AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene061145


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene061145.t1 MTR_4g068040 94.030 67 4 0 1 67 1 67 2.51e-41 129
MS.gene061145.t1 MTR_4g068040 100.000 63 0 0 1 63 1 63 9.29e-41 127
MS.gene061145.t1 MTR_2g018680 91.045 67 6 0 1 67 1 67 2.01e-39 124
MS.gene061145.t1 MTR_8g079485 89.552 67 7 0 1 67 1 67 4.58e-39 123
MS.gene061145.t1 MTR_2g018680 93.750 64 4 0 1 64 1 64 1.44e-38 122
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene061145.t1 AT3G59540 89.552 67 7 0 1 67 1 67 1.15e-39 125
MS.gene061145.t1 AT2G43460 89.552 67 7 0 1 67 1 67 1.15e-39 125

Find 11 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGCAAATCAATGAGATTA+AGG 0.290766 1.4:+77780660 MS.gene061145:CDS
TTGTTATAGGTGTAAGCTTA+AGG 0.368189 1.4:+77780965 MS.gene061145:intron
CAAAGATGTTGTCAAGTTCA+AGG 0.413071 1.4:+77780738 MS.gene061145:CDS
ACAAAGTGTGTACAAGTACT+TGG 0.506752 1.4:-77780770 None:intergenic
TTAATCTCATTGATTTGCTT+AGG 0.531275 1.4:-77780658 None:intergenic
TTGAAGCAATCACTTCCTCC+AGG 0.546677 1.4:+77780820 MS.gene061145:CDS
AGGACTTCCTCCTCACTGCT+AGG 0.557805 1.4:+77780680 MS.gene061145:CDS
CCTCCTCACTGCTAGGAGGA+AGG 0.586231 1.4:+77780687 MS.gene061145:CDS
CCTTCCTCCTAGCAGTGAGG+AGG 0.655712 1.4:-77780687 None:intergenic
CGTCCTTCCTCCTAGCAGTG+AGG 0.660436 1.4:-77780690 None:intergenic
ACTTCCTCCTCACTGCTAGG+AGG 0.666318 1.4:+77780683 MS.gene061145:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAACATTAAAAATCAAAAT+AGG - chr1.4:77780350-77780369 None:intergenic 10.0%
!! TTTATTTATTTATTTGGATT+TGG + chr1.4:77780571-77780590 MS.gene061145:intron 10.0%
!!! ATTTTATTTACTCAATTTTA+TGG + chr1.4:77780414-77780433 MS.gene061145:intron 10.0%
!! ACATTTCAATAAACATAAAA+AGG - chr1.4:77780636-77780655 None:intergenic 15.0%
!! ATAAGAAATTAAGAATTACA+AGG - chr1.4:77780882-77780901 None:intergenic 15.0%
!!! AAATTGTTGTTGTTTGTTAT+AGG + chr1.4:77780952-77780971 MS.gene061145:intron 20.0%
!!! TTATTTTTCGTCATATGTTA+TGG + chr1.4:77780853-77780872 MS.gene061145:intron 20.0%
! AAAAATAATTCTCACTAACC+TGG - chr1.4:77780841-77780860 None:intergenic 25.0%
! ATTATACACTGATCTGAATT+AGG + chr1.4:77780474-77780493 MS.gene061145:intron 25.0%
! TAAGCAAATCAATGAGATTA+AGG + chr1.4:77780660-77780679 MS.gene061145:CDS 25.0%
! TTCCTAAAAAAAACTGTGAA+TGG - chr1.4:77780305-77780324 None:intergenic 25.0%
!!! CACAGTTTTTTTTAGGAAAT+TGG + chr1.4:77780307-77780326 MS.gene061145:intron 25.0%
!!! TTAATCTCATTGATTTGCTT+AGG - chr1.4:77780661-77780680 None:intergenic 25.0%
!!! TTCCATTCACAGTTTTTTTT+AGG + chr1.4:77780300-77780319 MS.gene061145:intron 25.0%
ACTCCAATGTTTCAATTACA+TGG - chr1.4:77780449-77780468 None:intergenic 30.0%
GAACCATGTAATTGAAACAT+TGG + chr1.4:77780443-77780462 MS.gene061145:intron 30.0%
GATCTGAATTAGGTGATTTA+GGG + chr1.4:77780484-77780503 MS.gene061145:intron 30.0%
TGATCTGAATTAGGTGATTT+AGG + chr1.4:77780483-77780502 MS.gene061145:intron 30.0%
TTGTTATAGGTGTAAGCTTA+AGG + chr1.4:77780965-77780984 MS.gene061145:intron 30.0%
! CAAACTTGGTAGTTGTTAAA+GGG + chr1.4:77780518-77780537 MS.gene061145:intron 30.0%
! TCAAACTTGGTAGTTGTTAA+AGG + chr1.4:77780517-77780536 MS.gene061145:intron 30.0%
! TGGATTTTTGTGTTGTGATT+TGG + chr1.4:77780591-77780610 MS.gene061145:intron 30.0%
! TTTGCTTCTCTTGATTTTCA+CGG - chr1.4:77780722-77780741 None:intergenic 30.0%
AATAATTCTCACTAACCTGG+AGG - chr1.4:77780838-77780857 None:intergenic 35.0%
ACAAAGTGTGTACAAGTACT+TGG - chr1.4:77780773-77780792 None:intergenic 35.0%
CAAAGATGTTGTCAAGTTCA+AGG + chr1.4:77780738-77780757 MS.gene061145:CDS 35.0%
GAAACACTGCAAAGAATCAA+TGG - chr1.4:77780270-77780289 None:intergenic 35.0%
! TTGTGTTGTGATTTGGAAGA+TGG + chr1.4:77780598-77780617 MS.gene061145:intron 35.0%
! GGGCTTTTGATCTTCAAACT+TGG + chr1.4:77780504-77780523 MS.gene061145:intron 40.0%
TTGAAGCAATCACTTCCTCC+AGG + chr1.4:77780820-77780839 MS.gene061145:CDS 45.0%
!!! TTCTATTTTATTTATTTATT+TGG + chr1.4:77780565-77780584 MS.gene061145:intron 5.0%
ACTTCCTCCTCACTGCTAGG+AGG + chr1.4:77780683-77780702 MS.gene061145:CDS 55.0%
AGGACTTCCTCCTCACTGCT+AGG + chr1.4:77780680-77780699 MS.gene061145:CDS 55.0%
CCTCCTCACTGCTAGGAGGA+AGG + chr1.4:77780687-77780706 MS.gene061145:CDS 60.0%
CCTTCCTCCTAGCAGTGAGG+AGG - chr1.4:77780690-77780709 None:intergenic 60.0%
CGTCCTTCCTCCTAGCAGTG+AGG - chr1.4:77780693-77780712 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 77780248 77780993 77780248 ID=MS.gene061145
chr1.4 mRNA 77780248 77780993 77780248 ID=MS.gene061145.t1;Parent=MS.gene061145
chr1.4 exon 77780248 77780250 77780248 ID=MS.gene061145.t1.exon1;Parent=MS.gene061145.t1
chr1.4 CDS 77780248 77780250 77780248 ID=cds.MS.gene061145.t1;Parent=MS.gene061145.t1
chr1.4 exon 77780658 77780841 77780658 ID=MS.gene061145.t1.exon2;Parent=MS.gene061145.t1
chr1.4 CDS 77780658 77780841 77780658 ID=cds.MS.gene061145.t1;Parent=MS.gene061145.t1
chr1.4 exon 77780974 77780993 77780974 ID=MS.gene061145.t1.exon3;Parent=MS.gene061145.t1
chr1.4 CDS 77780974 77780993 77780974 ID=cds.MS.gene061145.t1;Parent=MS.gene061145.t1
Gene Sequence

>MS.gene061145

ATGGTATTTTTCTCTATCTCCATTGATTCTTTGCAGTGTTTCTGTATATTTCTTCCATTCACAGTTTTTTTTAGGAAATTGGAAGAATCTTAGCATTATCCTATTTTGATTTTTAATGTTTTTGATTCATGATTAGCTTAAATAATTTGATTTTCAGCTGCTATGAATTTTATTTACTCAATTTTATGGCTATCTGAACCATGTAATTGAAACATTGGAGTTTAGTATTATACACTGATCTGAATTAGGTGATTTAGGGCTTTTGATCTTCAAACTTGGTAGTTGTTAAAGGGAATGAAAATGCTTTGTTTTGATTATTCTATTTTATTTATTTATTTGGATTTGGATTTTTGTGTTGTGATTTGGAAGATGGTTCACATTGTAACCTTTTTATGTTTATTGAAATGTAGCCTAAGCAAATCAATGAGATTAAGGACTTCCTCCTCACTGCTAGGAGGAAGGACGCACGCTCCGTGAAAATCAAGAGAAGCAAAGATGTTGTCAAGTTCAAGGTTAGATGCTCCAAGTACTTGTACACACTTTGTGTGTTTGATACTGAGAAAGCTGATAAGTTGAAGCAATCACTTCCTCCAGGTTAGTGAGAATTATTTTTCGTCATATGTTATGGCTGCCTTGTAATTCTTAATTTCTTATCAACGTGCAAGTACTTTAAACTTTAGCTATAGTGAGTGAATTTCATAAACAAATTGTTGTTGTTTGTTATAGGTGTAAGCTTAAGGATGTAA

Protein sequence

>MS.gene061145.t1

MPKQINEIKDFLLTARRKDARSVKIKRSKDVVKFKVRCSKYLYTLCVFDTEKADKLKQSLPPGVSLRM