AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051677


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051677.t1 MTR_1g017780 97.516 161 4 0 1 161 1 161 5.34e-115 322
MS.gene051677.t1 MTR_8g076830 93.789 161 9 1 1 161 1 160 1.89e-98 280
MS.gene051677.t1 MTR_4g116410 93.168 161 10 1 1 161 1 160 3.69e-98 280
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051677.t1 AT5G23740 87.578 161 18 1 1 161 1 159 9.01e-93 266
MS.gene051677.t1 AT3G48930 86.335 161 21 1 1 161 1 160 3.51e-91 262
MS.gene051677.t1 AT4G30800 86.335 161 20 1 1 161 1 159 7.99e-89 256

Find 49 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGGGGATCATGTTATTAT+TGG 0.267190 1.3:-4955472 MS.gene051677:CDS
ATAATTCCTCCTAACAATAA+TGG 0.308146 1.3:+4955674 None:intergenic
AAGCGATTGCCACCCTTTCC+AGG 0.318925 1.3:+4956282 None:intergenic
TGAATAAAACCATTATTGTT+AGG 0.334061 1.3:-4955683 MS.gene051677:CDS
GACTCCTGTAAACGCCTTCT+TGG 0.362038 1.3:+4955247 None:intergenic
GGTGCCAAGAAGGCGTTTAC+AGG 0.366657 1.3:-4955251 MS.gene051677:CDS
GGGACACTTCTTGTCAATAT+AGG 0.373630 1.3:+4955767 None:intergenic
TTGCTTCAGAAAAGCCTTCT+CGG 0.396604 1.3:+4956350 None:intergenic
TTTGAGAAAGAAACCTTCAA+TGG 0.449940 1.3:+4956218 None:intergenic
CCCTAGGAGTCTTAAAACTA+AGG 0.476406 1.3:+4956244 None:intergenic
ACTCCTAGGGAAGCCATTGA+AGG 0.484194 1.3:-4956231 MS.gene051677:intron
GCTGGATCTTCTAGTGGTGC+CGG 0.487132 1.3:-4955272 MS.gene051677:CDS
ATGTTATTATTGGCCAATGC+AGG 0.499585 1.3:-4955462 MS.gene051677:intron
TACAATGATCTAACCTGCAT+TGG 0.500383 1.3:+4955449 None:intergenic
ATCCGAGGTCGTATCATATC+CGG 0.504599 1.3:-4955726 MS.gene051677:CDS
TCTGGGAAGGGGAAGAGACC+TGG 0.510724 1.3:-4956300 MS.gene051677:CDS
AACCTCACTGTCTTAGAAAG+TGG 0.510906 1.3:+4955317 None:intergenic
TAGTGGTGCCGGTGCCAAGA+AGG 0.518324 1.3:-4955261 MS.gene051677:CDS
GACAAGAAGTGTCCCTTCAC+TGG 0.524673 1.3:-4955759 MS.gene051677:CDS
ATCACCTTGTTTCCGAGTGA+AGG 0.529932 1.3:-4955494 MS.gene051677:CDS
AAGGGGAAGAGACCTGGAAA+GGG 0.530695 1.3:-4956294 MS.gene051677:CDS
CCTTGTTTCCGAGTGAAGGA+AGG 0.534218 1.3:-4955490 MS.gene051677:CDS
CCTTCCTTCACTCGGAAACA+AGG 0.542963 1.3:+4955490 None:intergenic
TGCTCGAAGATATCTGGGAA+GGG 0.550883 1.3:-4956312 MS.gene051677:CDS
CTTGTTTCCGAGTGAAGGAA+GGG 0.551830 1.3:-4955489 MS.gene051677:CDS
ATAAAACCATTATTGTTAGG+AGG 0.551945 1.3:-4955680 MS.gene051677:CDS
GTATTGAAAGTCATCCCAGC+TGG 0.559579 1.3:-4955290 MS.gene051677:CDS
GGGAAGAGACCTGGAAAGGG+TGG 0.564985 1.3:-4956291 MS.gene051677:CDS
TTTGAATTTGTAGACCGAGA+AGG 0.567346 1.3:-4956364 MS.gene051677:intron
GCACCACTAGAAGATCCAGC+TGG 0.568341 1.3:+4955275 None:intergenic
CAAACTAACTTGTTCAGCCA+TGG 0.568984 1.3:+4956463 None:intergenic
ATCCCAGCTGGATCTTCTAG+TGG 0.570183 1.3:-4955278 MS.gene051677:CDS
GAAGGGGAAGAGACCTGGAA+AGG 0.571357 1.3:-4956295 MS.gene051677:CDS
CGTGTGCAGGAATATTAGAA+TGG 0.572181 1.3:+4955518 None:intergenic
CTTAGCACTATGGCAAGTAC+CGG 0.576116 1.3:+4955707 None:intergenic
CATGATCCCCTTCCTTCACT+CGG 0.580378 1.3:+4955482 None:intergenic
GTGCTCGAAGATATCTGGGA+AGG 0.582495 1.3:-4956313 MS.gene051677:CDS
AAACCTTCAATGGCTTCCCT+AGG 0.582868 1.3:+4956228 None:intergenic
AAACAAGGTGATACGTGTGC+AGG 0.596227 1.3:+4955505 None:intergenic
GCTCGAAGATATCTGGGAAG+GGG 0.598893 1.3:-4956311 MS.gene051677:CDS
GATTGAGACATTACCAGTGA+AGG 0.618985 1.3:+4955746 None:intergenic
TTGTTTCCGAGTGAAGGAAG+GGG 0.622320 1.3:-4955488 MS.gene051677:CDS
ATTGAGACATTACCAGTGAA+GGG 0.624989 1.3:+4955747 None:intergenic
CACCACTAGAAGATCCAGCT+GGG 0.629304 1.3:+4955276 None:intergenic
ACTGGTAATGTCTCAATCCG+AGG 0.640857 1.3:-4955741 MS.gene051677:CDS
TGTAAACGCCTTCTTGGCAC+CGG 0.648607 1.3:+4955253 None:intergenic
ATTTCATTAAGAAATATCAG+AGG 0.666848 1.3:-4955647 MS.gene051677:intron
GGCCACTTTCTAAGACAGTG+AGG 0.709841 1.3:-4955319 MS.gene051677:CDS
TACCGGATATGATACGACCT+CGG 0.712271 1.3:+4955724 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTGTTTTGATAAATCT+TGG - chr1.3:4955293-4955312 MS.gene051677:CDS 15.0%
!! ATTTCATTAAGAAATATCAG+AGG - chr1.3:4956058-4956077 MS.gene051677:intron 20.0%
!! CAAATTATAGATTAATGTGA+AGG + chr1.3:4955271-4955290 None:intergenic 20.0%
!! GTATTAGATTACAAAAAGAA+AGG + chr1.3:4955896-4955915 None:intergenic 20.0%
!! GTTACCAATTTATTTACATA+AGG - chr1.3:4955869-4955888 MS.gene051677:intron 20.0%
!! TGAATAAAACCATTATTGTT+AGG - chr1.3:4956022-4956041 MS.gene051677:intron 20.0%
!! TTCCTATAAGATTAAGAAAA+AGG + chr1.3:4955918-4955937 None:intergenic 20.0%
!!! TACCTTTTTCTTAATCTTAT+AGG - chr1.3:4955913-4955932 MS.gene051677:intron 20.0%
!!! TAGATTGGTTTATTATTGAT+AGG - chr1.3:4955602-4955621 MS.gene051677:intron 20.0%
! AAGCTTATGAAAATAGCTTA+TGG + chr1.3:4955710-4955729 None:intergenic 25.0%
! AGGACCTTATGTAAATAAAT+TGG + chr1.3:4955876-4955895 None:intergenic 25.0%
! AGGACTTATTAAAACAGTTT+AGG + chr1.3:4955780-4955799 None:intergenic 25.0%
! ATAAAACCATTATTGTTAGG+AGG - chr1.3:4956025-4956044 MS.gene051677:intron 25.0%
! ATAATTCCTCCTAACAATAA+TGG + chr1.3:4956034-4956053 None:intergenic 25.0%
! TAAACCACGAATATGAAAAT+TGG + chr1.3:4955519-4955538 None:intergenic 25.0%
! TCTTGGATTTACTAACTAAT+TGG - chr1.3:4955310-4955329 MS.gene051677:CDS 25.0%
! TTTAAGAATCATAGGTAGAT+TGG - chr1.3:4955587-4955606 MS.gene051677:intron 25.0%
!! TTTTATTCATCTTAGCACTA+TGG + chr1.3:4956011-4956030 None:intergenic 25.0%
!! TTTTCATATTCGTGGTTTAA+TGG - chr1.3:4955520-4955539 MS.gene051677:CDS 25.0%
!!! AATCGCTTTTATAAATCTGT+TGG - chr1.3:4955438-4955457 MS.gene051677:intron 25.0%
!!! CATTGTGTTTTAAGAATCAT+AGG - chr1.3:4955579-4955598 MS.gene051677:intron 25.0%
!!! TTGTTTTGTTTATCCAAGTA+AGG - chr1.3:4956310-4956329 MS.gene051677:CDS 25.0%
CTCTGTTTGGTAAAAAATAG+TGG + chr1.3:4955687-4955706 None:intergenic 30.0%
TGTGTATGCTTGTTCTTATT+AGG - chr1.3:4956153-4956172 MS.gene051677:intron 30.0%
TTTGAGAAAGAAACCTTCAA+TGG + chr1.3:4955490-4955509 None:intergenic 30.0%
! GTTTCCAATTTTCATATTCG+TGG - chr1.3:4955512-4955531 MS.gene051677:CDS 30.0%
AAGCTTTCATGAAGAGCTTA+TGG - chr1.3:4955724-4955743 MS.gene051677:CDS 35.0%
ACAAATAGTTAACACACCTG+TGG + chr1.3:4956133-4956152 None:intergenic 35.0%
AGATAAGCTCAAATAAGCCA+TGG - chr1.3:4955837-4955856 MS.gene051677:intron 35.0%
AGCAGAAGTAAAGGTAATCA+AGG + chr1.3:4956358-4956377 None:intergenic 35.0%
ATGTTATTATTGGCCAATGC+AGG - chr1.3:4956243-4956262 MS.gene051677:CDS 35.0%
ATTGAGACATTACCAGTGAA+GGG + chr1.3:4955961-4955980 None:intergenic 35.0%
CACAAAAACAGTTCCTTACT+TGG + chr1.3:4956326-4956345 None:intergenic 35.0%
CTATGAACAAGCAGAAGTAA+AGG + chr1.3:4956367-4956386 None:intergenic 35.0%
CTTTACTTCTGCTTGTTCAT+AGG - chr1.3:4956365-4956384 MS.gene051677:intron 35.0%
GAAGGGGATCATGTTATTAT+TGG - chr1.3:4956233-4956252 MS.gene051677:CDS 35.0%
GCAGAAGTAAAGGTAATCAA+GGG + chr1.3:4956357-4956376 None:intergenic 35.0%
TACAATGATCTAACCTGCAT+TGG + chr1.3:4956259-4956278 None:intergenic 35.0%
TTACTGTATTTGTATGCCAC+AGG - chr1.3:4956114-4956133 MS.gene051677:intron 35.0%
TTTGAATTTGTAGACCGAGA+AGG - chr1.3:4955341-4955360 MS.gene051677:intron 35.0%
! AAATAGCTTATGGCTCTGTT+TGG + chr1.3:4955700-4955719 None:intergenic 35.0%
! TTGGTAACATAAACATGCCA+TGG + chr1.3:4955857-4955876 None:intergenic 35.0%
! TTTTGTGCTCGAAGATATCT+GGG - chr1.3:4955388-4955407 MS.gene051677:intron 35.0%
! TTTTTGTGCTCGAAGATATC+TGG - chr1.3:4955387-4955406 MS.gene051677:intron 35.0%
!!! CCTTAGTTTTAAGACTCCTA+GGG - chr1.3:4955461-4955480 MS.gene051677:intron 35.0%
AACCTCACTGTCTTAGAAAG+TGG + chr1.3:4956391-4956410 None:intergenic 40.0%
ATTCATTCCCCTTTCTTACC+AGG - chr1.3:4956082-4956101 MS.gene051677:intron 40.0%
CCCTAGGAGTCTTAAAACTA+AGG + chr1.3:4955464-4955483 None:intergenic 40.0%
CGTGTGCAGGAATATTAGAA+TGG + chr1.3:4956190-4956209 None:intergenic 40.0%
GATTGAGACATTACCAGTGA+AGG + chr1.3:4955962-4955981 None:intergenic 40.0%
GGGACACTTCTTGTCAATAT+AGG + chr1.3:4955941-4955960 None:intergenic 40.0%
TTCATTCCCCTTTCTTACCA+GGG - chr1.3:4956083-4956102 MS.gene051677:intron 40.0%
TTGCTTCAGAAAAGCCTTCT+CGG + chr1.3:4955358-4955377 None:intergenic 40.0%
!!! GCCTTAGTTTTAAGACTCCT+AGG - chr1.3:4955460-4955479 MS.gene051677:intron 40.0%
AAACAAGGTGATACGTGTGC+AGG + chr1.3:4956203-4956222 None:intergenic 45.0%
AAACCTTCAATGGCTTCCCT+AGG + chr1.3:4955480-4955499 None:intergenic 45.0%
ATCCGAGGTCGTATCATATC+CGG - chr1.3:4955979-4955998 MS.gene051677:intron 45.0%
CTTAGCACTATGGCAAGTAC+CGG + chr1.3:4956001-4956020 None:intergenic 45.0%
CTTGTTTCCGAGTGAAGGAA+GGG - chr1.3:4956216-4956235 MS.gene051677:intron 45.0%
GTATTGAAAGTCATCCCAGC+TGG - chr1.3:4956415-4956434 MS.gene051677:intron 45.0%
TACCGGATATGATACGACCT+CGG + chr1.3:4955984-4956003 None:intergenic 45.0%
TGCTCGAAGATATCTGGGAA+GGG - chr1.3:4955393-4955412 MS.gene051677:intron 45.0%
TTGTTTCCGAGTGAAGGAAG+GGG - chr1.3:4956217-4956236 MS.gene051677:intron 45.0%
! ACTGGTAATGTCTCAATCCG+AGG - chr1.3:4955964-4955983 MS.gene051677:intron 45.0%
! ATCACCTTGTTTCCGAGTGA+AGG - chr1.3:4956211-4956230 MS.gene051677:intron 45.0%
AAGGGGAAGAGACCTGGAAA+GGG - chr1.3:4955411-4955430 MS.gene051677:intron 50.0%
ACTCCTAGGGAAGCCATTGA+AGG - chr1.3:4955474-4955493 MS.gene051677:CDS 50.0%
ATACAGTAAACTGCGCACCC+TGG + chr1.3:4956103-4956122 None:intergenic 50.0%
ATCCCAGCTGGATCTTCTAG+TGG - chr1.3:4956427-4956446 MS.gene051677:intron 50.0%
CACCACTAGAAGATCCAGCT+GGG + chr1.3:4956432-4956451 None:intergenic 50.0%
CATGATCCCCTTCCTTCACT+CGG + chr1.3:4956226-4956245 None:intergenic 50.0%
CCTTCCTTCACTCGGAAACA+AGG + chr1.3:4956218-4956237 None:intergenic 50.0%
GACTCCTGTAAACGCCTTCT+TGG + chr1.3:4956461-4956480 None:intergenic 50.0%
GCTCGAAGATATCTGGGAAG+GGG - chr1.3:4955394-4955413 MS.gene051677:intron 50.0%
GTGACATCATTTGCGTTGCG+AGG + chr1.3:4955800-4955819 None:intergenic 50.0%
GTGCTCGAAGATATCTGGGA+AGG - chr1.3:4955392-4955411 MS.gene051677:intron 50.0%
TGTAAACGCCTTCTTGGCAC+CGG + chr1.3:4956455-4956474 None:intergenic 50.0%
! CCTTGTTTCCGAGTGAAGGA+AGG - chr1.3:4956215-4956234 MS.gene051677:intron 50.0%
!! GACAAGAAGTGTCCCTTCAC+TGG - chr1.3:4955946-4955965 MS.gene051677:intron 50.0%
!! GGCCACTTTCTAAGACAGTG+AGG - chr1.3:4956386-4956405 MS.gene051677:intron 50.0%
AAGCGATTGCCACCCTTTCC+AGG + chr1.3:4955426-4955445 None:intergenic 55.0%
ACTGCGCACCCTGGTAAGAA+AGG + chr1.3:4956094-4956113 None:intergenic 55.0%
CTGCGCACCCTGGTAAGAAA+GGG + chr1.3:4956093-4956112 None:intergenic 55.0%
GAAGGGGAAGAGACCTGGAA+AGG - chr1.3:4955410-4955429 MS.gene051677:intron 55.0%
GCACCACTAGAAGATCCAGC+TGG + chr1.3:4956433-4956452 None:intergenic 55.0%
GCTGGATCTTCTAGTGGTGC+CGG - chr1.3:4956433-4956452 MS.gene051677:intron 55.0%
TGCGCACCCTGGTAAGAAAG+GGG + chr1.3:4956092-4956111 None:intergenic 55.0%
!! GGTGCCAAGAAGGCGTTTAC+AGG - chr1.3:4956454-4956473 MS.gene051677:intron 55.0%
GGGAAGAGACCTGGAAAGGG+TGG - chr1.3:4955414-4955433 MS.gene051677:intron 60.0%
TCTGGGAAGGGGAAGAGACC+TGG - chr1.3:4955405-4955424 MS.gene051677:intron 60.0%
!! TAGTGGTGCCGGTGCCAAGA+AGG - chr1.3:4956444-4956463 MS.gene051677:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 4955244 4956483 4955244 ID=MS.gene051677
chr1.3 mRNA 4955244 4956483 4955244 ID=MS.gene051677.t1;Parent=MS.gene051677
chr1.3 exon 4956472 4956483 4956472 ID=MS.gene051677.t1.exon1;Parent=MS.gene051677.t1
chr1.3 CDS 4956472 4956483 4956472 ID=cds.MS.gene051677.t1;Parent=MS.gene051677.t1
chr1.3 exon 4956232 4956373 4956232 ID=MS.gene051677.t1.exon2;Parent=MS.gene051677.t1
chr1.3 CDS 4956232 4956373 4956232 ID=cds.MS.gene051677.t1;Parent=MS.gene051677.t1
chr1.3 exon 4955648 4955792 4955648 ID=MS.gene051677.t1.exon3;Parent=MS.gene051677.t1
chr1.3 CDS 4955648 4955792 4955648 ID=cds.MS.gene051677.t1;Parent=MS.gene051677.t1
chr1.3 exon 4955463 4955552 4955463 ID=MS.gene051677.t1.exon4;Parent=MS.gene051677.t1
chr1.3 CDS 4955463 4955552 4955463 ID=cds.MS.gene051677.t1;Parent=MS.gene051677.t1
chr1.3 exon 4955244 4955340 4955244 ID=MS.gene051677.t1.exon5;Parent=MS.gene051677.t1
chr1.3 CDS 4955244 4955340 4955244 ID=cds.MS.gene051677.t1;Parent=MS.gene051677.t1
Gene Sequence

>MS.gene051677

ATGGCTGAACAAGTTAGTTTGTTACCTTCACATTAATCTATAATTTGAATTTTTTGTTTTGATAAATCTTGGATTTACTAACTAATTGGTTTGTGATTTTGAATTTGTAGACCGAGAAGGCTTTTCTGAAGCAAAATAAAGTGTTTTTGTGCTCGAAGATATCTGGGAAGGGGAAGAGACCTGGAAAGGGTGGCAATCGCTTTTATAAATCTGTTGGCCTTAGTTTTAAGACTCCTAGGGAAGCCATTGAAGGTTTCTTTCTCAAATTGTTTCCAATTTTCATATTCGTGGTTTAATGGAGTAATTATATACTCATAAACTCACTTTTTAATTCACATTGTGTTTTAAGAATCATAGGTAGATTGGTTTATTATTGATAGGTTTGTATATATGAAACTGTAGTTACTCAGATTGTATGACATTCAATTGTTTTAAGCTATCCACTATTTTTTACCAAACAGAGCCATAAGCTATTTTCATAAGCTTTCATGAAGAGCTTATGGAAATAAGCTGAAAACAGCGTATGAATATGTCCTAAACTGTTTTAATAAGTCCTCGCAACGCAAATGATGTCACAAGTGCTTATGTCAAATAGATAAGCTCAAATAAGCCATGGCATGTTTATGTTACCAATTTATTTACATAAGGTCCTTTCTTTTTGTAATCTAATACCTTTTTCTTAATCTTATAGGAACCTATATTGACAAGAAGTGTCCCTTCACTGGTAATGTCTCAATCCGAGGTCGTATCATATCCGGTACTTGCCATAGTGCTAAGATGAATAAAACCATTATTGTTAGGAGGAATTATCTTCATTTCATTAAGAAATATCAGAGGTATTCATTCCCCTTTCTTACCAGGGTGCGCAGTTTACTGTATTTGTATGCCACAGGTGTGTTAACTATTTGTTGTGTATGCTTGTTCTTATTAGGTATGAGAAGCGCCATTCTAATATTCCTGCACACGTATCACCTTGTTTCCGAGTGAAGGAAGGGGATCATGTTATTATTGGCCAATGCAGGTTAGATCATTGTAGAATTGTAGAATAATAACGCTTTTTTTGTTTTTGTTTTGTTTATCCAAGTAAGGAACTGTTTTTGTGTGTTTTAGCCCTTGATTACCTTTACTTCTGCTTGTTCATAGGCCACTTTCTAAGACAGTGAGGTTCAATGTATTGAAAGTCATCCCAGCTGGATCTTCTAGTGGTGCCGGTGCCAAGAAGGCGTTTACAGGAGTCTGA

Protein sequence

>MS.gene051677.t1

MAEQTEKAFLKQNKVFLCSKISGKGKRPGKGGNRFYKSVGLSFKTPREAIEGTYIDKKCPFTGNVSIRGRIISGTCHSAKMNKTIIVRRNYLHFIKKYQRYEKRHSNIPAHVSPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSSGAGAKKAFTGV