45.0%
ACTAGTCCACAGGCATTAGG+TGG + chr7.2:19833235-19833254 MS.gene017672:CDS 50.0%
CCCCATATGGAATGGAGAGA+TGG - chr7.2:19833368-19833387 None:intergenic 50.0%
TCTCCATTCCATATGGGGTG+TGG + chr7.2:19833370-19833389 MS.gene017672:CDS 50.0%
TGATGACCACCTAATGCCTG+TGG - chr7.2:19833244-19833263 None:intergenic 50.0%
GTGCAACAAGGGGAAGGAGA+AGG + chr7.2:19832970-19832989 MS.gene017672:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 19832968 19833663 19832968 ID=MS.gene017672
chr7.2 mRNA 19832968 19833663 19832968 ID=MS.gene017672.t1;Parent=MS.gene017672
chr7.2 exon 19832968 19833663 19832968 ID=MS.gene017672.t1.exon1;Parent=MS.gene017672.t1
chr7.2 CDS 19832968 19833663 19832968 ID=cds.MS.gene017672.t1;Parent=MS.gene017672.t1
Gene Sequence

>MS.gene017672

ATGTGCAACAAGGGGAAGGAGAAGGTGAATGAAGAATCAGTAGCCAATTTGAAGATGATGGAAAATCAGAACAAGAGAAAGGCAATTGTGCTGGAAGAATCTCATGTTGAAACTCAGAATTCAAGGACTCCCCAAAAAGATGTTGTTGAAGAAGAATCGACTGATTCTTCTAAAGAAATTTCTCCATTTCTTCTTTTTGGATTCATTGTTGATCACAGGAAAAGTATTCAAAAGGCTTACTCGTGCAAATTTTGTAGCAGAAAGTTCACTAGTCCACAGGCATTAGGTGGTCATCAAAATTCTCACAAATTAGAGAGAAGTCTCAAAAAAAGGATCCAAGCTTTTAACAATGCTTGGATAAATTACTCAAATGGTGATCAAGGGATAAGTCTAAACACCATCTCTCCATTCCATATGGGGTGTGGATATCATTATTATGGATTTAACAATATGATTCAGCATGCAGGGTCTACAAACTTTTATGCAGGGAATTTGTATGGTGCATTGCAGCATATTCCAGAGATAGATGAAGCAGATGAAGCTAATCAAAGCATAATGAGTCAAAAAGTTAATATGTCTGAGATTGAAGTTGGTTCAGTTTCAAAGGGAGGTGTTGTTAGTGATGAAGTTGATCAGGAAGACAAAGAGACTCAAGAGGAGGAAGCATCCAAGATTGATTTGACCCTTAAGCTTTGA
Protein sequence

>MS.gene017672.t1

MCNKGKEKVNEESVANLKMMENQNKRKAIVLEESHVETQNSRTPQKDVVEEESTDSSKEISPFLLFGFIVDHRKSIQKAYSCKFCSRKFTSPQALGGHQNSHKLERSLKKRIQAFNNAWINYSNGDQGISLNTISPFHMGCGYHYYGFNNMIQHAGSTNFYAGNLYGALQHIPEIDEADEANQSIMSQKVNMSEIEVGSVSKGGVVSDEVDQEDKETQEEEASKIDLTLKL