AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96235

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96235.t1 MTR_2g019410 90.421 261 25 0 1 261 1 261 2.53e-175 483
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96235.t1 AT2G34530 38.424 203 111 5 70 259 67 268 1.92e-30 115
MS.gene96235.t1 AT2G34530 38.424 203 111 5 70 259 77 278 2.36e-30 115
MS.gene96235.t1 AT2G34530 38.424 203 111 5 70 259 111 312 4.17e-30 115
MS.gene96235.t1 AT2G34530 43.885 139 75 2 70 206 77 214 2.12e-25 100
MS.gene96235.t1 AT2G34530 43.885 139 75 2 70 206 67 204 4.73e-25 100

Find 54 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTCTCTATCTTTCGACTTA+TGG 0.180793 2.2:-65227725 MS.gene96235:CDS
CTCTTTCAATCTATCCAATA+TGG 0.186585 2.2:+65227607 None:intergenic
TCTTGATTTAATAAAGATTC+AGG 0.264321 2.2:-65227504 MS.gene96235:intron
GTCTCTATCTTTCGACTTAT+GGG 0.294022 2.2:-65227724 MS.gene96235:CDS
AGTGCAATACAAGAATTATC+AGG 0.313725 2.2:-65226299 MS.gene96235:CDS
GCCGTTGTTATTGTCATCCT+TGG 0.313936 2.2:-65227749 MS.gene96235:CDS
AGTAGAAATGCTCATCTATA+AGG 0.325228 2.2:-65227227 MS.gene96235:intron
TGAGCTTGAGCTTCGACTTT+CGG 0.331242 2.2:+65227696 None:intergenic
GAATTCATTCCAACATTCAT+TGG 0.362634 2.2:+65226394 None:intergenic
GAACTTATAAAGAGAAAATT+CGG 0.363931 2.2:+65226346 None:intergenic
TCATAGTGGAAAACCCATAT+TGG 0.366180 2.2:-65227621 MS.gene96235:CDS
TTTCCGTGTTTCCCTTCATT+TGG 0.370913 2.2:+65226420 None:intergenic
AGATATGTTGCAGCAAGCTT+TGG 0.373596 2.2:-65227365 MS.gene96235:intron
TTCATGATAATTTGAAGAAA+GGG 0.388116 2.2:+65227838 None:intergenic
ACGGTCAAAGTGTCCGGACT+TGG 0.391154 2.2:+65227670 None:intergenic
TCTTTCAATCTATCCAATAT+GGG 0.393501 2.2:+65227608 None:intergenic
CTTCATGATAATTTGAAGAA+AGG 0.402053 2.2:+65227837 None:intergenic
AGATTCTGCGGTGGAAATAC+TGG 0.405408 2.2:-65227317 MS.gene96235:CDS
CTTCAATTGGCAGGGAGAGC+TGG 0.406149 2.2:-65226818 MS.gene96235:intron
CTCAAGCTCACGCCCAAGTC+CGG 0.417252 2.2:-65227683 MS.gene96235:CDS
CCGTTGTTATTGTCATCCTT+GGG 0.433089 2.2:-65227748 MS.gene96235:CDS
GGCAATTATATACCAAATGA+AGG 0.439320 2.2:-65226432 MS.gene96235:CDS
TTTCAAGCATGTACGGTTCA+AGG 0.445106 2.2:+65226789 None:intergenic
CATATTGGATAGATTGAAAG+AGG 0.477246 2.2:-65227606 MS.gene96235:CDS
CCGGACACTTTGACCGTACA+AGG 0.481049 2.2:-65227664 MS.gene96235:CDS
TGCTCGACGCCCACTGTACA+AGG 0.484519 2.2:-65226749 MS.gene96235:intron
GCAGCAAGCTTTGGAAAAGC+TGG 0.488777 2.2:-65227356 MS.gene96235:intron
ACTGGAAAATGCCGTAAAGA+AGG 0.511553 2.2:-65227299 MS.gene96235:CDS
TAACGATCCATGACCTTGTA+CGG 0.512166 2.2:+65227651 None:intergenic
ACAAGAATTATCAGGGAGGA+AGG 0.520561 2.2:-65226291 MS.gene96235:CDS
CCTTGTACGGTCAAAGTGTC+CGG 0.522757 2.2:+65227664 None:intergenic
CGGTCAAAGTGTCCGGACTT+GGG 0.540111 2.2:+65227671 None:intergenic
AATCATCTTTCAAGCATGTA+CGG 0.563613 2.2:+65226782 None:intergenic
TAAAGAGAAAATTCGGTGCA+AGG 0.565220 2.2:+65226353 None:intergenic
ACTTTGACCGTACAAGGTCA+TGG 0.569622 2.2:-65227658 MS.gene96235:CDS
GTGCAATACAAGAATTATCA+GGG 0.569824 2.2:-65226298 MS.gene96235:CDS
AAATATCAAGATGGCAACAC+TGG 0.574878 2.2:-65227771 MS.gene96235:CDS
CGACTCAAGTATGAATCACC+TGG 0.592794 2.2:-65227882 None:intergenic
GCAATTATATACCAAATGAA+GGG 0.605208 2.2:-65226431 MS.gene96235:CDS
CAAGAATTATCAGGGAGGAA+GGG 0.609044 2.2:-65226290 MS.gene96235:CDS
TTGGAAAAGCTGGAAATGAG+TGG 0.622925 2.2:-65227346 MS.gene96235:CDS
GTATGAGTTAAATATCAAGA+TGG 0.627283 2.2:-65227780 MS.gene96235:CDS
GAACGTGTACCTTGTACAGT+GGG 0.633465 2.2:+65226740 None:intergenic
GGAACGTGTACCTTGTACAG+TGG 0.634635 2.2:+65226739 None:intergenic
ATACCAAATGAAGGGAAACA+CGG 0.638175 2.2:-65226423 MS.gene96235:CDS
AAGGAGGATCTTGTACCGCA+AGG 0.649015 2.2:+65226372 None:intergenic
ATCGTTAGAGAAATTCATAG+TGG 0.664835 2.2:-65227635 MS.gene96235:CDS
TCGAAAGATAGAGACTCCCA+AGG 0.672047 2.2:+65227732 None:intergenic
CCCAAGGATGACAATAACAA+CGG 0.691024 2.2:+65227748 None:intergenic
TGGAAGTGAAGATTCTGCGG+TGG 0.692864 2.2:-65227326 MS.gene96235:CDS
AGAGAAAATTCGGTGCAAGG+AGG 0.706718 2.2:+65226356 None:intergenic
GAGTGGAAGTGAAGATTCTG+CGG 0.718050 2.2:-65227329 MS.gene96235:CDS
ATGTTGGAATGAATTCCTTG+CGG 0.756613 2.2:-65226387 MS.gene96235:CDS
CAATACAAGAATTATCAGGG+AGG 0.773135 2.2:-65226295 MS.gene96235:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAGTTTATTTACATTTT+TGG - chr2.2:65227003-65227022 MS.gene96235:intron 10.0%
!! TTATAAGTTCAAAAAAAATG+TGG - chr2.2:65227822-65227841 MS.gene96235:CDS 15.0%
!!! AATGAACTTTTATAATCTAA+TGG - chr2.2:65227172-65227191 MS.gene96235:intron 15.0%
!!! TAATTTAGGTATATATGTTT+TGG - chr2.2:65227030-65227049 MS.gene96235:intron 15.0%
!! AACATATATACCTAAATTAG+AGG + chr2.2:65227029-65227048 None:intergenic 20.0%
!! AATGACCTAAAACAAATTAT+TGG - chr2.2:65227243-65227262 MS.gene96235:CDS 20.0%
!! ACGAAATTAATGTTAAATCT+TGG - chr2.2:65227201-65227220 MS.gene96235:intron 20.0%
!! CAATAAATCTTAGTATATGA+AGG + chr2.2:65226695-65226714 None:intergenic 20.0%
!! GAACTTATAAAGAGAAAATT+CGG + chr2.2:65227812-65227831 None:intergenic 20.0%
!! TATGAAAAGAAAACTTCAAT+TGG - chr2.2:65227324-65227343 MS.gene96235:CDS 20.0%
!! TCTTGATTTAATAAAGATTC+AGG - chr2.2:65226651-65226670 MS.gene96235:intron 20.0%
!! TTCATGATAATTTGAAGAAA+GGG + chr2.2:65226320-65226339 None:intergenic 20.0%
!!! CATTGAAATTTCAAGTTATT+AGG + chr2.2:65227227-65227246 None:intergenic 20.0%
!!! TATTTGATAATTTAGATGAG+AGG + chr2.2:65227462-65227481 None:intergenic 20.0%
!!! TTGATTCTTTCTTTTTTTAC+AGG - chr2.2:65227702-65227721 MS.gene96235:CDS 20.0%
! AACAATTATCTAACGTACTT+AGG + chr2.2:65226728-65226747 None:intergenic 25.0%
! CTGATCACATAAAATTTATC+TGG - chr2.2:65227518-65227537 MS.gene96235:CDS 25.0%
! CTTCATGATAATTTGAAGAA+AGG + chr2.2:65226321-65226340 None:intergenic 25.0%
! GCAATTATATACCAAATGAA+GGG - chr2.2:65227724-65227743 MS.gene96235:CDS 25.0%
! GTATGAGTTAAATATCAAGA+TGG - chr2.2:65226375-65226394 MS.gene96235:CDS 25.0%
! TAAAACAAATTATTGGACGA+TGG - chr2.2:65227250-65227269 MS.gene96235:CDS 25.0%
! TAAAGAAAAATTGATGGGAA+GGG + chr2.2:65227123-65227142 None:intergenic 25.0%
! TCTTTCAATCTATCCAATAT+GGG + chr2.2:65226550-65226569 None:intergenic 25.0%
!! CAGATAAATTTTATGTGATC+AGG + chr2.2:65227520-65227539 None:intergenic 25.0%
!! CTCTCTAAAGAAAAATTGAT+GGG + chr2.2:65227128-65227147 None:intergenic 25.0%
!! TTTTAATCAAAGAATCGACA+AGG + chr2.2:65227647-65227666 None:intergenic 25.0%
!!! ACAAACTAAGAAAGTTTTGA+AGG - chr2.2:65226609-65226628 MS.gene96235:intron 25.0%
!!! ATCGTCCAATAATTTGTTTT+AGG + chr2.2:65227251-65227270 None:intergenic 25.0%
!!! TTAGTTTGTTTTAATGTTGC+AGG + chr2.2:65226598-65226617 None:intergenic 25.0%
AAAAGAAAACTTCAATTGGC+AGG - chr2.2:65227328-65227347 MS.gene96235:CDS 30.0%
AAAGAAAACTTCAATTGGCA+GGG - chr2.2:65227329-65227348 MS.gene96235:CDS 30.0%
AATCATCTTTCAAGCATGTA+CGG + chr2.2:65227376-65227395 None:intergenic 30.0%
ACAATTGAGAAACTACAATC+AGG + chr2.2:65227073-65227092 None:intergenic 30.0%
AGTAGAAATGCTCATCTATA+AGG - chr2.2:65226928-65226947 MS.gene96235:intron 30.0%
AGTGCAATACAAGAATTATC+AGG - chr2.2:65227856-65227875 MS.gene96235:CDS 30.0%
ATCGTTAGAGAAATTCATAG+TGG - chr2.2:65226520-65226539 MS.gene96235:intron 30.0%
CATATTGGATAGATTGAAAG+AGG - chr2.2:65226549-65226568 MS.gene96235:intron 30.0%
CTAAAGAAAAATTGATGGGA+AGG + chr2.2:65227124-65227143 None:intergenic 30.0%
CTCTTTCAATCTATCCAATA+TGG + chr2.2:65226551-65226570 None:intergenic 30.0%
GAATTCATTCCAACATTCAT+TGG + chr2.2:65227764-65227783 None:intergenic 30.0%
GGCAATTATATACCAAATGA+AGG - chr2.2:65227723-65227742 MS.gene96235:CDS 30.0%
GTGCAATACAAGAATTATCA+GGG - chr2.2:65227857-65227876 MS.gene96235:CDS 30.0%
TCAAAAACCTTGTGCTTTAT+CGG - chr2.2:65227485-65227504 MS.gene96235:intron 30.0%
TCACGATCAACTTATTTCAA+AGG - chr2.2:65227567-65227586 MS.gene96235:CDS 30.0%
! AATTGATCAACTTTTCTACC+AGG + chr2.2:65226294-65226313 None:intergenic 30.0%
! CCTCTCTAAAGAAAAATTGA+TGG + chr2.2:65227129-65227148 None:intergenic 30.0%
! GTATGCAAGTTGAAATGATA+AGG + chr2.2:65227440-65227459 None:intergenic 30.0%
!! CCATCAATTTTTCTTTAGAG+AGG - chr2.2:65227126-65227145 MS.gene96235:intron 30.0%
!!! ACATTTTTGGCCTCTAATTT+AGG - chr2.2:65227016-65227035 MS.gene96235:intron 30.0%
AAATATCAAGATGGCAACAC+TGG - chr2.2:65226384-65226403 MS.gene96235:CDS 35.0%
AGTCTCTATCTTTCGACTTA+TGG - chr2.2:65226430-65226449 MS.gene96235:CDS 35.0%
ATACCAAATGAAGGGAAACA+CGG - chr2.2:65227732-65227751 MS.gene96235:CDS 35.0%
ATGTTGGAATGAATTCCTTG+CGG - chr2.2:65227768-65227787 MS.gene96235:CDS 35.0%
CAATACAAGAATTATCAGGG+AGG - chr2.2:65227860-65227879 MS.gene96235:CDS 35.0%
CGGAAAAAACCAATGAATGT+TGG - chr2.2:65227752-65227771 MS.gene96235:CDS 35.0%
GAAGATGTGCATTCGATTAT+TGG + chr2.2:65227625-65227644 None:intergenic 35.0%
GTCTCTATCTTTCGACTTAT+GGG - chr2.2:65226431-65226450 MS.gene96235:CDS 35.0%
TTATGATCCGATAAAGCACA+AGG + chr2.2:65227495-65227514 None:intergenic 35.0%
! TCATAGTGGAAAACCCATAT+TGG - chr2.2:65226534-65226553 MS.gene96235:intron 35.0%
!! ATGGTGTTGCAAATGACATA+GGG - chr2.2:65227269-65227288 MS.gene96235:CDS 35.0%
!! TAAAGAGAAAATTCGGTGCA+AGG + chr2.2:65227805-65227824 None:intergenic 35.0%
AAATTGATGGGAAGGGTTGA+AGG + chr2.2:65227116-65227135 None:intergenic 40.0%
AATTGATGGGAAGGGTTGAA+GGG + chr2.2:65227115-65227134 None:intergenic 40.0%
ACAAGAATTATCAGGGAGGA+AGG - chr2.2:65227864-65227883 MS.gene96235:CDS 40.0%
ACTGGAAAATGCCGTAAAGA+AGG - chr2.2:65226856-65226875 MS.gene96235:intron 40.0%
AGATATGTTGCAGCAAGCTT+TGG - chr2.2:65226790-65226809 MS.gene96235:CDS 40.0%
CAAGAATTATCAGGGAGGAA+GGG - chr2.2:65227865-65227884 MS.gene96235:CDS 40.0%
CCCAAGGATGACAATAACAA+CGG + chr2.2:65226410-65226429 None:intergenic 40.0%
TAACGATCCATGACCTTGTA+CGG + chr2.2:65226507-65226526 None:intergenic 40.0%
TTGGAAAAGCTGGAAATGAG+TGG - chr2.2:65226809-65226828 MS.gene96235:intron 40.0%
TTTCAAGCATGTACGGTTCA+AGG + chr2.2:65227369-65227388 None:intergenic 40.0%
TTTCCGTGTTTCCCTTCATT+TGG + chr2.2:65227738-65227757 None:intergenic 40.0%
! CCGTTGTTATTGTCATCCTT+GGG - chr2.2:65226407-65226426 MS.gene96235:CDS 40.0%
! CGCATTTTCAGCCTTCTTTA+CGG + chr2.2:65226870-65226889 None:intergenic 40.0%
!! GATGGTGTTGCAAATGACAT+AGG - chr2.2:65227268-65227287 MS.gene96235:CDS 40.0%
!! TGGTGTTGCAAATGACATAG+GGG - chr2.2:65227270-65227289 MS.gene96235:CDS 40.0%
ACTTTGACCGTACAAGGTCA+TGG - chr2.2:65226497-65226516 MS.gene96235:intron 45.0%
AGATTCTGCGGTGGAAATAC+TGG - chr2.2:65226838-65226857 MS.gene96235:intron 45.0%
GAACGTGTACCTTGTACAGT+GGG + chr2.2:65227418-65227437 None:intergenic 45.0%
GAGTGGAAGTGAAGATTCTG+CGG - chr2.2:65226826-65226845 MS.gene96235:intron 45.0%
TCGAAAGATAGAGACTCCCA+AGG + chr2.2:65226426-65226445 None:intergenic 45.0%
TGAGCTTGAGCTTCGACTTT+CGG + chr2.2:65226462-65226481 None:intergenic 45.0%
! GCCGTTGTTATTGTCATCCT+TGG - chr2.2:65226406-65226425 MS.gene96235:CDS 45.0%
!! AGAGAAAATTCGGTGCAAGG+AGG + chr2.2:65227802-65227821 None:intergenic 45.0%
AAGGAGGATCTTGTACCGCA+AGG + chr2.2:65227786-65227805 None:intergenic 50.0%
GGAACGTGTACCTTGTACAG+TGG + chr2.2:65227419-65227438 None:intergenic 50.0%
TGGAAGTGAAGATTCTGCGG+TGG - chr2.2:65226829-65226848 MS.gene96235:intron 50.0%
! CCTTGTACGGTCAAAGTGTC+CGG + chr2.2:65226494-65226513 None:intergenic 50.0%
!! GCAGCAAGCTTTGGAAAAGC+TGG - chr2.2:65226799-65226818 MS.gene96235:CDS 50.0%
CCGGACACTTTGACCGTACA+AGG - chr2.2:65226491-65226510 MS.gene96235:intron 55.0%
CTTCAATTGGCAGGGAGAGC+TGG - chr2.2:65227337-65227356 MS.gene96235:CDS 55.0%
! ACGGTCAAAGTGTCCGGACT+TGG + chr2.2:65226488-65226507 None:intergenic 55.0%
! CGGTCAAAGTGTCCGGACTT+GGG + chr2.2:65226487-65226506 None:intergenic 55.0%
CTCAAGCTCACGCCCAAGTC+CGG - chr2.2:65226472-65226491 MS.gene96235:intron 60.0%
TGCTCGACGCCCACTGTACA+AGG - chr2.2:65227406-65227425 MS.gene96235:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 65226283 65227894 65226283 ID=MS.gene96235
chr2.2 mRNA 65226283 65227894 65226283 ID=MS.gene96235.t1;Parent=MS.gene96235
chr2.2 exon 65227505 65227894 65227505 ID=MS.gene96235.t1.exon1;Parent=MS.gene96235.t1
chr2.2 CDS 65227505 65227894 65227505 ID=cds.MS.gene96235.t1;Parent=MS.gene96235.t1
chr2.2 exon 65227228 65227374 65227228 ID=MS.gene96235.t1.exon2;Parent=MS.gene96235.t1
chr2.2 CDS 65227228 65227374 65227228 ID=cds.MS.gene96235.t1;Parent=MS.gene96235.t1
chr2.2 exon 65226750 65226827 65226750 ID=MS.gene96235.t1.exon3;Parent=MS.gene96235.t1
chr2.2 CDS 65226750 65226827 65226750 ID=cds.MS.gene96235.t1;Parent=MS.gene96235.t1
chr2.2 exon 65226283 65226453 65226283 ID=MS.gene96235.t1.exon4;Parent=MS.gene96235.t1
chr2.2 CDS 65226283 65226453 65226283 ID=cds.MS.gene96235.t1;Parent=MS.gene96235.t1
Gene Sequence

>MS.gene96235

ATGAATCACCTGGTAGAAAAGTTGATCAATTTATCCCTTTCTTCAAATTATCATGAAGATATGCGAAAATTCATCTTAGCTTTCACATCTAAGTATGAGTTAAATATCAAGATGGCAACACTGGCCGTTGTTATTGTCATCCTTGGGAGTCTCTATCTTTCGACTTATGGGTCAAACCGAAAGTCGAAGCTCAAGCTCACGCCCAAGTCCGGACACTTTGACCGTACAAGGTCATGGATCGTTAGAGAAATTCATAGTGGAAAACCCATATTGGATAGATTGAAAGAGGATTTCAATAAAGCTCGAGTAAATCCTGCAACATTAAAACAAACTAAGAAAGTTTTGAAGGCTTTACTCAAAGAAGAATATCTTGATTTAATAAAGATTCAGGTAACATATTTTACAAGTTCCTTCATATACTAAGATTTATTGTTAACAATATCCTAAGTACGTTAGATAATTGTTTTAACACTAAGAAATGACAATGTGATTCATATTCTAACTAAGAGATATGTTGCAGCAAGCTTTGGAAAAGCTGGAAATGAGTGGAAGTGAAGATTCTGCGGTGGAAATACTGGAAAATGCCGTAAAGAAGGCTGAAAATGCGAACAAAGCACATGAAGCTTATGAAATTGAAATGTTACTAGTAGAAATGCTCATCTATAAGGTTGAAAAATCTCAACTTGTCACTATACTCTATTAACATATTTATTTTTAAAATTTAAGTTTATTTACATTTTTGGCCTCTAATTTAGGTATATATGTTTTGGTTTCTCAATTTTTTTTACCTGATTGTAGTTTCTCAATTGTCTAATTTTTGCATTTCAGTCCCTTCAACCCTTCCCATCAATTTTTCTTTAGAGAGGAACAATCAACTTTGAAAGTGACAAATGAACTTTTATAATCTAATGGATCTATACGAAATTAATGTTAAATCTTGGCCTAATAACTTGAAATTTCAATGACCTAAAACAAATTATTGGACGATGGTGTTGCAAATGACATAGGGGTGTGTACTTTGTTGTGAATTCTTTATCTATTTATGAAAAGAAAACTTCAATTGGCAGGGAGAGCTGGACAGTGCCTTGAACCGTACATGCTTGAAAGATGATTCGCTTAAAGATGCTCGACGCCCACTGTACAAGGTACACGTTCCTTATCATTTCAACTTGCATACCTCTCATCTAAATTATCAAATAATCTCAAAAACCTTGTGCTTTATCGGATCATAACTCCTGATCACATAAAATTTATCTGGAGATACAATTCGATCAATGTCGTTTATCACGATCAACTTATTTCAAAGGTTGAACAATTCACGATGAGCATATAGCAGTTTCCAATAATCGAATGCACATCTTCCTTGTCGATTCTTTGATTAAAAATATAAAGAAAGACTTGTCAAATTAAGTTTGCTCATTGATTCTTTCTTTTTTTACAGGCAATTATATACCAAATGAAGGGAAACACGGAAAAAACCAATGAATGTTGGAATGAATTCCTTGCGGTACAAGATCCTCCTTGCACCGAATTTTCTCTTTATAAGTTCAAAAAAAATGTGGAACGACTTCAAAGTGCAATACAAGAATTATCAGGGAGGAAGGGACAATAA
Protein sequence

>MS.gene96235.t1

MNHLVEKLINLSLSSNYHEDMRKFILAFTSKYELNIKMATLAVVIVILGSLYLSTYGSNRKSKLKLTPKSGHFDRTRSWIVREIHSGKPILDRLKEDFNKARVNPATLKQTKKVLKALLKEEYLDLIKIQQALEKLEMSGSEDSAVEILENAVKKAENANKAHEAYEIEMLLVEMLIYKGELDSALNRTCLKDDSLKDARRPLYKAIIYQMKGNTEKTNECWNEFLAVQDPPCTEFSLYKFKKNVERLQSAIQELSGRKGQ