AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0716430


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0716430 MtrunA17_Chr5g0403881 90.323 62 6 0 1 62 1 62 3.27e-33 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0716430 AT3G50685.1 66.258 163 50 2 6 168 1 158 5.05e-67 201

Find 45 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATCTCAATTCCTGTTAT+AGG 0.193029 5_1:+9873367 Msa0716430:CDS
CTCCCTGCTGATCAGTGTTT+TGG 0.233472 5_1:+9873658 Msa0716430:CDS
GGTCTTCCTAATGGTCCTTT+TGG 0.235150 5_1:+9873535 Msa0716430:CDS
ATGTCTTTGGTGTTGATATT+GGG 0.276572 5_1:-9873207 None:intergenic
GAATGGTTTGTGAATGTCTT+TGG 0.291190 5_1:-9873220 None:intergenic
TGTTGAAGGGTTGTCATATT+TGG 0.326036 5_1:+9873570 Msa0716430:CDS
AATGTCTTTGGTGTTGATAT+TGG 0.344494 5_1:-9873208 None:intergenic
TTTCAACAAGGTTACATTCC+TGG 0.368209 5_1:+9873631 Msa0716430:CDS
GGGTTATTAGGTGCTGTTGA+AGG 0.373371 5_1:+9873556 Msa0716430:CDS
GCTATTGCTGCTATCTCTGT+TGG 0.385488 5_1:-9873337 None:intergenic
TGCTGCTATCTCTGTTGGGC+TGG 0.397920 5_1:-9873332 None:intergenic
ACTGGTTCTGGTCTTCCTAA+TGG 0.397978 5_1:+9873526 Msa0716430:CDS
CCAGGACCAGGTGGATCAAT+TGG 0.412152 5_1:+9873433 Msa0716430:CDS
CTCTACACTCTCAAAACAAC+TGG 0.418846 5_1:+9873397 Msa0716430:CDS
AATAACCCAAAAGGACCATT+AGG 0.423242 5_1:-9873541 None:intergenic
TAGAGAGACCAACCTATAAC+AGG 0.435409 5_1:-9873379 None:intergenic
GGAGAATAGTAACATCTTTG+AGG 0.445427 5_1:-9873185 None:intergenic
GGATCAATTGGTGCATTAGA+AGG 0.445690 5_1:+9873445 Msa0716430:CDS
TATCCAAAACACTGATCAGC+AGG 0.446026 5_1:-9873661 None:intergenic
CTATTGCTGCTATCTCTGTT+GGG 0.455946 5_1:-9873336 None:intergenic
TGTAAGTTATCTTGTAGTTG+TGG 0.468651 5_1:+9873468 Msa0716430:CDS
GTAAGTTATCTTGTAGTTGT+GGG 0.479034 5_1:+9873469 Msa0716430:CDS
TAACATCTTTGAGGCTTCCA+TGG 0.494683 5_1:-9873176 None:intergenic
TAGTTGTGGGAATTGTTGCT+TGG 0.495156 5_1:+9873482 Msa0716430:CDS
CCAATTGATCCACCTGGTCC+TGG 0.509784 5_1:-9873433 None:intergenic
GGTTATTAGGTGCTGTTGAA+GGG 0.510819 5_1:+9873557 Msa0716430:CDS
TGTGGTCTTCCACCAGGACC+AGG 0.516068 5_1:+9873421 Msa0716430:CDS
AGGGTTGTCATATTTGGCAT+TGG 0.526933 5_1:+9873576 Msa0716430:CDS
TGTCTTTGGTGTTGATATTG+GGG 0.527176 5_1:-9873206 None:intergenic
TCTCAATTCCTGTTATAGGT+TGG 0.527179 5_1:+9873371 Msa0716430:CDS
TGATCAGCAGGGAGAGGACC+AGG 0.529852 5_1:-9873649 None:intergenic
ACAGAGATAGCAGCAATAGC+AGG 0.544713 5_1:+9873340 Msa0716430:CDS
ACAGCACCTAATAACCCAAA+AGG 0.547610 5_1:-9873550 None:intergenic
GAGATAGCAGCAATAGCAGG+TGG 0.565377 5_1:+9873343 Msa0716430:CDS
AAACACTGATCAGCAGGGAG+AGG 0.597184 5_1:-9873655 None:intergenic
ACTCTCAAAACAACTGGTTG+TGG 0.598063 5_1:+9873403 Msa0716430:CDS
ATAACAAACATGGCAAAGGA+AGG 0.600615 5_1:+9873295 Msa0716430:CDS
ACTGGTTGTGGTCTTCCACC+AGG 0.608557 5_1:+9873415 Msa0716430:CDS
CAAGATAACAAACATGGCAA+AGG 0.614035 5_1:+9873291 Msa0716430:CDS
CAAACTCAAGATAACAAACA+TGG 0.620939 5_1:+9873285 Msa0716430:CDS
ATTGATCCACCTGGTCCTGG+TGG 0.622088 5_1:-9873430 None:intergenic
GGTCTTCCACCAGGACCAGG+TGG 0.646487 5_1:+9873424 Msa0716430:CDS
AATGCACCAATTGATCCACC+TGG 0.654079 5_1:-9873439 None:intergenic
AGATAGCAGCAATAGCAGGT+GGG 0.659143 5_1:+9873344 Msa0716430:CDS
ATCCAAAACACTGATCAGCA+GGG 0.675935 5_1:-9873660 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATATACCAAAAATAAAAC+TGG + chr5_1:9873508-9873527 Msa0716430:CDS 15.0%
!!! TTCTAAGTGGTTTTTTTGAA+TGG - chr5_1:9873240-9873259 None:intergenic 25.0%
! TTAATCTCAATTCCTGTTAT+AGG + chr5_1:9873367-9873386 Msa0716430:CDS 25.0%
!! ATGTCTTTGGTGTTGATATT+GGG - chr5_1:9873210-9873229 None:intergenic 30.0%
!! AATGTCTTTGGTGTTGATAT+TGG - chr5_1:9873211-9873230 None:intergenic 30.0%
! TGAGATTTTTGCTTTCTAAG+TGG - chr5_1:9873253-9873272 None:intergenic 30.0%
CAAACTCAAGATAACAAACA+TGG + chr5_1:9873285-9873304 Msa0716430:CDS 30.0%
TGTAAGTTATCTTGTAGTTG+TGG + chr5_1:9873468-9873487 Msa0716430:CDS 30.0%
GTAAGTTATCTTGTAGTTGT+GGG + chr5_1:9873469-9873488 Msa0716430:CDS 30.0%
! ACCAAAAATAAAACTGGTTC+TGG + chr5_1:9873514-9873533 Msa0716430:CDS 30.0%
!!! ACCAGAACCAGTTTTATTTT+TGG - chr5_1:9873518-9873537 None:intergenic 30.0%
!!! GTTGCTATTGTTGTTGTTTT+TGG + chr5_1:9873598-9873617 Msa0716430:CDS 30.0%
GGAGAATAGTAACATCTTTG+AGG - chr5_1:9873188-9873207 None:intergenic 35.0%
!! TGTCTTTGGTGTTGATATTG+GGG - chr5_1:9873209-9873228 None:intergenic 35.0%
! GAATGGTTTGTGAATGTCTT+TGG - chr5_1:9873223-9873242 None:intergenic 35.0%
CAAGATAACAAACATGGCAA+AGG + chr5_1:9873291-9873310 Msa0716430:CDS 35.0%
ATAACAAACATGGCAAAGGA+AGG + chr5_1:9873295-9873314 Msa0716430:CDS 35.0%
TCTCAATTCCTGTTATAGGT+TGG + chr5_1:9873371-9873390 Msa0716430:CDS 35.0%
AATAACCCAAAAGGACCATT+AGG - chr5_1:9873544-9873563 None:intergenic 35.0%
!!! AATGGTCCTTTTGGGTTATT+AGG + chr5_1:9873544-9873563 Msa0716430:CDS 35.0%
TGTTGAAGGGTTGTCATATT+TGG + chr5_1:9873570-9873589 Msa0716430:CDS 35.0%
! GGTTTGCAGTATTTTCAACA+AGG + chr5_1:9873619-9873638 Msa0716430:CDS 35.0%
TTTCAACAAGGTTACATTCC+TGG + chr5_1:9873631-9873650 Msa0716430:CDS 35.0%
CTATTGCTGCTATCTCTGTT+GGG - chr5_1:9873339-9873358 None:intergenic 40.0%
TAGAGAGACCAACCTATAAC+AGG - chr5_1:9873382-9873401 None:intergenic 40.0%
CTCTACACTCTCAAAACAAC+TGG + chr5_1:9873397-9873416 Msa0716430:CDS 40.0%
ACTCTCAAAACAACTGGTTG+TGG + chr5_1:9873403-9873422 Msa0716430:CDS 40.0%
GGATCAATTGGTGCATTAGA+AGG + chr5_1:9873445-9873464 Msa0716430:CDS 40.0%
TAGTTGTGGGAATTGTTGCT+TGG + chr5_1:9873482-9873501 Msa0716430:CDS 40.0%
! GTCTTCCTAATGGTCCTTTT+GGG + chr5_1:9873536-9873555 Msa0716430:CDS 40.0%
ACAGCACCTAATAACCCAAA+AGG - chr5_1:9873553-9873572 None:intergenic 40.0%
!! GGTTATTAGGTGCTGTTGAA+GGG + chr5_1:9873557-9873576 Msa0716430:CDS 40.0%
AGGGTTGTCATATTTGGCAT+TGG + chr5_1:9873576-9873595 Msa0716430:CDS 40.0%
ATCCAAAACACTGATCAGCA+GGG - chr5_1:9873663-9873682 None:intergenic 40.0%
TATCCAAAACACTGATCAGC+AGG - chr5_1:9873664-9873683 None:intergenic 40.0%
GCTATTGCTGCTATCTCTGT+TGG - chr5_1:9873340-9873359 None:intergenic 45.0%
ACAGAGATAGCAGCAATAGC+AGG + chr5_1:9873340-9873359 Msa0716430:CDS 45.0%
AGATAGCAGCAATAGCAGGT+GGG + chr5_1:9873344-9873363 Msa0716430:CDS 45.0%
AATGCACCAATTGATCCACC+TGG - chr5_1:9873442-9873461 None:intergenic 45.0%
!! ACTGGTTCTGGTCTTCCTAA+TGG + chr5_1:9873526-9873545 Msa0716430:CDS 45.0%
! GGTCTTCCTAATGGTCCTTT+TGG + chr5_1:9873535-9873554 Msa0716430:CDS 45.0%
!! GGGTTATTAGGTGCTGTTGA+AGG + chr5_1:9873556-9873575 Msa0716430:CDS 45.0%
GAGATAGCAGCAATAGCAGG+TGG + chr5_1:9873343-9873362 Msa0716430:CDS 50.0%
AAACACTGATCAGCAGGGAG+AGG - chr5_1:9873658-9873677 None:intergenic 50.0%
! CTCCCTGCTGATCAGTGTTT+TGG + chr5_1:9873658-9873677 Msa0716430:CDS 50.0%
TGCTGCTATCTCTGTTGGGC+TGG - chr5_1:9873335-9873354 None:intergenic 55.0%
ACTGGTTGTGGTCTTCCACC+AGG + chr5_1:9873415-9873434 Msa0716430:CDS 55.0%
ATTGATCCACCTGGTCCTGG+TGG - chr5_1:9873433-9873452 None:intergenic 55.0%
CCAATTGATCCACCTGGTCC+TGG - chr5_1:9873436-9873455 None:intergenic 55.0%
CCAGGACCAGGTGGATCAAT+TGG + chr5_1:9873433-9873452 Msa0716430:CDS 55.0%
TGTGGTCTTCCACCAGGACC+AGG + chr5_1:9873421-9873440 Msa0716430:CDS 60.0%
TGATCAGCAGGGAGAGGACC+AGG - chr5_1:9873652-9873671 None:intergenic 60.0%
GGTCTTCCACCAGGACCAGG+TGG + chr5_1:9873424-9873443 Msa0716430:CDS 65.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 9873178 9873684 9873178 ID=Msa0716430;Name=Msa0716430
chr5_1 mRNA 9873178 9873684 9873178 ID=Msa0716430-mRNA-1;Parent=Msa0716430;Name=Msa0716430-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|168
chr5_1 exon 9873178 9873684 9873178 ID=Msa0716430-mRNA-1:exon:3890;Parent=Msa0716430-mRNA-1
chr5_1 CDS 9873178 9873684 9873178 ID=Msa0716430-mRNA-1:cds;Parent=Msa0716430-mRNA-1
Gene Sequence

>Msa0716430

ATGGAAGCCTCAAAGATGTTACTATTCTCCCCAATATCAACACCAAAGACATTCACAAACCATTCAAAAAAACCACTTAGAAAGCAAAAATCTCATCATGTGAGACTCAAACTCAAGATAACAAACATGGCAAAGGAAGGAAGCGACACTAACACCAGCCCAACAGAGATAGCAGCAATAGCAGGTGGGTTAATCTCAATTCCTGTTATAGGTTGGTCTCTCTACACTCTCAAAACAACTGGTTGTGGTCTTCCACCAGGACCAGGTGGATCAATTGGTGCATTAGAAGGTGTAAGTTATCTTGTAGTTGTGGGAATTGTTGCTTGGTCTTTATATACCAAAAATAAAACTGGTTCTGGTCTTCCTAATGGTCCTTTTGGGTTATTAGGTGCTGTTGAAGGGTTGTCATATTTGGCATTGGTTGCTATTGTTGTTGTTTTTGGTTTGCAGTATTTTCAACAAGGTTACATTCCTGGTCCTCTCCCTGCTGATCAGTGTTTTGGATAG

Protein sequence

>Msa0716430

MEASKMLLFSPISTPKTFTNHSKKPLRKQKSHHVRLKLKITNMAKEGSDTNTSPTEIAAIAGGLISIPVIGWSLYTLKTTGCGLPPGPGGSIGALEGVSYLVVVGIVAWSLYTKNKTGSGLPNGPFGLLGAVEGLSYLALVAIVVVFGLQYFQQGYIPGPLPADQCFG*