AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39522

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39522.t1 MTR_4g088335 96.602 206 7 0 1 206 1 206 6.17e-150 414
MS.gene39522.t1 MTR_2g014550 71.066 197 57 0 10 206 14 210 8.15e-106 303
MS.gene39522.t1 MTR_2g014520 71.066 197 57 0 10 206 11 207 1.23e-104 300
MS.gene39522.t1 MTR_4g078870 53.623 207 93 3 1 206 1 205 3.88e-72 218
MS.gene39522.t1 MTR_5g044580 42.778 180 103 0 21 200 35 214 6.53e-49 159
MS.gene39522.t1 MTR_7g010890 41.714 175 102 0 26 200 40 214 2.62e-46 152
MS.gene39522.t1 MTR_2g020850 41.279 172 98 2 35 206 21 189 2.26e-42 141
MS.gene39522.t1 MTR_4g118470 40.212 189 105 3 19 206 18 199 1.53e-41 140
MS.gene39522.t1 MTR_4g118480 41.379 174 98 2 34 206 27 197 1.91e-39 134
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39522.t1 AT4G18425 65.193 181 63 0 26 206 33 213 1.25e-88 259
MS.gene39522.t1 AT5G46090 58.738 206 80 2 6 206 9 214 4.36e-88 258
MS.gene39522.t1 AT3G02430 47.027 185 92 2 21 201 28 210 1.77e-62 194
MS.gene39522.t1 AT4G28485 52.486 181 85 1 27 206 20 200 2.38e-60 187
MS.gene39522.t1 AT4G24310 48.889 180 86 2 31 206 32 209 4.41e-59 185
MS.gene39522.t1 AT1G09157 40.761 184 97 2 29 200 56 239 1.94e-43 145
MS.gene39522.t1 AT5G39650 40.761 184 97 2 29 200 57 240 4.90e-42 142
MS.gene39522.t1 AT3G21550 41.071 168 94 1 35 202 10 172 2.24e-39 133
MS.gene39522.t1 AT3G21520 37.500 168 100 2 35 201 24 187 4.39e-36 125
MS.gene39522.t1 AT5G27370 35.556 180 101 3 36 200 7 186 1.27e-30 111
MS.gene39522.t1 AT4G28485 56.436 101 44 0 106 206 65 165 3.05e-30 109

Find 38 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCCACACTTAGAGGCTTA+TGG 0.290450 4.2:-22936218 MS.gene39522:CDS
CCTACTCATGGACATGGAAT+TGG 0.314672 4.2:-22935964 MS.gene39522:CDS
TATGGATTTGCCACACTTAG+AGG 0.326553 4.2:-22936225 MS.gene39522:CDS
GATAGCTTCAAAGACAATAA+AGG 0.336132 4.2:-22936258 MS.gene39522:CDS
TTGCCTTGGTTTGTGAATAT+TGG 0.340750 4.2:+22936360 None:intergenic
GCATGCAATTATGTCAATCT+TGG 0.353966 4.2:-22936124 MS.gene39522:CDS
ACTGCATTGCCTGTTGGAAT+TGG 0.372342 4.2:-22936018 MS.gene39522:CDS
TGAATATTGGTGATAGAAGT+TGG 0.394112 4.2:+22936373 None:intergenic
ATCTCCATGTTGTGAAGAAA+TGG 0.396573 4.2:+22936498 None:intergenic
AGAGGCTTATGGATCATTGA+TGG 0.412901 4.2:-22936207 MS.gene39522:CDS
ATAGCTTCAAAGACAATAAA+GGG 0.414287 4.2:-22936257 MS.gene39522:CDS
AGATGTTAATTTGTTGAAAG+TGG 0.417439 4.2:+22935937 None:intergenic
TTTGTTACATTTCCTACTCA+TGG 0.420011 4.2:-22935976 MS.gene39522:CDS
AATAAAGGGAACATATGTTA+TGG 0.425934 4.2:-22936243 MS.gene39522:CDS
GAAGCATGAGGCACCACATA+AGG 0.455779 4.2:+22936296 None:intergenic
GATTGATGGCTCTATGCAAA+AGG 0.462025 4.2:+22936457 None:intergenic
ATCCTTACTGCATTGCCTGT+TGG 0.464824 4.2:-22936024 MS.gene39522:CDS
CTATGCAAAAGGTTCCTTTG+TGG 0.472887 4.2:+22936468 None:intergenic
GATGTTAATTTGTTGAAAGT+GGG 0.482749 4.2:+22935938 None:intergenic
GTGATAGAAGTTGGAATGAA+AGG 0.491481 4.2:+22936382 None:intergenic
AGCTATCAGTGAAGCATAGT+AGG 0.500815 4.2:+22936274 None:intergenic
CAGAAAACACCAATTCCAAC+AGG 0.507539 4.2:+22936009 None:intergenic
TTGATGCAAAATATAAACTA+AGG 0.516003 4.2:-22936161 MS.gene39522:CDS
TAACGTGGTCACACTTGCCT+TGG 0.522411 4.2:+22936346 None:intergenic
TTCCAACAGGCAATGCAGTA+AGG 0.522793 4.2:+22936022 None:intergenic
AGTGCCTGTTGGTAAAAGAT+TGG 0.523234 4.2:+22936407 None:intergenic
CGCATCTCATATGAAGGTGA+TGG 0.549812 4.2:+22936051 None:intergenic
ATTTGACGCATCTCATATGA+AGG 0.568010 4.2:+22936045 None:intergenic
CCAATTCCATGTCCATGAGT+AGG 0.587119 4.2:+22935964 None:intergenic
TGCAATGTTTGATCATAATG+TGG 0.607647 4.2:-22936088 MS.gene39522:CDS
ACATTTCCTACTCATGGACA+TGG 0.611411 4.2:-22935970 MS.gene39522:CDS
GCTACCATTTCTTCACAACA+TGG 0.625275 4.2:-22936502 MS.gene39522:CDS
TCACCAATATTCACAAACCA+AGG 0.630187 4.2:-22936363 MS.gene39522:CDS
GAAGCATAGTAGGAAGCATG+AGG 0.656130 4.2:+22936284 None:intergenic
GATCCATAAGCCTCTAAGTG+TGG 0.659503 4.2:+22936215 None:intergenic
TGGAGATTGTAGAACCACAA+AGG 0.686595 4.2:-22936482 MS.gene39522:CDS
AATGAAAGGACAGTGCCTGT+TGG 0.722317 4.2:+22936396 None:intergenic
AAGTCATTAACTGTGTAACG+TGG 0.724428 4.2:+22936331 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGATGCAAAATATAAACTA+AGG - chr4.2:22936321-22936340 MS.gene39522:CDS 20.0%
! AATAAAGGGAACATATGTTA+TGG - chr4.2:22936239-22936258 MS.gene39522:CDS 25.0%
! ATAGCTTCAAAGACAATAAA+GGG - chr4.2:22936225-22936244 MS.gene39522:CDS 25.0%
!!! TTATCACTTTTATCCTTATG+TGG - chr4.2:22936173-22936192 MS.gene39522:CDS 25.0%
GATAGCTTCAAAGACAATAA+AGG - chr4.2:22936224-22936243 MS.gene39522:CDS 30.0%
TGCAATGTTTGATCATAATG+TGG - chr4.2:22936394-22936413 MS.gene39522:CDS 30.0%
TTTGTTACATTTCCTACTCA+TGG - chr4.2:22936506-22936525 MS.gene39522:CDS 30.0%
! GCTTTTACATGTTTGATTGA+TGG + chr4.2:22936042-22936061 None:intergenic 30.0%
! TATTTTGCATCAAGTTCATG+TGG + chr4.2:22936314-22936333 None:intergenic 30.0%
! TGAATATTGGTGATAGAAGT+TGG + chr4.2:22936112-22936131 None:intergenic 30.0%
AAGTCATTAACTGTGTAACG+TGG + chr4.2:22936154-22936173 None:intergenic 35.0%
ATCTCCATGTTGTGAAGAAA+TGG + chr4.2:22935987-22936006 None:intergenic 35.0%
ATTTGACGCATCTCATATGA+AGG + chr4.2:22936440-22936459 None:intergenic 35.0%
GCATGCAATTATGTCAATCT+TGG - chr4.2:22936358-22936377 MS.gene39522:CDS 35.0%
GTGATAGAAGTTGGAATGAA+AGG + chr4.2:22936103-22936122 None:intergenic 35.0%
TCACCAATATTCACAAACCA+AGG - chr4.2:22936119-22936138 MS.gene39522:CDS 35.0%
! GTAGCTTTTGTTCATCATAG+AGG + chr4.2:22935965-22935984 None:intergenic 35.0%
! TTAGCCAATCTTTTACCAAC+AGG - chr4.2:22936071-22936090 MS.gene39522:CDS 35.0%
!! TTGCCTTGGTTTGTGAATAT+TGG + chr4.2:22936125-22936144 None:intergenic 35.0%
ACATTTCCTACTCATGGACA+TGG - chr4.2:22936512-22936531 MS.gene39522:CDS 40.0%
AGAGGCTTATGGATCATTGA+TGG - chr4.2:22936275-22936294 MS.gene39522:CDS 40.0%
AGCTATCAGTGAAGCATAGT+AGG + chr4.2:22936211-22936230 None:intergenic 40.0%
CAGAAAACACCAATTCCAAC+AGG + chr4.2:22936476-22936495 None:intergenic 40.0%
CTATGCAAAAGGTTCCTTTG+TGG + chr4.2:22936017-22936036 None:intergenic 40.0%
GCTACCATTTCTTCACAACA+TGG - chr4.2:22935980-22935999 MS.gene39522:CDS 40.0%
TATGGATTTGCCACACTTAG+AGG - chr4.2:22936257-22936276 MS.gene39522:CDS 40.0%
TGGAGATTGTAGAACCACAA+AGG - chr4.2:22936000-22936019 MS.gene39522:CDS 40.0%
! AGTGCCTGTTGGTAAAAGAT+TGG + chr4.2:22936078-22936097 None:intergenic 40.0%
! GATTGATGGCTCTATGCAAA+AGG + chr4.2:22936028-22936047 None:intergenic 40.0%
AATGAAAGGACAGTGCCTGT+TGG + chr4.2:22936089-22936108 None:intergenic 45.0%
ACTGCATTGCCTGTTGGAAT+TGG - chr4.2:22936464-22936483 MS.gene39522:CDS 45.0%
ATCCTTACTGCATTGCCTGT+TGG - chr4.2:22936458-22936477 MS.gene39522:CDS 45.0%
CCAATTCCATGTCCATGAGT+AGG + chr4.2:22936521-22936540 None:intergenic 45.0%
CCTACTCATGGACATGGAAT+TGG - chr4.2:22936518-22936537 MS.gene39522:CDS 45.0%
CGCATCTCATATGAAGGTGA+TGG + chr4.2:22936434-22936453 None:intergenic 45.0%
GATCCATAAGCCTCTAAGTG+TGG + chr4.2:22936270-22936289 None:intergenic 45.0%
TTCCAACAGGCAATGCAGTA+AGG + chr4.2:22936463-22936482 None:intergenic 45.0%
TTGCCACACTTAGAGGCTTA+TGG - chr4.2:22936264-22936283 MS.gene39522:CDS 45.0%
! GAAGCATAGTAGGAAGCATG+AGG + chr4.2:22936201-22936220 None:intergenic 45.0%
TAACGTGGTCACACTTGCCT+TGG + chr4.2:22936139-22936158 None:intergenic 50.0%
! GAAGCATGAGGCACCACATA+AGG + chr4.2:22936189-22936208 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 22935942 22936562 22935942 ID=MS.gene39522
chr4.2 mRNA 22935942 22936562 22935942 ID=MS.gene39522.t1;Parent=MS.gene39522
chr4.2 exon 22935942 22936562 22935942 ID=MS.gene39522.t1.exon1;Parent=MS.gene39522.t1
chr4.2 CDS 22935942 22936562 22935942 ID=cds.MS.gene39522.t1;Parent=MS.gene39522.t1
Gene Sequence

>MS.gene39522

ATGGATGTTAAAGTATCAAACCTCTATGATGAACAAAAGCTACCATTTCTTCACAACATGGAGATTGTAGAACCACAAAGGAACCTTTTGCATAGAGCCATCAATCAAACATGTAAAAGCACAGCTCATTTAGCCAATCTTTTACCAACAGGCACTGTCCTTTCATTCCAACTTCTATCACCAATATTCACAAACCAAGGCAAGTGTGACCACGTTACACAGTTAATGACTTTATCACTTTTATCCTTATGTGGTGCCTCATGCTTCCTACTATGCTTCACTGATAGCTTCAAAGACAATAAAGGGAACATATGTTATGGATTTGCCACACTTAGAGGCTTATGGATCATTGATGGATCAGCTACACTTCCACATGAACTTGATGCAAAATATAAACTAAGGTTCATTGATTTCATGCATGCAATTATGTCAATCTTGGTTTTTTCAGCTATTGCAATGTTTGATCATAATGTGGTTAACTGTTTCTTTCCATCACCTTCATATGAGATGCGTCAAATCCTTACTGCATTGCCTGTTGGAATTGGTGTTTTCTGTAGCATGCTGTTTGTTACATTTCCTACTCATGGACATGGAATTGGCTTCCCACTTTCAACAAATTAA
Protein sequence

>MS.gene39522.t1

MDVKVSNLYDEQKLPFLHNMEIVEPQRNLLHRAINQTCKSTAHLANLLPTGTVLSFQLLSPIFTNQGKCDHVTQLMTLSLLSLCGASCFLLCFTDSFKDNKGNICYGFATLRGLWIIDGSATLPHELDAKYKLRFIDFMHAIMSILVFSAIAMFDHNVVNCFFPSPSYEMRQILTALPVGIGVFCSMLFVTFPTHGHGIGFPLSTN