AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0280006993.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006993.01.T01 MTR_2g018680 100.000 61 0 0 1 61 4 64 9.98e-38 121
MsG0280006993.01.T01 MTR_2g018680 100.000 61 0 0 1 61 4 64 1.16e-37 121
MsG0280006993.01.T01 MTR_4g068040 95.082 61 3 0 1 61 4 64 1.24e-35 116
MsG0280006993.01.T01 MTR_4g068040 95.000 60 3 0 1 60 4 63 5.25e-35 114
MsG0280006993.01.T01 MTR_8g079485 91.803 61 5 0 1 61 4 64 1.14e-34 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0280006993.01.T01 AT3G59540 90.164 61 6 0 1 61 4 64 5.13e-34 112
MsG0280006993.01.T01 AT2G43460 90.164 61 6 0 1 61 4 64 5.13e-34 112

Find 27 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTCTCCATTTCATCCATT+TGG 0.273233 2:+9112461 None:intergenic
TAAGCAAATCAACGAGATTA+AGG 0.294566 2:-9113349 None:intergenic
ATCTCTCCAAATGGATGAAA+TGG 0.308166 2:-9112467 MsG0280006993.01.T01:CDS
TGAGTGTTCAAGACCTTTAG+AGG 0.372905 2:-9112614 MsG0280006993.01.T01:intron
TGACCTCGCATCCTTCCTTC+TGG 0.376233 2:+9113311 None:intergenic
TGGAGAGATATAGATCCATT+TGG 0.428839 2:+9112481 None:intergenic
TGGATCTATATCTCTCCAAA+TGG 0.457727 2:-9112476 MsG0280006993.01.T01:CDS
TTCTCATCCAATACCTCTAA+AGG 0.468641 2:+9112601 None:intergenic
GAGTTAAGATCCTCTCCATT+TGG 0.475407 2:+9112436 None:intergenic
AGTGAGAATCAAGAGGAGTA+AGG 0.485084 2:-9113289 MsG0280006993.01.T01:CDS
TAAGGATGTGGTTAAGTTCA+AGG 0.499148 2:-9113271 MsG0280006993.01.T01:CDS
AAGGGTAAAGATCCTCCAAA+TGG 0.506011 2:-9112496 MsG0280006993.01.T01:CDS
GAAATGGAGAGAATACCAAA+TGG 0.517514 2:-9112451 MsG0280006993.01.T01:CDS
ATGTGGTTAAGTTCAAGGTC+AGG 0.518401 2:-9113266 MsG0280006993.01.T01:CDS
AATCAAGAGGAGTAAGGATG+TGG 0.526249 2:-9113283 MsG0280006993.01.T01:CDS
ACTAAGTGTGTAGAGGTACT+TGG 0.532503 2:+9113239 None:intergenic
CCTTCTCACTGCCAGAAGGA+AGG 0.537276 2:-9113322 MsG0280006993.01.T01:CDS
TTGAAGCAATCACTTCCTCC+AGG 0.552717 2:-9113189 MsG0280006993.01.T01:CDS
AGAGATATAGATCCATTTGG+AGG 0.564353 2:+9112484 None:intergenic
CCTTCCTTCTGGCAGTGAGA+AGG 0.565796 2:+9113322 None:intergenic
ATTTCCTTCTCACTGCCAGA+AGG 0.584170 2:-9113326 MsG0280006993.01.T01:CDS
TGTAAATCCAACTACAGACC+TGG 0.609614 2:+9113171 None:intergenic
CGAGGTCAGTGAGAATCAAG+AGG 0.618562 2:-9113296 MsG0280006993.01.T01:CDS
GGAGAGAATACCAAATGGAG+AGG 0.623091 2:-9112446 MsG0280006993.01.T01:CDS
CTGCCAGAAGGAAGGATGCG+AGG 0.654921 2:-9113314 MsG0280006993.01.T01:CDS
CAAACACACTAAGTGTGTAG+AGG 0.657075 2:+9113232 None:intergenic
AAATCCAACTACAGACCTGG+AGG 0.697593 2:+9113174 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTATATTTATTTAGCCT+AGG - Chr2:9112618-9112637 MsG0280006993.01.T01:CDS 15.0%
!!! ATTTTTAACTCAATTTATCT+TGG - Chr2:9112805-9112824 MsG0280006993.01.T01:intron 15.0%
!! AAATTGATATGGTTAAAGAA+GGG + Chr2:9113068-9113087 None:intergenic 20.0%
!! CTTTATCATGTTACAATATT+TGG + Chr2:9112976-9112995 None:intergenic 20.0%
!! TAGTTCAATTGTCTATATTT+AGG - Chr2:9112657-9112676 MsG0280006993.01.T01:intron 20.0%
!! TTACAATATTTGGTTACTAT+TGG + Chr2:9112966-9112985 None:intergenic 20.0%
!!! ATCCATTTTAATTTTCCAAA+AGG + Chr2:9113037-9113056 None:intergenic 20.0%
!!! TTCCTTTTGGAAAATTAAAA+TGG - Chr2:9113032-9113051 MsG0280006993.01.T01:intron 20.0%
! ACATATAGCACAAATTGATA+TGG + Chr2:9113079-9113098 None:intergenic 25.0%
! ATTAAACTGTTGATACAAAC+AGG + Chr2:9112684-9112703 None:intergenic 25.0%
! CAAATTGATATGGTTAAAGA+AGG + Chr2:9113069-9113088 None:intergenic 25.0%
! TCAAATAAGTCAATTCAATC+CGG - Chr2:9112932-9112951 MsG0280006993.01.T01:intron 25.0%
! TTAAACTGTTGATACAAACA+GGG + Chr2:9112683-9112702 None:intergenic 25.0%
AATTGAACTAGTTGAACTGT+TGG + Chr2:9112647-9112666 None:intergenic 30.0%
ATTTGGTTACTATTGGCAAA+AGG + Chr2:9112959-9112978 None:intergenic 30.0%
CTTATTTGAGGAACATATCT+TGG + Chr2:9112921-9112940 None:intergenic 30.0%
GATAAAGTTAACATTAGCAC+TGG - Chr2:9112989-9113008 MsG0280006993.01.T01:intron 30.0%
TTTGGTTACTATTGGCAAAA+GGG + Chr2:9112958-9112977 None:intergenic 30.0%
! GGATTGAATTGACTTATTTG+AGG + Chr2:9112933-9112952 None:intergenic 30.0%
! TTTCTTCTATGTCTTCCTTT+TGG - Chr2:9113019-9113038 MsG0280006993.01.T01:intron 30.0%
!! TTTGTGAGTTGATCTTGTAA+GGG - Chr2:9113245-9113264 MsG0280006993.01.T01:CDS 30.0%
!!! TTTTGTGAGTTGATCTTGTA+AGG - Chr2:9113244-9113263 MsG0280006993.01.T01:CDS 30.0%
AGAGATATAGATCCATTTGG+AGG + Chr2:9113278-9113297 None:intergenic 35.0%
ATCTCTCCAAATGGATGAAA+TGG - Chr2:9113292-9113311 MsG0280006993.01.T01:CDS 35.0%
GAAATGGAGAGAATACCAAA+TGG - Chr2:9113308-9113327 MsG0280006993.01.T01:CDS 35.0%
TAAACACTTGTGAGACTGTT+TGG + Chr2:9112896-9112915 None:intergenic 35.0%
TAAGGATGTGGTTAAGTTCA+AGG - Chr2:9112488-9112507 MsG0280006993.01.T01:CDS 35.0%
TGGAGAGATATAGATCCATT+TGG + Chr2:9113281-9113300 None:intergenic 35.0%
TGGATCTATATCTCTCCAAA+TGG - Chr2:9113283-9113302 MsG0280006993.01.T01:CDS 35.0%
TTCTCATCCAATACCTCTAA+AGG + Chr2:9113161-9113180 None:intergenic 35.0%
TTCTCTCCATTTCATCCATT+TGG + Chr2:9113301-9113320 None:intergenic 35.0%
! ACAATGCTCTTGATGTTTTC+AGG - Chr2:9113120-9113139 MsG0280006993.01.T01:intron 35.0%
! TTCAAGACCTTTAGAGGTAT+TGG - Chr2:9113151-9113170 MsG0280006993.01.T01:intron 35.0%
!! AGGTATTGGATGAGAAATCA+AGG - Chr2:9113165-9113184 MsG0280006993.01.T01:intron 35.0%
AAGGGTAAAGATCCTCCAAA+TGG - Chr2:9113263-9113282 MsG0280006993.01.T01:CDS 40.0%
AATCAAGAGGAGTAAGGATG+TGG - Chr2:9112476-9112495 MsG0280006993.01.T01:CDS 40.0%
AGTGAGAATCAAGAGGAGTA+AGG - Chr2:9112470-9112489 MsG0280006993.01.T01:CDS 40.0%
AGTTGAACTGTTGGTATCCT+AGG + Chr2:9112638-9112657 None:intergenic 40.0%
ATGTGGTTAAGTTCAAGGTC+AGG - Chr2:9112493-9112512 MsG0280006993.01.T01:CDS 40.0%
CAAACACACTAAGTGTGTAG+AGG + Chr2:9112530-9112549 None:intergenic 40.0%
GAGTTAAGATCCTCTCCATT+TGG + Chr2:9113326-9113345 None:intergenic 40.0%
TGAGTGTTCAAGACCTTTAG+AGG - Chr2:9113145-9113164 MsG0280006993.01.T01:intron 40.0%
TGTAAATCCAACTACAGACC+TGG + Chr2:9112591-9112610 None:intergenic 40.0%
TTGGATGAGAAATCAAGGAG+AGG - Chr2:9113170-9113189 MsG0280006993.01.T01:intron 40.0%
!! ACTAAGTGTGTAGAGGTACT+TGG + Chr2:9112523-9112542 None:intergenic 40.0%
AAATCCAACTACAGACCTGG+AGG + Chr2:9112588-9112607 None:intergenic 45.0%
ATTTCCTTCTCACTGCCAGA+AGG - Chr2:9112433-9112452 MsG0280006993.01.T01:CDS 45.0%
GGAGAGAATACCAAATGGAG+AGG - Chr2:9113313-9113332 MsG0280006993.01.T01:CDS 45.0%
GTTACTATTGGCAAAAGGGC+CGG + Chr2:9112954-9112973 None:intergenic 45.0%
TTGAAGCAATCACTTCCTCC+AGG - Chr2:9112570-9112589 MsG0280006993.01.T01:intron 45.0%
ACTTCCTCCAGGTCTGTAGT+TGG - Chr2:9112581-9112600 MsG0280006993.01.T01:intron 50.0%
CGAGGTCAGTGAGAATCAAG+AGG - Chr2:9112463-9112482 MsG0280006993.01.T01:CDS 50.0%
CCTTCCTTCTGGCAGTGAGA+AGG + Chr2:9112440-9112459 None:intergenic 55.0%
CCTTCTCACTGCCAGAAGGA+AGG - Chr2:9112437-9112456 MsG0280006993.01.T01:CDS 55.0%
TGACCTCGCATCCTTCCTTC+TGG + Chr2:9112451-9112470 None:intergenic 55.0%
CTGCCAGAAGGAAGGATGCG+AGG - Chr2:9112445-9112464 MsG0280006993.01.T01:CDS 60.0%
Chromosome Type Strat End Strand Name
Chr2 gene 9112414 9113367 9112414 ID=MsG0280006993.01;Name=MsG0280006993.01
Chr2 mRNA 9112414 9113367 9112414 ID=MsG0280006993.01.T01;Parent=MsG0280006993.01;Name=MsG0280006993.01.T01;_AED=0.49;_eAED=0.49;_QI=0|0|0|1|0|0.33|3|0|102
Chr2 exon 9113186 9113367 9113186 ID=MsG0280006993.01.T01:exon:2161;Parent=MsG0280006993.01.T01
Chr2 exon 9112615 9112639 9112615 ID=MsG0280006993.01.T01:exon:2160;Parent=MsG0280006993.01.T01
Chr2 exon 9112414 9112515 9112414 ID=MsG0280006993.01.T01:exon:2159;Parent=MsG0280006993.01.T01
Chr2 CDS 9113186 9113367 9113186 ID=MsG0280006993.01.T01:cds;Parent=MsG0280006993.01.T01
Chr2 CDS 9112615 9112639 9112615 ID=MsG0280006993.01.T01:cds;Parent=MsG0280006993.01.T01
Chr2 CDS 9112414 9112515 9112414 ID=MsG0280006993.01.T01:cds;Parent=MsG0280006993.01.T01
Gene Sequence

>MsG0280006993.01.T01

CAAATCAACGAGATTAAGGATTTCCTTCTCACTGCCAGAAGGAAGGATGCGAGGTCAGTGAGAATCAAGAGGAGTAAGGATGTGGTTAAGTTCAAGGTCAGGTGTTCCAAGTACCTCTACACACTTAGTGTGTTTGACGTTGAGAAAGCTGACAAATTGAAGCAATCACTTCCTCCAGGTCTGTTTGAGTGTTCAAGACCTTTAGAGGGTAAAGATCCTCCAAATGGATCTATATCTCTCCAAATGGATGAAATGGAGAGAATACCAAATGGAGAGGATCTTAACTCATCTTGTAACTTGAGATTGTAG

Protein sequence

>MsG0280006993.01.T01

QINEIKDFLLTARRKDARSVRIKRSKDVVKFKVRCSKYLYTLSVFDVEKADKLKQSLPPGLFECSRPLEGKDPPNGSISLQMDEMERIPNGEDLNSSCNLRL*