AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059439


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGGTTTGAATGGTCTTTC+AGG 0.210529 2.3:-25582058 MS.gene059439:CDS
GATAGCCTTCCGATATCTTT+CGG 0.293306 2.3:+25581812 None:intergenic
GTGAAAGTTTAGAGACATTA+GGG 0.300992 2.3:-25582009 MS.gene059439:CDS
TTCAACTTACTGATTGATTT+CGG 0.301958 2.3:+25582100 None:intergenic
ATAGCCTTCCGATATCTTTC+GGG 0.309741 2.3:+25581813 None:intergenic
CAGATAACAATCTTGTTAAC+TGG 0.317415 2.3:-25582516 MS.gene059439:CDS
GATTGATTTCGGAATGATTC+CGG 0.356406 2.3:+25582111 None:intergenic
TGTGAAAGTTTAGAGACATT+AGG 0.362670 2.3:-25582010 MS.gene059439:CDS
GGTGAGCTTCCTCCTGAGAT+TGG 0.377990 2.3:-25581893 MS.gene059439:CDS
TTGCATCAAAATTCATTGAT+TGG 0.396275 2.3:-25581842 MS.gene059439:CDS
ATTTATAGCAATAACTTAAC+CGG 0.396748 2.3:-25582130 MS.gene059439:CDS
CTGATTCAACTCCATGCAAT+TGG 0.400059 2.3:-25582486 MS.gene059439:CDS
GGAACAATTCCACCTGAGTT+AGG 0.401869 2.3:-25581749 MS.gene059439:CDS
CTACTAATGTTTCCAATCTC+AGG 0.407052 2.3:+25581881 None:intergenic
GATGCAAAGCAAGTAATTCA+AGG 0.412372 2.3:+25581858 None:intergenic
TGTGTCTTGCACTGATTCAT+TGG 0.423366 2.3:-25582458 MS.gene059439:intron
GTTATAAGAGCAGGTTTGAA+TGG 0.426502 2.3:-25582067 MS.gene059439:CDS
TAGGAATGATACCAATCAAA+TGG 0.442970 2.3:+25581688 None:intergenic
GGTGATGTCCCGAAAGATAT+CGG 0.455528 2.3:-25581821 MS.gene059439:CDS
TTAGCACAGAATCAGTTAGT+AGG 0.456826 2.3:-25581986 MS.gene059439:CDS
ATGTATACTAATCAGTTGAA+TGG 0.471288 2.3:-25581770 MS.gene059439:CDS
AAGCTTAGAGTTATAAGAGC+AGG 0.482503 2.3:-25582076 MS.gene059439:CDS
GAAGGCTATCGCGGTTGAAG+AGG 0.534774 2.3:-25581799 MS.gene059439:CDS
TTAGTACAGTTTCCTAACTC+AGG 0.546213 2.3:+25581737 None:intergenic
GACACACCAGTCCAATTGCA+TGG 0.558122 2.3:+25582475 None:intergenic
TCACACTCACTAATTTCTGA+AGG 0.563210 2.3:+25582028 None:intergenic
TTGCATGGAGTTGAATCAGA+AGG 0.585213 2.3:+25582490 None:intergenic
GTACAGTTTCCTAACTCAGG+TGG 0.599486 2.3:+25581740 None:intergenic
AAGATATCGGAAGGCTATCG+CGG 0.624637 2.3:-25581808 MS.gene059439:CDS
ATGTCCCGAAAGATATCGGA+AGG 0.629291 2.3:-25581817 MS.gene059439:CDS
TGGAGAACTAACATCACTTG+AGG 0.633179 2.3:-25582161 MS.gene059439:CDS
TCAACTCCATGCAATTGGAC+TGG 0.636613 2.3:-25582481 MS.gene059439:CDS
CTAATGTTTCCAATCTCAGG+AGG 0.648464 2.3:+25581884 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATTACAGTTATCAAAAAA+AGG + chr2.3:25581912-25581931 None:intergenic 15.0%
!!! AACTTACTAATTTGATTTTA+TGG - chr2.3:25582291-25582310 MS.gene059439:intron 15.0%
!! ATTTATAGCAATAACTTAAC+CGG - chr2.3:25582092-25582111 MS.gene059439:CDS 20.0%
! AGATTCAACTCAACTAAATA+TGG + chr2.3:25581855-25581874 None:intergenic 25.0%
! ATGTATACTAATCAGTTGAA+TGG - chr2.3:25582452-25582471 MS.gene059439:intron 25.0%
! CTTTGTGAAAATTACATGTA+TGG - chr2.3:25582020-25582039 MS.gene059439:CDS 25.0%
! TCAAAAAAAGGTTCAGAAAT+TGG + chr2.3:25581900-25581919 None:intergenic 25.0%
! TGATAACTGTAATAAACTTG+AGG - chr2.3:25581917-25581936 MS.gene059439:CDS 25.0%
! TTCCAAATAAGAGATAGAAA+TGG + chr2.3:25581975-25581994 None:intergenic 25.0%
! TTGCATCAAAATTCATTGAT+TGG - chr2.3:25582380-25582399 MS.gene059439:intron 25.0%
!! CATACATGTAATTTTCACAA+AGG + chr2.3:25582022-25582041 None:intergenic 25.0%
!! TTCAACTTACTGATTGATTT+CGG + chr2.3:25582125-25582144 None:intergenic 25.0%
!! TTTTAGACCTTTGTACTAAT+AGG - chr2.3:25581940-25581959 MS.gene059439:CDS 25.0%
CAGATAACAATCTTGTTAAC+TGG - chr2.3:25581706-25581725 MS.gene059439:CDS 30.0%
CTTTCCAAAAATTTCATCTC+TGG - chr2.3:25581873-25581892 MS.gene059439:CDS 30.0%
GACCATTTCTATCTCTTATT+TGG - chr2.3:25581970-25581989 MS.gene059439:CDS 30.0%
GTGAAAGTTTAGAGACATTA+GGG - chr2.3:25582213-25582232 MS.gene059439:intron 30.0%
TATGGAAGGTTACATATAGT+AGG + chr2.3:25581837-25581856 None:intergenic 30.0%
TCAACTCAACTAAATATGGA+AGG + chr2.3:25581851-25581870 None:intergenic 30.0%
TGTGAAAGTTTAGAGACATT+AGG - chr2.3:25582212-25582231 MS.gene059439:intron 30.0%
! TTATGGCAAAACTCTTTTTC+TGG - chr2.3:25582308-25582327 MS.gene059439:intron 30.0%
AACTACCAGAGAGATTAAAG+TGG + chr2.3:25581809-25581828 None:intergenic 35.0%
AAGCTTAGAGTTATAAGAGC+AGG - chr2.3:25582146-25582165 MS.gene059439:CDS 35.0%
CATGAAGCCTATTAGTACAA+AGG + chr2.3:25581950-25581969 None:intergenic 35.0%
CTACTAATGTTTCCAATCTC+AGG + chr2.3:25582344-25582363 None:intergenic 35.0%
CTTTACCACTTTAATCTCTC+TGG - chr2.3:25581801-25581820 MS.gene059439:CDS 35.0%
CTTTGTACTAATAGGCTTCA+TGG - chr2.3:25581948-25581967 MS.gene059439:CDS 35.0%
GATGCAAAGCAAGTAATTCA+AGG + chr2.3:25582367-25582386 None:intergenic 35.0%
GGTGAAATTCCAAATGAGAT+TGG - chr2.3:25582041-25582060 MS.gene059439:CDS 35.0%
GTTATAAGAGCAGGTTTGAA+TGG - chr2.3:25582155-25582174 MS.gene059439:CDS 35.0%
TCACACTCACTAATTTCTGA+AGG + chr2.3:25582197-25582216 None:intergenic 35.0%
TTAGCACAGAATCAGTTAGT+AGG - chr2.3:25582236-25582255 MS.gene059439:intron 35.0%
TTAGTACAGTTTCCTAACTC+AGG + chr2.3:25582488-25582507 None:intergenic 35.0%
! GATTGATTTCGGAATGATTC+CGG + chr2.3:25582114-25582133 None:intergenic 35.0%
! GTTAGTTCTCCAATCTCATT+TGG + chr2.3:25582053-25582072 None:intergenic 35.0%
! TGGACCAGAGATGAAATTTT+TGG + chr2.3:25581880-25581899 None:intergenic 35.0%
!!! TGAAGCTTTTGAAGCTCTTT+CGG + chr2.3:25582269-25582288 None:intergenic 35.0%
ATAGCCTTCCGATATCTTTC+GGG + chr2.3:25582412-25582431 None:intergenic 40.0%
CTAATGTTTCCAATCTCAGG+AGG + chr2.3:25582341-25582360 None:intergenic 40.0%
CTGATTCAACTCCATGCAAT+TGG - chr2.3:25581736-25581755 MS.gene059439:CDS 40.0%
GATAGCCTTCCGATATCTTT+CGG + chr2.3:25582413-25582432 None:intergenic 40.0%
TGGAGAACTAACATCACTTG+AGG - chr2.3:25582061-25582080 MS.gene059439:CDS 40.0%
TTGCATGGAGTTGAATCAGA+AGG + chr2.3:25581735-25581754 None:intergenic 40.0%
!! TGTGTCTTGCACTGATTCAT+TGG - chr2.3:25581764-25581783 MS.gene059439:CDS 40.0%
AAGATATCGGAAGGCTATCG+CGG - chr2.3:25582414-25582433 MS.gene059439:intron 45.0%
ATGTCCCGAAAGATATCGGA+AGG - chr2.3:25582405-25582424 MS.gene059439:intron 45.0%
GCAGGTTTGAATGGTCTTTC+AGG - chr2.3:25582164-25582183 MS.gene059439:CDS 45.0%
GGAACAATTCCACCTGAGTT+AGG - chr2.3:25582473-25582492 MS.gene059439:CDS 45.0%
GGTGATGTCCCGAAAGATAT+CGG - chr2.3:25582401-25582420 MS.gene059439:intron 45.0%
GTACAGTTTCCTAACTCAGG+TGG + chr2.3:25582485-25582504 None:intergenic 45.0%
TCAACTCCATGCAATTGGAC+TGG - chr2.3:25581741-25581760 MS.gene059439:CDS 45.0%
GACACACCAGTCCAATTGCA+TGG + chr2.3:25581750-25581769 None:intergenic 50.0%
GAAGGCTATCGCGGTTGAAG+AGG - chr2.3:25582423-25582442 MS.gene059439:intron 55.0%
GGTGAGCTTCCTCCTGAGAT+TGG - chr2.3:25582329-25582348 MS.gene059439:intron 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 25581703 25582541 25581703 ID=MS.gene059439
chr2.3 mRNA 25581703 25582541 25581703 ID=MS.gene059439.t1;Parent=MS.gene059439
chr2.3 exon 25582459 25582541 25582459 ID=MS.gene059439.t1.exon1;Parent=MS.gene059439.t1
chr2.3 CDS 25582459 25582541 25582459 ID=cds.MS.gene059439.t1;Parent=MS.gene059439.t1
chr2.3 exon 25581703 25582185 25581703 ID=MS.gene059439.t1.exon2;Parent=MS.gene059439.t1
chr2.3 CDS 25581703 25582185 25581703 ID=cds.MS.gene059439.t1;Parent=MS.gene059439.t1
Gene Sequence

>MS.gene059439

ATTCAGATAACAATCTTGTTAACTGGAATCCTTCTGATTCAACTCCATGCAATTGGACTGGTGTGTCTTGCACTGATTCATTGGTAACTTCTGTTAATCTTTACCACTTTAATCTCTCTGGTAGTTTGTCTCCTACTATATGTAACCTTCCATATTTAGTTGAGTTGAATCTTTCCAAAAATTTCATCTCTGGTCCAATTTCTGAACCTTTTTTTGATAACTGTAATAAACTTGAGGTTTTAGACCTTTGTACTAATAGGCTTCATGGACCATTTCTATCTCTTATTTGGAAAATCAAAACACTTAGAAAACTTTACCTTTGTGAAAATTACATGTATGGTGAAATTCCAAATGAGATTGGAGAACTAACATCACTTGAGGAGTTAGTTATTTATAGCAATAACTTAACCGGAATCATTCCGAAATCAATCAGTAAGTTGAAGAAGCTTAGAGTTATAAGAGCAGGTTTGAATGGTCTTTCAGGAACATTACCTTCAGAAATTAGTGAGTGTGAAAGTTTAGAGACATTAGGGTTAGCACAGAATCAGTTAGTAGGTTCTATTCCGAAAGAGCTTCAAAAGCTTCAGAAACTTACTAATTTGATTTTATGGCAAAACTCTTTTTCTGGTGAGCTTCCTCCTGAGATTGGAAACATTAGTAGCCTTGAATTACTTGCTTTGCATCAAAATTCATTGATTGGTGATGTCCCGAAAGATATCGGAAGGCTATCGCGGTTGAAGAGGTTGTACATGTATACTAATCAGTTGAATGGAACAATTCCACCTGAGTTAGGAAACTGTACTAATGCTGTTGAGATTGATCTTTCAGAAACCATTTGA

Protein sequence

>MS.gene059439.t1

IQITILLTGILLIQLHAIGLVCLALIHULENUHHLRSULFIAITUPESFRNQSVSURSLELUEQVUMVFQEHYLQKLVSVKVURHUGUHRISUUVLFRKSFKSFRNLLIUFYGKTLFLVSFLLRLETLVALNYLLCIKIHULVMSRKISEGYRGURGCTCILISUMEQFHLSUETVLMLLRLIFQKPF