AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52853


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 37 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTGGCAAGGAAGGCTTAA+AGG 0.244002 3.3:+1459719 MS.gene52853:CDS
AGAGTTCCGTCTTGGTTAAA+TGG 0.267555 3.3:+1459686 MS.gene52853:CDS
ACCACAAGGTTTAAATGAAT+TGG 0.278023 3.3:-1458854 None:intergenic
CTCACCTGAGTTGCCTTTAT+AGG 0.288772 3.3:-1459848 None:intergenic
AAAAGAGCGGAAATTGTCTT+TGG 0.330350 3.3:+1459661 MS.gene52853:CDS
GGATAATTTGTCAGCTCAAC+TGG 0.331316 3.3:+1459619 MS.gene52853:CDS
TTTAGAAGGAACGAAGTTCT+TGG 0.347265 3.3:-1458812 None:intergenic
AATTATACGAACTTGGAATC+AGG 0.387815 3.3:+1459771 MS.gene52853:CDS
TCCAGACATATATCCTATAA+AGG 0.391852 3.3:+1459835 MS.gene52853:CDS
CTCAACTGGATGTTCTTGTA+AGG 0.439096 3.3:+1459633 MS.gene52853:CDS
GGAAATCTCCTTGGCAAGGA+AGG 0.464112 3.3:+1459711 MS.gene52853:CDS
CTCCGACAAAGAAAAGGATA+AGG 0.475675 3.3:+1459591 MS.gene52853:CDS
TTCCGTCTTGGTTAAATGGA+TGG 0.483104 3.3:+1459690 MS.gene52853:CDS
TTGGAATCAGGATTAGAGAA+AGG 0.488890 3.3:+1459783 MS.gene52853:CDS
CTCGTTCTCCGACAAAGAAA+AGG 0.491299 3.3:+1459585 MS.gene52853:CDS
CTTTGGAGAGAGTTCCGTCT+TGG 0.491832 3.3:+1459678 MS.gene52853:CDS
AAAGAAAAGGATAAGGGAGT+TGG 0.492650 3.3:+1459598 MS.gene52853:CDS
TCCAATTCATTTAAACCTTG+TGG 0.499872 3.3:+1458853 MS.gene52853:CDS
GCCTTTATAGGATATATGTC+TGG 0.504217 3.3:-1459836 None:intergenic
CTTCGTAGGTACGGGAGTTG+TGG 0.524597 3.3:+1458775 None:intergenic
GAGGAAGAATTATACGAACT+TGG 0.526932 3.3:+1459764 MS.gene52853:CDS
TTCCATCCATTTAACCAAGA+CGG 0.547637 3.3:-1459692 None:intergenic
CCTTTAAGCCTTCCTTGCCA+AGG 0.550309 3.3:-1459719 None:intergenic
TAAATGGATGGAAATCTCCT+TGG 0.554988 3.3:+1459702 MS.gene52853:CDS
TCCGACAAAGAAAAGGATAA+GGG 0.559478 3.3:+1459592 MS.gene52853:CDS
ATATCCTATAAAGGCAACTC+AGG 0.566710 3.3:+1459844 MS.gene52853:CDS
TTACATTCCCAGGCAAGGCA+TGG 0.576004 3.3:+1459560 MS.gene52853:intron
TTATAGGATATATGTCTGGA+TGG 0.582429 3.3:-1459832 None:intergenic
GGCGGTGAGCTAATTAAACT+AGG 0.601575 3.3:+1459740 MS.gene52853:CDS
TCAACTGGATGTTCTTGTAA+GGG 0.604338 3.3:+1459634 MS.gene52853:CDS
GGATGGAAATCTCCTTGGCA+AGG 0.610408 3.3:+1459707 MS.gene52853:CDS
TAATCCTCGTCAAACAAACT+CGG 0.636648 3.3:-1459809 None:intergenic
TGAGCTAATTAAACTAGGAG+AGG 0.639606 3.3:+1459745 MS.gene52853:CDS
GTTTCCGAGTTTGTTTGACG+AGG 0.659643 3.3:+1459805 MS.gene52853:CDS
TGAATTGGAGTACATCCTTG+AGG 0.660520 3.3:-1458839 None:intergenic
TTGTAAGGGATGTAAAAGAG+CGG 0.687987 3.3:+1459648 MS.gene52853:CDS
TGGCAAGGAAGGCTTAAAGG+CGG 0.730530 3.3:+1459722 MS.gene52853:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAATGATAGTTTAAACTA+TGG + chr3.3:1459481-1459500 MS.gene52853:intron 15.0%
!! GTTGGTTATATATATATAAT+AGG + chr3.3:1458936-1458955 MS.gene52853:intron 15.0%
!! TTAATGATAGTTTAAACTAT+GGG + chr3.3:1459482-1459501 MS.gene52853:intron 15.0%
!! AACTATCATTAATAACAAGT+TGG - chr3.3:1459474-1459493 None:intergenic 20.0%
!! TTAAGTCTATGAAATTATGT+TGG + chr3.3:1458918-1458937 MS.gene52853:intron 20.0%
!!! TATAATCATTTCAAAGTGTT+TGG - chr3.3:1459035-1459054 None:intergenic 20.0%
! CACATACATAAAATCTAAGT+GGG - chr3.3:1459397-1459416 None:intergenic 25.0%
!! ATTTTATGCAGTTGAAATGA+AGG + chr3.3:1459428-1459447 MS.gene52853:intron 25.0%
!! GTAATTTTCTCAACAATTGA+AGG + chr3.3:1458875-1458894 MS.gene52853:intron 25.0%
!! TTAGATTTTATGTATGTGCT+TGG + chr3.3:1459399-1459418 MS.gene52853:intron 25.0%
!! TTTTATGCAGTTGAAATGAA+GGG + chr3.3:1459429-1459448 MS.gene52853:intron 25.0%
AATTATACGAACTTGGAATC+AGG + chr3.3:1459771-1459790 MS.gene52853:CDS 30.0%
AATTATCATACTCTTCCGTT+TGG - chr3.3:1459528-1459547 None:intergenic 30.0%
ACCACAAGGTTTAAATGAAT+TGG - chr3.3:1458857-1458876 None:intergenic 30.0%
CTACATCTATGTCTAACTAT+TGG - chr3.3:1459231-1459250 None:intergenic 30.0%
GCACATACATAAAATCTAAG+TGG - chr3.3:1459398-1459417 None:intergenic 30.0%
TAAAAACCGTGTCATGTATT+AGG - chr3.3:1459297-1459316 None:intergenic 30.0%
TCCAATTCATTTAAACCTTG+TGG + chr3.3:1458853-1458872 MS.gene52853:CDS 30.0%
TCCAGACATATATCCTATAA+AGG + chr3.3:1459835-1459854 MS.gene52853:CDS 30.0%
TCTTGAGTTACTTACTTGTT+TGG + chr3.3:1459057-1459076 MS.gene52853:intron 30.0%
TTATAGGATATATGTCTGGA+TGG - chr3.3:1459835-1459854 None:intergenic 30.0%
TTGTTGAGAAAATTACCACA+AGG - chr3.3:1458871-1458890 None:intergenic 30.0%
TTTGCATTGCTAATTGCAAA+TGG + chr3.3:1458995-1459014 MS.gene52853:intron 30.0%
! AATACATGACACGGTTTTTA+TGG + chr3.3:1459297-1459316 MS.gene52853:intron 30.0%
! ACAGACTATTTTCACAAAGT+GGG - chr3.3:1459347-1459366 None:intergenic 30.0%
! TCATTTTCTGCTTACAGTTT+AGG - chr3.3:1459097-1459116 None:intergenic 30.0%
! TTCCTTCTAAAAATTCCTCA+AGG + chr3.3:1458824-1458843 MS.gene52853:CDS 30.0%
!! ATCCTTGAGGAATTTTTAGA+AGG - chr3.3:1458829-1458848 None:intergenic 30.0%
AAAAGAGCGGAAATTGTCTT+TGG + chr3.3:1459661-1459680 MS.gene52853:CDS 35.0%
AAAGAAAAGGATAAGGGAGT+TGG + chr3.3:1459598-1459617 MS.gene52853:CDS 35.0%
ATATCCTATAAAGGCAACTC+AGG + chr3.3:1459844-1459863 MS.gene52853:CDS 35.0%
ATTAGCAATGCAAACTTAGC+TGG - chr3.3:1458989-1459008 None:intergenic 35.0%
CCACAGATAAACCATAAAAC+TGG - chr3.3:1459273-1459292 None:intergenic 35.0%
GAGGAAGAATTATACGAACT+TGG + chr3.3:1459764-1459783 MS.gene52853:CDS 35.0%
GATGTAGAGCAAGATTAAGA+AGG + chr3.3:1459244-1459263 MS.gene52853:intron 35.0%
GCCTTTATAGGATATATGTC+TGG - chr3.3:1459839-1459858 None:intergenic 35.0%
TAAATGGATGGAAATCTCCT+TGG + chr3.3:1459702-1459721 MS.gene52853:CDS 35.0%
TAATCCTCGTCAAACAAACT+CGG - chr3.3:1459812-1459831 None:intergenic 35.0%
TCAACTGGATGTTCTTGTAA+GGG + chr3.3:1459634-1459653 MS.gene52853:CDS 35.0%
TCCGACAAAGAAAAGGATAA+GGG + chr3.3:1459592-1459611 MS.gene52853:CDS 35.0%
TGAGCTAATTAAACTAGGAG+AGG + chr3.3:1459745-1459764 MS.gene52853:CDS 35.0%
TTCCATCCATTTAACCAAGA+CGG - chr3.3:1459695-1459714 None:intergenic 35.0%
TTGGAATCAGGATTAGAGAA+AGG + chr3.3:1459783-1459802 MS.gene52853:CDS 35.0%
TTGTAAGGGATGTAAAAGAG+CGG + chr3.3:1459648-1459667 MS.gene52853:CDS 35.0%
TTGTGTTAATAGAGGATGGT+CGG + chr3.3:1459171-1459190 MS.gene52853:intron 35.0%
TTTAGAAGGAACGAAGTTCT+TGG - chr3.3:1458815-1458834 None:intergenic 35.0%
! CACAGACTATTTTCACAAAG+TGG - chr3.3:1459348-1459367 None:intergenic 35.0%
! TAAGAAGGATGCCAGTTTTA+TGG + chr3.3:1459259-1459278 MS.gene52853:intron 35.0%
! TCCCTTATCCTTTTCTTTGT+CGG - chr3.3:1459596-1459615 None:intergenic 35.0%
! TGACTTGTGTTAATAGAGGA+TGG + chr3.3:1459167-1459186 MS.gene52853:intron 35.0%
!! CCAGTTTTATGGTTTATCTG+TGG + chr3.3:1459270-1459289 MS.gene52853:intron 35.0%
AGAGTTCCGTCTTGGTTAAA+TGG + chr3.3:1459686-1459705 MS.gene52853:CDS 40.0%
CTCAACTGGATGTTCTTGTA+AGG + chr3.3:1459633-1459652 MS.gene52853:CDS 40.0%
CTCCGACAAAGAAAAGGATA+AGG + chr3.3:1459591-1459610 MS.gene52853:CDS 40.0%
TAGTGCTATGTTACATTCCC+AGG + chr3.3:1459550-1459569 MS.gene52853:intron 40.0%
TCTATTAACACAAGTCAGCG+AGG - chr3.3:1459164-1459183 None:intergenic 40.0%
TGAATTGGAGTACATCCTTG+AGG - chr3.3:1458842-1458861 None:intergenic 40.0%
TGTGGACCTAATACATGACA+CGG + chr3.3:1459288-1459307 MS.gene52853:intron 40.0%
TGTGTTAATAGAGGATGGTC+GGG + chr3.3:1459172-1459191 MS.gene52853:intron 40.0%
TTCCGTCTTGGTTAAATGGA+TGG + chr3.3:1459690-1459709 MS.gene52853:CDS 40.0%
! GGATAATTTGTCAGCTCAAC+TGG + chr3.3:1459619-1459638 MS.gene52853:CDS 40.0%
!! TCGCTGACTTGTGTTAATAG+AGG + chr3.3:1459163-1459182 MS.gene52853:intron 40.0%
!! TGGCATTGATTGATCAATGC+AGG + chr3.3:1459317-1459336 MS.gene52853:intron 40.0%
CTATGTTACATTCCCAGGCA+AGG + chr3.3:1459555-1459574 MS.gene52853:intron 45.0%
CTCGTTCTCCGACAAAGAAA+AGG + chr3.3:1459585-1459604 MS.gene52853:CDS 45.0%
GGCGGTGAGCTAATTAAACT+AGG + chr3.3:1459740-1459759 MS.gene52853:CDS 45.0%
TAATAGAGGATGGTCGGGTT+TGG + chr3.3:1459177-1459196 MS.gene52853:intron 45.0%
! GTTTCCGAGTTTGTTTGACG+AGG + chr3.3:1459805-1459824 MS.gene52853:CDS 45.0%
CCTTGGCAAGGAAGGCTTAA+AGG + chr3.3:1459719-1459738 MS.gene52853:CDS 50.0%
CCTTTAAGCCTTCCTTGCCA+AGG - chr3.3:1459722-1459741 None:intergenic 50.0%
CTAACCGCTTCTTGGCCAAA+CGG + chr3.3:1459510-1459529 MS.gene52853:intron 50.0%
GGAAATCTCCTTGGCAAGGA+AGG + chr3.3:1459711-1459730 MS.gene52853:CDS 50.0%
GGATGGAAATCTCCTTGGCA+AGG + chr3.3:1459707-1459726 MS.gene52853:CDS 50.0%
TCTTCCGTTTGGCCAAGAAG+CGG - chr3.3:1459517-1459536 None:intergenic 50.0%
TGGCAAGGAAGGCTTAAAGG+CGG + chr3.3:1459722-1459741 MS.gene52853:CDS 50.0%
TTACATTCCCAGGCAAGGCA+TGG + chr3.3:1459560-1459579 MS.gene52853:intron 50.0%
TTTGGCCAAGAAGCGGTTAG+TGG - chr3.3:1459510-1459529 None:intergenic 50.0%
! ATGGTCGGGTTTGGTAAGGA+GGG + chr3.3:1459186-1459205 MS.gene52853:intron 50.0%
! CTTTGGAGAGAGTTCCGTCT+TGG + chr3.3:1459678-1459697 MS.gene52853:CDS 50.0%
AACGAGTTCCATGCCTTGCC+TGG - chr3.3:1459571-1459590 None:intergenic 55.0%
ACGAGTTCCATGCCTTGCCT+GGG - chr3.3:1459570-1459589 None:intergenic 55.0%
! GAGGATGGTCGGGTTTGGTA+AGG + chr3.3:1459182-1459201 MS.gene52853:intron 55.0%
! GATGGTCGGGTTTGGTAAGG+AGG + chr3.3:1459185-1459204 MS.gene52853:intron 55.0%
GGGCGCCACTAACCGCTTCT+TGG + chr3.3:1459502-1459521 MS.gene52853:intron 65.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 1458783 1459865 1458783 ID=MS.gene52853
chr3.3 mRNA 1458783 1459865 1458783 ID=MS.gene52853.t1;Parent=MS.gene52853
chr3.3 exon 1458783 1458874 1458783 ID=MS.gene52853.t1.exon1;Parent=MS.gene52853.t1
chr3.3 CDS 1458783 1458874 1458783 ID=cds.MS.gene52853.t1;Parent=MS.gene52853.t1
chr3.3 exon 1459572 1459865 1459572 ID=MS.gene52853.t1.exon2;Parent=MS.gene52853.t1
chr3.3 CDS 1459572 1459865 1459572 ID=cds.MS.gene52853.t1;Parent=MS.gene52853.t1
Gene Sequence

>MS.gene52853

GTACGGGAGTTGTGGAAAGACATTACAGACCAAGAACTTCGTTCCTTCTAAAAATTCCTCAAGGATGTACTCCAATTCATTTAAACCTTGTGGTAATTTTCTCAACAATTGAAGGATAGTTATTTATTTAGTTAATTAAGTCTATGAAATTATGTTGGTTATATATATATAATAGGTTTTATCATATATTTTTTGAATTGATACCAGCTAAGTTTGCATTGCTAATTGCAAATGGAAATTAAATGTTTGCCAAACACTTTGAAATGATTATATGTCTTGAGTTACTTACTTGTTTGGTTTGCTTCAGTGAGCCTAAACTGTAAGCAGAAAATGAAAAGTATTTAAGAGATTGAATCACACAGCATAGTGTTGATGCAGCCTCGCTGACTTGTGTTAATAGAGGATGGTCGGGTTTGGTAAGGAGGGATGACGAGATAGAGAGAGTCCAATAGTTAGACATAGATGTAGAGCAAGATTAAGAAGGATGCCAGTTTTATGGTTTATCTGTGGACCTAATACATGACACGGTTTTTATGGCATTGATTGATCAATGCAGGTGATCCCACTTTGTGAAAATAGTCTGTGTTGTTGTTGTTGTGTTGTATCATCTACCCACTTAGATTTTATGTATGTGCTTGGATGAGAATTTTATGCAGTTGAAATGAAGGGTTAATCTTTTCTAAATTGTCCAACTTGTTATTAATGATAGTTTAAACTATGGGCGCCACTAACCGCTTCTTGGCCAAACGGAAGAGTATGATAATTGATAGTGCTATGTTACATTCCCAGGCAAGGCATGGAACTCGTTCTCCGACAAAGAAAAGGATAAGGGAGTTGGATAATTTGTCAGCTCAACTGGATGTTCTTGTAAGGGATGTAAAAGAGCGGAAATTGTCTTTGGAGAGAGTTCCGTCTTGGTTAAATGGATGGAAATCTCCTTGGCAAGGAAGGCTTAAAGGCGGTGAGCTAATTAAACTAGGAGAGGAAGAATTATACGAACTTGGAATCAGGATTAGAGAAAGGTTTCCGAGTTTGTTTGACGAGGATTACCATCCAGACATATATCCTATAAAGGCAACTCAG

Protein sequence

>MS.gene52853.t1

VRELWKDITDQELRSFUKFLKDVLQFIUTLWQGMELVLRQRKGUGSWIICQLNWMFLUGMUKSGNCLWREFRLGUMDGNLLGKEGLKAVSULNUERKNYTNLESGLEKGFRVCLTRITIQTYILURQL