AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90375

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90375.t1 MTR_2g105340 74.815 135 17 3 1 133 1 120 9.17e-39 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 51 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCCATTTCTTTCAGTTTCC+CGG 0.179440 2.1:+626457 None:intergenic
TTAACTGTGCCAGCAACTTC+TGG 0.273818 2.1:-626279 MS.gene90375:CDS
AAGAGAGTAGAAAGACATAT+TGG 0.339499 2.1:+627124 None:intergenic
GAGTTGGCCCAGGATTATAT+TGG 0.353506 2.1:+626310 None:intergenic
TCCCGGGAAACTGAAAGAAA+TGG 0.360508 2.1:-626459 MS.gene90375:CDS
AGTTGGCCCAGGATTATATT+GGG 0.360873 2.1:+626311 None:intergenic
AGAGATTAGGAGGAGAATTC+TGG 0.378079 2.1:+626226 None:intergenic
CCCGGGAAACTGAAAGAAAT+GGG 0.394159 2.1:-626458 MS.gene90375:CDS
CAGAGCGTCTGCGGCGGGAG+TGG 0.394365 2.1:+626365 None:intergenic
GTTGGGTTTCCAGAAGTTGC+TGG 0.414499 2.1:+626270 None:intergenic
AAAATATGTATCTGAGCTGT+TGG 0.415022 2.1:+626252 None:intergenic
CCCGGCGAATGGTGCGGAGG+TGG 0.417570 2.1:+626414 None:intergenic
CCTCCTCCCCAATATAATCC+TGG 0.422464 2.1:-626318 MS.gene90375:CDS
CCCATTTCTTTCAGTTTCCC+GGG 0.433130 2.1:+626458 None:intergenic
GAATGGTGCGGAGGTGGTGG+TGG 0.448834 2.1:+626420 None:intergenic
TATAATCCTGGGCCAACTCC+AGG 0.450650 2.1:-626306 MS.gene90375:CDS
GGAGAATTCAGTTTCTGAAC+TGG 0.452981 2.1:+626390 None:intergenic
AGAGCGTCTGCGGCGGGAGT+GGG 0.453808 2.1:+626366 None:intergenic
GGCGAATGGTGCGGAGGTGG+TGG 0.454424 2.1:+626417 None:intergenic
TTATATTGGGGAGGAGGTGG+TGG 0.459881 2.1:+626324 None:intergenic
ACCACCTCCGCACCATTCGC+CGG 0.460281 2.1:-626415 MS.gene90375:CDS
TTCAGTTTCTGAACTGGTCC+CGG 0.467126 2.1:+626396 None:intergenic
GGATTATATTGGGGAGGAGG+TGG 0.471962 2.1:+626321 None:intergenic
GCTGAAGCTGCAAAGAGATT+AGG 0.479618 2.1:+626213 None:intergenic
AAATATGTATCTGAGCTGTT+GGG 0.496619 2.1:+626253 None:intergenic
AAGAGCCCTGGAGTTGGCCC+AGG 0.496989 2.1:+626300 None:intergenic
TAGAAACAAACAGCAAGGCT+TGG 0.507692 2.1:+627088 None:intergenic
CTCCTCCCCAATATAATCCT+GGG 0.521004 2.1:-626317 MS.gene90375:CDS
TGTCTCAGAGCGTCTGCGGC+GGG 0.521606 2.1:+626360 None:intergenic
TCTGAACTGGTCCCGGCGAA+TGG 0.523874 2.1:+626403 None:intergenic
CCACCTCCGCACCATTCGCC+GGG 0.524394 2.1:-626414 MS.gene90375:CDS
GCTGGCACAGTTAAGAGCCC+TGG 0.549638 2.1:+626288 None:intergenic
CCAGGATTATATTGGGGAGG+AGG 0.552901 2.1:+626318 None:intergenic
CAGCAAGCATCTAGCTTCTG+TGG 0.554315 2.1:+627062 None:intergenic
TAGAAACTGAATTCTCCTCC+CGG 0.559431 2.1:-626476 MS.gene90375:CDS
GAAGCTGCAAAGAGATTAGG+AGG 0.563505 2.1:+626216 None:intergenic
ACAGTTAAGAGCCCTGGAGT+TGG 0.564303 2.1:+626294 None:intergenic
ACTGGTCCCGGCGAATGGTG+CGG 0.568557 2.1:+626408 None:intergenic
AGAAACTGAATTCTCCTCCC+GGG 0.573887 2.1:-626475 MS.gene90375:CDS
GCGTCTGCGGCGGGAGTGGG+AGG 0.581224 2.1:+626369 None:intergenic
CTGTTGCAGACTATGTCACT+AGG 0.582810 2.1:-627042 MS.gene90375:intron
ATGTCTCAGAGCGTCTGCGG+CGG 0.587729 2.1:+626359 None:intergenic
ATAATCCTGGGCCAACTCCA+GGG 0.596363 2.1:-626305 MS.gene90375:CDS
GGTCCCGGCGAATGGTGCGG+AGG 0.622064 2.1:+626411 None:intergenic
GTTGGCCCAGGATTATATTG+GGG 0.622956 2.1:+626312 None:intergenic
GGCCCAGGATTATATTGGGG+AGG 0.624273 2.1:+626315 None:intergenic
CCGGGAAACTGAAAGAAATG+GGG 0.639431 2.1:-626457 MS.gene90375:CDS
GGCAGTAGAAACAAACAGCA+AGG 0.643990 2.1:+627083 None:intergenic
ATGATGTCTCAGAGCGTCTG+CGG 0.676100 2.1:+626356 None:intergenic
CGGGAAACTGAAAGAAATGG+GGG 0.677386 2.1:-626456 MS.gene90375:CDS
ATTTCTTTCAGTTTCCCGGG+AGG 0.690454 2.1:+626461 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATTCTTATTAGTTAT+TGG - chr2.1:626474-626493 MS.gene90375:CDS 10.0%
!! AATTATTCTTATTAGTTATT+GGG - chr2.1:626475-626494 MS.gene90375:CDS 10.0%
!!! TAAAAGAATTTTATTTGAAT+TGG + chr2.1:626394-626413 None:intergenic 10.0%
!! AAACAATATATTTATGTGAT+TGG + chr2.1:626755-626774 None:intergenic 15.0%
!! GAAAATATAATATAACGAAA+TGG - chr2.1:626568-626587 MS.gene90375:intron 15.0%
!! TATTTATGTGATTGGAATAA+TGG + chr2.1:626747-626766 None:intergenic 20.0%
!!! AAGAATTTTATTTGAATTGG+AGG + chr2.1:626391-626410 None:intergenic 20.0%
!!! AATATTTTTTCAGTTACATG+AGG + chr2.1:626724-626743 None:intergenic 20.0%
!!! AGAATTTTATTTGAATTGGA+GGG + chr2.1:626390-626409 None:intergenic 20.0%
!!! TATTTTGTTTTGAATATGTG+CGG + chr2.1:626428-626447 None:intergenic 20.0%
AAAATATGTATCTGAGCTGT+TGG + chr2.1:627095-627114 None:intergenic 30.0%
AAATATGTATCTGAGCTGTT+GGG + chr2.1:627094-627113 None:intergenic 30.0%
AAGAGAGTAGAAAGACATAT+TGG + chr2.1:626223-626242 None:intergenic 30.0%
ACGAAATGGTTGAATTTAAG+TGG - chr2.1:626582-626601 MS.gene90375:intron 30.0%
!!! GATATCTTTTTGAGTTCGAA+TGG + chr2.1:626693-626712 None:intergenic 30.0%
TCAGTTACATGAGGTGAAAA+AGG + chr2.1:626715-626734 None:intergenic 35.0%
AGAGATTAGGAGGAGAATTC+TGG + chr2.1:627121-627140 None:intergenic 40.0%
AGTTGGCCCAGGATTATATT+GGG + chr2.1:627036-627055 None:intergenic 40.0%
GGAGAATTCAGTTTCTGAAC+TGG + chr2.1:626957-626976 None:intergenic 40.0%
TAGAAACAAACAGCAAGGCT+TGG + chr2.1:626259-626278 None:intergenic 40.0%
TAGAAACTGAATTCTCCTCC+CGG - chr2.1:626868-626887 MS.gene90375:intron 40.0%
AGAAACTGAATTCTCCTCCC+GGG - chr2.1:626869-626888 MS.gene90375:intron 45.0%
ATTTCTTTCAGTTTCCCGGG+AGG + chr2.1:626886-626905 None:intergenic 45.0%
CCCATTTCTTTCAGTTTCCC+GGG + chr2.1:626889-626908 None:intergenic 45.0%
CCCCATTTCTTTCAGTTTCC+CGG + chr2.1:626890-626909 None:intergenic 45.0%
CCCGGGAAACTGAAAGAAAT+GGG - chr2.1:626886-626905 MS.gene90375:intron 45.0%
CCGGGAAACTGAAAGAAATG+GGG - chr2.1:626887-626906 MS.gene90375:intron 45.0%
CGGGAAACTGAAAGAAATGG+GGG - chr2.1:626888-626907 MS.gene90375:intron 45.0%
CTCCTCCCCAATATAATCCT+GGG - chr2.1:627027-627046 MS.gene90375:intron 45.0%
CTGTTGCAGACTATGTCACT+AGG - chr2.1:626302-626321 MS.gene90375:CDS 45.0%
GAAGCTGCAAAGAGATTAGG+AGG + chr2.1:627131-627150 None:intergenic 45.0%
GAGTTGGCCCAGGATTATAT+TGG + chr2.1:627037-627056 None:intergenic 45.0%
GCTGAAGCTGCAAAGAGATT+AGG + chr2.1:627134-627153 None:intergenic 45.0%
GGCAGTAGAAACAAACAGCA+AGG + chr2.1:626264-626283 None:intergenic 45.0%
GTTGGCCCAGGATTATATTG+GGG + chr2.1:627035-627054 None:intergenic 45.0%
TCCCGGGAAACTGAAAGAAA+TGG - chr2.1:626885-626904 MS.gene90375:intron 45.0%
TTAACTGTGCCAGCAACTTC+TGG - chr2.1:627065-627084 MS.gene90375:CDS 45.0%
TTCAGTTTCTGAACTGGTCC+CGG + chr2.1:626951-626970 None:intergenic 45.0%
!! AATTGGAGGGAGTACTGACT+AGG + chr2.1:626377-626396 None:intergenic 45.0%
!! TATAATATAATATAATTAGT+TGG - chr2.1:626510-626529 MS.gene90375:intron 5.0%
ACAGTTAAGAGCCCTGGAGT+TGG + chr2.1:627053-627072 None:intergenic 50.0%
ATAATCCTGGGCCAACTCCA+GGG - chr2.1:627039-627058 MS.gene90375:intron 50.0%
CCAGGATTATATTGGGGAGG+AGG + chr2.1:627029-627048 None:intergenic 50.0%
CCTCCTCCCCAATATAATCC+TGG - chr2.1:627026-627045 MS.gene90375:intron 50.0%
GGATTATATTGGGGAGGAGG+TGG + chr2.1:627026-627045 None:intergenic 50.0%
GTTGGGTTTCCAGAAGTTGC+TGG + chr2.1:627077-627096 None:intergenic 50.0%
TATAATCCTGGGCCAACTCC+AGG - chr2.1:627038-627057 MS.gene90375:intron 50.0%
TTATATTGGGGAGGAGGTGG+TGG + chr2.1:627023-627042 None:intergenic 50.0%
! ATGATGTCTCAGAGCGTCTG+CGG + chr2.1:626991-627010 None:intergenic 50.0%
! CAGCAAGCATCTAGCTTCTG+TGG + chr2.1:626285-626304 None:intergenic 50.0%
GGCCCAGGATTATATTGGGG+AGG + chr2.1:627032-627051 None:intergenic 55.0%
GCTGGCACAGTTAAGAGCCC+TGG + chr2.1:627059-627078 None:intergenic 60.0%
TCTGAACTGGTCCCGGCGAA+TGG + chr2.1:626944-626963 None:intergenic 60.0%
! ATGTCTCAGAGCGTCTGCGG+CGG + chr2.1:626988-627007 None:intergenic 60.0%
AAGAGCCCTGGAGTTGGCCC+AGG + chr2.1:627047-627066 None:intergenic 65.0%
ACCACCTCCGCACCATTCGC+CGG - chr2.1:626929-626948 MS.gene90375:intron 65.0%
ACTGGTCCCGGCGAATGGTG+CGG + chr2.1:626939-626958 None:intergenic 65.0%
! GAATGGTGCGGAGGTGGTGG+TGG + chr2.1:626927-626946 None:intergenic 65.0%
! TGTCTCAGAGCGTCTGCGGC+GGG + chr2.1:626987-627006 None:intergenic 65.0%
CCACCTCCGCACCATTCGCC+GGG - chr2.1:626930-626949 MS.gene90375:intron 70.0%
GGCGAATGGTGCGGAGGTGG+TGG + chr2.1:626930-626949 None:intergenic 70.0%
! AGAGCGTCTGCGGCGGGAGT+GGG + chr2.1:626981-627000 None:intergenic 70.0%
CCCGGCGAATGGTGCGGAGG+TGG + chr2.1:626933-626952 None:intergenic 75.0%
GGTCCCGGCGAATGGTGCGG+AGG + chr2.1:626936-626955 None:intergenic 75.0%
! CAGAGCGTCTGCGGCGGGAG+TGG + chr2.1:626982-627001 None:intergenic 75.0%
! GCGTCTGCGGCGGGAGTGGG+AGG + chr2.1:626978-626997 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 626209 627157 626209 ID=MS.gene90375
chr2.1 mRNA 626209 627157 626209 ID=MS.gene90375.t1;Parent=MS.gene90375
chr2.1 exon 627043 627157 627043 ID=MS.gene90375.t1.exon1;Parent=MS.gene90375.t1
chr2.1 CDS 627043 627157 627043 ID=cds.MS.gene90375.t1;Parent=MS.gene90375.t1
chr2.1 exon 626209 626495 626209 ID=MS.gene90375.t1.exon2;Parent=MS.gene90375.t1
chr2.1 CDS 626209 626495 626209 ID=cds.MS.gene90375.t1;Parent=MS.gene90375.t1
Gene Sequence

>MS.gene90375

ATGAAGACTCTCCAATATGTCTTTCTACTCTCTTCACTCTTTGCATTCCAAGCCTTGCTGTTTGTTTCTACTGCCACAGAAGCTAGATGCTTGCTGTTGCAGACTATGTCACTAGGTAAATTCTTTACTTATAGCTTATTAACTTATATGTGCATGCACTTTGTACCTAGTCAGTACTCCCTCCAATTCAAATAAAATTCTTTTAAAGCTTTTTCGCCGCACATATTCAAAACAAAATAAATGAACAAAGTGTAATAATCTTTTAAAATTATTCTTATTAGTTATTGGGTTGTATAGTACGTATAATATAATATAATTAGTTGGACGTAAAATTGAAAAATTAATTAATTGATTGTCTTGAAAATATAATATAACGAAATGGTTGAATTTAAGTGGTTAATAAATTTTATTTTAAATAATTCAAAAGAACACGAATTTAAAATTTTAAATAAAATAATCATTGATCAAGCTATACTTATATCCATTCGAACTCAAAAAGATATCCTTTTTCACCTCATGTAACTGAAAAAATATTCCATTATTCCAATCACATAAATATATTGTTTAGAAAAAGAAAAGCATATCACAATGTCAGTTTGTCATACTAGTTATTAATATATTTTCACAAATATTTATACAACTAGACGTGATTTGATGTATAGAAACTGAATTCTCCTCCCGGGAAACTGAAAGAAATGGGGGAAGACATCATGCACCACCACCACCTCCGCACCATTCGCCGGGACCAGTTCAGAAACTGAATTCTCCTCCCACTCCCGCCGCAGACGCTCTGAGACATCATCGACACTCACCACCACCTCCTCCCCAATATAATCCTGGGCCAACTCCAGGGCTCTTAACTGTGCCAGCAACTTCTGGAAACCCAACAGCTCAGATACATATTTTGTACCAGAATTCTCCTCCTAATCTCTTTGCAGCTTCAGCCTGA
Protein sequence

>MS.gene90375.t1

MKTLQYVFLLSSLFAFQALLFVSTATEARCLLLQTMSLETEFSSRETERNGGRHHAPPPPPHHSPGPVQKLNSPPTPAADALRHHRHSPPPPPQYNPGPTPGLLTVPATSGNPTAQIHILYQNSPPNLFAASA