AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54086

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54086.t1 MTR_1g010050 97.600 125 3 0 1 125 1 125 5.62e-89 254
MS.gene54086.t1 MTR_1g010050 97.938 97 2 0 1 97 1 97 2.40e-66 196
MS.gene54086.t1 MTR_1g010050 96.341 82 3 0 1 82 1 82 1.25e-53 163
MS.gene54086.t1 MTR_1g071100 34.951 103 62 2 23 125 11 108 2.83e-17 72.0
MS.gene54086.t1 MTR_1g076640 38.393 112 61 2 14 125 4 107 1.82e-13 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54086.t1 AT3G63420 36.170 94 56 2 32 125 8 97 4.12e-16 68.6
MS.gene54086.t1 AT3G63420 36.170 94 56 2 32 125 8 97 4.12e-16 68.6
MS.gene54086.t1 AT3G63420 39.759 83 46 2 32 114 48 126 4.48e-16 69.7
MS.gene54086.t1 AT3G22942 44.000 75 40 1 45 119 21 93 1.89e-11 57.0

Find 27 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTCTTTCCCTGGCTTCTA+TGG 0.223765 1.2:+10099024 MS.gene54086:CDS
CTGGTTCTGGTTGGGATAGA+TGG 0.293101 1.2:+10099915 MS.gene54086:CDS
TAACATGCTTGCAGGATTAA+AGG 0.337522 1.2:+10099881 MS.gene54086:intron
TCTGGTTGGGATAGATGGTT+TGG 0.341402 1.2:+10099920 MS.gene54086:CDS
GGTCCAGTTGATGCTGGTTC+TGG 0.360151 1.2:+10099902 MS.gene54086:CDS
TGACCTGGAGAATATTGATT+TGG 0.373161 1.2:-10099086 None:intergenic
GTTGGAACTGTTTCTTTCCC+TGG 0.413466 1.2:+10099015 MS.gene54086:CDS
GAATATTGATTTGGTTATTG+AGG 0.423057 1.2:-10099077 None:intergenic
TTGGTTATTGAGGTTAGATA+TGG 0.427698 1.2:-10099067 None:intergenic
CAACCAGAACCAGCATCAAC+TGG 0.434691 1.2:-10099905 None:intergenic
CCTACTTCATTTGCACAAGT+TGG 0.435219 1.2:+10098997 MS.gene54086:CDS
GAAGTAACAGATTCAGAAGA+TGG 0.458262 1.2:+10098934 MS.gene54086:CDS
TACCATGGAAGCATAGGATC+TGG 0.459697 1.2:-10099561 None:intergenic
GGTTGGGATAGATGGTTTGG+AGG 0.467119 1.2:+10099923 MS.gene54086:CDS
AGTTGATGCTGGTTCTGGTT+GGG 0.472706 1.2:+10099907 MS.gene54086:CDS
TATGATAATGCAGGAAGAGT+TGG 0.480511 1.2:+10099370 MS.gene54086:intron
ATTCATTGAAAAGAAAGAAA+AGG 0.487861 1.2:+10098972 MS.gene54086:CDS
CAGTTGATGCTGGTTCTGGT+TGG 0.505214 1.2:+10099906 MS.gene54086:CDS
ATTAAAGGTCCAGTTGATGC+TGG 0.509550 1.2:+10099896 MS.gene54086:CDS
CCAACTTGTGCAAATGAAGT+AGG 0.510578 1.2:-10098997 None:intergenic
TACTGATTGCTGTCTATCCA+TGG 0.514312 1.2:-10098911 None:intergenic
TAACCAAATCAATATTCTCC+AGG 0.514948 1.2:+10099083 MS.gene54086:CDS
TGCCAGATCCTATGCTTCCA+TGG 0.550978 1.2:+10099559 MS.gene54086:CDS
ACTCTCGAAATCATAAGCGA+TGG 0.594105 1.2:+10099954 MS.gene54086:CDS
TGGAAGCATAGGATCTGGCA+TGG 0.601609 1.2:-10099556 None:intergenic
TGCTTACTCATTGCAGACCG+TGG 0.621212 1.2:-10099420 None:intergenic
AACAATAGGTGAATCTTCCA+CGG 0.624066 1.2:+10099403 MS.gene54086:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATACATGTTATATATA+TGG + chr1.2:10099307-10099326 MS.gene54086:intron 10.0%
!!! AAAACAAATACTTTTTAAAT+TGG + chr1.2:10099454-10099473 MS.gene54086:intron 10.0%
!!! AATTAGATATAGTTTTTTTT+TGG - chr1.2:10099249-10099268 None:intergenic 10.0%
!!! ATTAGATATAGTTTTTTTTT+GGG - chr1.2:10099248-10099267 None:intergenic 10.0%
!!! AAATACTTTTTAAATTGGAT+TGG + chr1.2:10099459-10099478 MS.gene54086:intron 15.0%
!!! ATTGTTGTGTATTTTTTAAA+CGG + chr1.2:10099639-10099658 MS.gene54086:intron 15.0%
!! ATTCATTGAAAAGAAAGAAA+AGG + chr1.2:10098972-10098991 MS.gene54086:CDS 20.0%
!! CAAAAACTTATATATCTTCT+TGG + chr1.2:10099168-10099187 MS.gene54086:intron 20.0%
!!! ACTCACAATATTACATTTTA+AGG + chr1.2:10099610-10099629 MS.gene54086:intron 20.0%
!!! TTAATTAAAAGCACAATGAA+TGG - chr1.2:10099509-10099528 None:intergenic 20.0%
!!! TTGTTGTGTATTTTTTAAAC+GGG + chr1.2:10099640-10099659 MS.gene54086:intron 20.0%
! TGCAGAACTATATATATTCT+TGG + chr1.2:10099278-10099297 MS.gene54086:intron 25.0%
! TTACATGTTATCAACTCATA+TGG - chr1.2:10099864-10099883 None:intergenic 25.0%
! TTGGAAAAACTTGAAACAAT+AGG + chr1.2:10099389-10099408 MS.gene54086:CDS 25.0%
!! AGATGATCTTAATTTTACCA+TGG - chr1.2:10099579-10099598 None:intergenic 25.0%
!! ATTTGAACTTATGATAATGC+AGG + chr1.2:10099361-10099380 MS.gene54086:intron 25.0%
!!! GAATATTGATTTGGTTATTG+AGG - chr1.2:10099080-10099099 None:intergenic 25.0%
!!! TGCTATTTTTCATCATTGAA+TGG + chr1.2:10099482-10099501 MS.gene54086:intron 25.0%
TAACCAAATCAATATTCTCC+AGG + chr1.2:10099083-10099102 MS.gene54086:CDS 30.0%
TGTTATCAACTCATATGGTT+AGG - chr1.2:10099859-10099878 None:intergenic 30.0%
TTGGTTATTGAGGTTAGATA+TGG - chr1.2:10099070-10099089 None:intergenic 30.0%
!! TAATTTTACCATGGAAGCAT+AGG - chr1.2:10099570-10099589 None:intergenic 30.0%
!! TTAAAAAGGGTCTTGTTAAC+CGG - chr1.2:10099795-10099814 None:intergenic 30.0%
AACAATAGGTGAATCTTCCA+CGG + chr1.2:10099403-10099422 MS.gene54086:CDS 35.0%
ATAACATGTAACATGCTTGC+AGG + chr1.2:10099873-10099892 MS.gene54086:intron 35.0%
GAAGTAACAGATTCAGAAGA+TGG + chr1.2:10098934-10098953 MS.gene54086:CDS 35.0%
TAACATGCTTGCAGGATTAA+AGG + chr1.2:10099881-10099900 MS.gene54086:intron 35.0%
! TATGATAATGCAGGAAGAGT+TGG + chr1.2:10099370-10099389 MS.gene54086:intron 35.0%
! TATGTTTTCCATAGAAGCCA+GGG - chr1.2:10099035-10099054 None:intergenic 35.0%
! TGACCTGGAGAATATTGATT+TGG - chr1.2:10099089-10099108 None:intergenic 35.0%
AAATGAGATGAGAGTTGACC+TGG - chr1.2:10099104-10099123 None:intergenic 40.0%
ACTCTCGAAATCATAAGCGA+TGG + chr1.2:10099954-10099973 MS.gene54086:CDS 40.0%
CCAACTTGTGCAAATGAAGT+AGG - chr1.2:10099000-10099019 None:intergenic 40.0%
CCTACTTCATTTGCACAAGT+TGG + chr1.2:10098997-10099016 MS.gene54086:CDS 40.0%
! ATTAAAGGTCCAGTTGATGC+TGG + chr1.2:10099896-10099915 MS.gene54086:CDS 40.0%
! CTATGTTTTCCATAGAAGCC+AGG - chr1.2:10099036-10099055 None:intergenic 40.0%
GTTTCTTTCCCTGGCTTCTA+TGG + chr1.2:10099024-10099043 MS.gene54086:CDS 45.0%
TCTGGTTGGGATAGATGGTT+TGG + chr1.2:10099920-10099939 MS.gene54086:CDS 45.0%
! GTTGGAACTGTTTCTTTCCC+TGG + chr1.2:10099015-10099034 MS.gene54086:CDS 45.0%
! TACCATGGAAGCATAGGATC+TGG - chr1.2:10099564-10099583 None:intergenic 45.0%
!! AGTTGATGCTGGTTCTGGTT+GGG + chr1.2:10099907-10099926 MS.gene54086:CDS 45.0%
!!! ATTATTTGTTATATTTAAAA+AGG - chr1.2:10099809-10099828 None:intergenic 5.0%
!!! TTATTTATATTTTAGTATTA+TGG + chr1.2:10099127-10099146 MS.gene54086:intron 5.0%
!!! TTATTTGTTATATTTAAAAA+GGG - chr1.2:10099808-10099827 None:intergenic 5.0%
AACTAGTGTCGCGTGAACAC+CGG + chr1.2:10099773-10099792 MS.gene54086:intron 50.0%
CAACCAGAACCAGCATCAAC+TGG - chr1.2:10099908-10099927 None:intergenic 50.0%
TGCCAGATCCTATGCTTCCA+TGG + chr1.2:10099559-10099578 MS.gene54086:CDS 50.0%
TGCTTACTCATTGCAGACCG+TGG - chr1.2:10099423-10099442 None:intergenic 50.0%
! GGTTGGGATAGATGGTTTGG+AGG + chr1.2:10099923-10099942 MS.gene54086:CDS 50.0%
! TGGAAGCATAGGATCTGGCA+TGG - chr1.2:10099559-10099578 None:intergenic 50.0%
!! CAGTTGATGCTGGTTCTGGT+TGG + chr1.2:10099906-10099925 MS.gene54086:CDS 50.0%
!! CTGGTTCTGGTTGGGATAGA+TGG + chr1.2:10099915-10099934 MS.gene54086:CDS 50.0%
!! GGTCCAGTTGATGCTGGTTC+TGG + chr1.2:10099902-10099921 MS.gene54086:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 10098913 10099982 10098913 ID=MS.gene54086
chr1.2 mRNA 10098913 10099982 10098913 ID=MS.gene54086.t1;Parent=MS.gene54086
chr1.2 exon 10098913 10099104 10098913 ID=MS.gene54086.t1.exon1;Parent=MS.gene54086.t1
chr1.2 CDS 10098913 10099104 10098913 ID=cds.MS.gene54086.t1;Parent=MS.gene54086.t1
chr1.2 exon 10099383 10099435 10099383 ID=MS.gene54086.t1.exon2;Parent=MS.gene54086.t1
chr1.2 CDS 10099383 10099435 10099383 ID=cds.MS.gene54086.t1;Parent=MS.gene54086.t1
chr1.2 exon 10099536 10099580 10099536 ID=MS.gene54086.t1.exon3;Parent=MS.gene54086.t1
chr1.2 CDS 10099536 10099580 10099536 ID=cds.MS.gene54086.t1;Parent=MS.gene54086.t1
chr1.2 exon 10099895 10099982 10099895 ID=MS.gene54086.t1.exon4;Parent=MS.gene54086.t1
chr1.2 CDS 10099895 10099982 10099895 ID=cds.MS.gene54086.t1;Parent=MS.gene54086.t1
Gene Sequence

>MS.gene54086

ATGGATAGACAGCAATCAGTAGAAGTAACAGATTCAGAAGATGGAAGAGAATCAGAAGAATTCATTGAAAAGAAAGAAAAGGTTCCTACTTCATTTGCACAAGTTGGAACTGTTTCTTTCCCTGGCTTCTATGGAAAACATAGATTGCAAGCTTCCATATCTAACCTCAATAACCAAATCAATATTCTCCAGGTCAACTCTCATCTCATTTCACTTATTTATATTTTAGTATTATGGTCTATTTTGTTTAATCTGCAAAAACTTATATATCTTCTTGGTATATCTCATTTACATATTATATATATGCATAATTAACTAGAAGAGTTTTTGTACCCAAAAAAAAACTATATCTAATTTCTTTAGTTTGCAGAACTATATATATTCTTGGTATATCTAATATACATGTTATATATATGGATAACTAACTAGAATAAATTGATATTGAATAATTTGAACTTATGATAATGCAGGAAGAGTTGGAAAAACTTGAAACAATAGGTGAATCTTCCACGGTCTGCAATGAGTAAGCAAAGCAAAAATAAAAACAAATACTTTTTAAATTGGATTGGTGCTATTTTTCATCATTGAATGGTCCATTCATTGTGCTTTTAATTAATTTGCAGTGTCATTTCAAGCGTTGAATCCATGCCAGATCCTATGCTTCCATGGTAAAATTAAGATCATCTTGATTTTTGATACTCACAATATTACATTTTAAGGATTCATATTGTTGTGTATTTTTTAAACGGGAAATTTATTTTAGAAAAGATTCTCTTGAAAATTATGTGTTCTACTTTTTGAAAGTTGAAAGTGTTTTTTTACGCAAAAACTTAATTATTTTTTTCTATTTTTAGTTTGTTAACTAGTGTCGCGTGAACACCGGTTAACAAGACCCTTTTTAAATATAACAAATAATAAAGATTAATACACACATGTATATAGTCCTAACCATATGAGTTGATAACATGTAACATGCTTGCAGGATTAAAGGTCCAGTTGATGCTGGTTCTGGTTGGGATAGATGGTTTGGAGGAGCACACAACTCTCGAAATCATAAGCGATGGATTTAG
Protein sequence

>MS.gene54086.t1

MDRQQSVEVTDSEDGRESEEFIEKKEKVPTSFAQVGTVSFPGFYGKHRLQASISNLNNQINILQEELEKLETIGESSTVCNDVISSVESMPDPMLPWIKGPVDAGSGWDRWFGGAHNSRNHKRWI