AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052302


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052302.t1 MTR_4g076090 96.825 63 2 0 1 63 1 63 5.61e-40 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052302.t1 AT3G22210 62.295 61 22 1 5 65 6 65 7.04e-20 76.6

Find 22 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAATTCGCTCTTCCAGTTT+TGG 0.231911 4.2:-33060143 MS.gene052302:CDS
TGATGTGTGGCGAGCATTAC+TGG 0.309464 4.2:-33058948 MS.gene052302:CDS
GTCTTCTAGCTCGCCTCTCT+CGG 0.346161 4.2:+33059913 None:intergenic
GACAGAAATCACTTCAAGAT+TGG 0.349085 4.2:-33059983 MS.gene052302:intron
GCTGCAACAATGCCCAAAAC+TGG 0.365881 4.2:+33060130 None:intergenic
AGCATTAAACTTTATTATCA+AGG 0.372958 4.2:+33058867 None:intergenic
AGCTCGCCTCTCTCGGGAGC+TGG 0.374844 4.2:+33059920 None:intergenic
CTCTCTCGGGAGCTGGATGT+TGG 0.452110 4.2:+33059927 None:intergenic
GGTCATCTTCATCACCATAC+TGG 0.459278 4.2:-33058916 MS.gene052302:CDS
TTGATACTCGTAATCCAGTA+TGG 0.459701 4.2:+33058902 None:intergenic
ACAGAAATCACTTCAAGATT+GGG 0.482353 4.2:-33059982 MS.gene052302:intron
ATTGAAACTCACTGCATAGA+AGG 0.485260 4.2:+33060096 None:intergenic
TCTTCTAGCTCGCCTCTCTC+GGG 0.500761 4.2:+33059914 None:intergenic
AAACTTTATTATCAAGGGAA+GGG 0.504724 4.2:+33058873 None:intergenic
TAAACTTTATTATCAAGGGA+AGG 0.509711 4.2:+33058872 None:intergenic
GCATTAAACTTTATTATCAA+GGG 0.548046 4.2:+33058868 None:intergenic
GAGCATTACTGGATTGTCTA+CGG 0.582425 4.2:-33058937 MS.gene052302:CDS
CAACATCCAGCTCCCGAGAG+AGG 0.612999 4.2:-33059926 MS.gene052302:CDS
GATGATTCTGAATCAGACAA+TGG 0.634322 4.2:-33059960 MS.gene052302:CDS
GAGTTTCAATGAGATTAGAG+AGG 0.641117 4.2:-33060083 MS.gene052302:intron
GATTCTGAATCAGACAATGG+AGG 0.655225 4.2:-33059957 MS.gene052302:CDS
CTCGATATAACACTGATGTG+TGG 0.707696 4.2:-33058961 MS.gene052302:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGAATAGTATTTTTTTTTT+TGG - chr4.2:33059700-33059719 MS.gene052302:intron 10.0%
!! ATAACATTGAAATTTGAAAA+CGG + chr4.2:33059500-33059519 None:intergenic 15.0%
!!! ATACTCCTTTTATATTTTAA+TGG - chr4.2:33059518-33059537 MS.gene052302:intron 15.0%
!!! TACATTTTTCTAATAGAAAA+TGG + chr4.2:33059329-33059348 None:intergenic 15.0%
!! AAAATTAAGGAAAATACTTC+GGG + chr4.2:33060025-33060044 None:intergenic 20.0%
!! CAAAATTAAGGAAAATACTT+CGG + chr4.2:33060026-33060045 None:intergenic 20.0%
!! CTAGACCATTAAAATATAAA+AGG + chr4.2:33059526-33059545 None:intergenic 20.0%
!! TAACATTGAAATTTGAAAAC+GGG + chr4.2:33059499-33059518 None:intergenic 20.0%
!! TGATCACTAAAAAGTAATAT+CGG - chr4.2:33059841-33059860 MS.gene052302:intron 20.0%
!! TGTCAAAAAGAAAAACATAT+AGG + chr4.2:33059618-33059637 None:intergenic 20.0%
!!! AGTATTTTCCTTAATTTTGT+TGG - chr4.2:33060027-33060046 MS.gene052302:intron 20.0%
!!! ATAGTAGTTTTTTATTACGT+CGG - chr4.2:33059730-33059749 MS.gene052302:intron 20.0%
!!! ATTTCTTTATTTTTGATGCT+TGG - chr4.2:33059209-33059228 MS.gene052302:intron 20.0%
!!! TTTTTTGGATAATAATACGT+AGG - chr4.2:33059756-33059775 MS.gene052302:intron 20.0%
! AAACTTTATTATCAAGGGAA+GGG + chr4.2:33060155-33060174 None:intergenic 25.0%
! AACATTGAAATTTGAAAACG+GGG + chr4.2:33059498-33059517 None:intergenic 25.0%
! GATCACTAAAAAGTAATATC+GGG - chr4.2:33059842-33059861 MS.gene052302:intron 25.0%
! TAAACTTTATTATCAAGGGA+AGG + chr4.2:33060156-33060175 None:intergenic 25.0%
! TCTCATTGCTAATATAGTTT+AGG + chr4.2:33059649-33059668 None:intergenic 25.0%
!! AAATGAACATGCAACTATTT+TGG + chr4.2:33059446-33059465 None:intergenic 25.0%
!!! TTATTACGTCGGTTTTTTTT+TGG - chr4.2:33059741-33059760 MS.gene052302:intron 25.0%
!!! TTGCTGTTGAAGTTATTTTT+TGG + chr4.2:33059153-33059172 None:intergenic 25.0%
AAGAACAGGTGACTTAAATT+TGG - chr4.2:33059794-33059813 MS.gene052302:intron 30.0%
AAGTTGAGCCAACAAAATTA+AGG + chr4.2:33060038-33060057 None:intergenic 30.0%
ACAGAAATCACTTCAAGATT+GGG - chr4.2:33059043-33059062 MS.gene052302:intron 30.0%
ACATTGAAATTTGAAAACGG+GGG + chr4.2:33059497-33059516 None:intergenic 30.0%
ACCAACAAGAACTATTGAAA+AGG + chr4.2:33059283-33059302 None:intergenic 30.0%
AGTAGCAAATTGTTTGTACT+AGG - chr4.2:33059249-33059268 MS.gene052302:intron 30.0%
! ACCTTTTCAATAGTTCTTGT+TGG - chr4.2:33059279-33059298 MS.gene052302:intron 30.0%
!!! ACATTTTTTGTGTTTTCTCC+AGG - chr4.2:33059381-33059400 MS.gene052302:intron 30.0%
!!! CATTTTTTGTGTTTTCTCCA+GGG - chr4.2:33059382-33059401 MS.gene052302:intron 30.0%
ATTGAAACTCACTGCATAGA+AGG + chr4.2:33058932-33058951 None:intergenic 35.0%
GACAGAAATCACTTCAAGAT+TGG - chr4.2:33059042-33059061 MS.gene052302:intron 35.0%
GAGTTTCAATGAGATTAGAG+AGG - chr4.2:33058942-33058961 MS.gene052302:CDS 35.0%
GATGATTCTGAATCAGACAA+TGG - chr4.2:33059065-33059084 MS.gene052302:intron 35.0%
TCTCATTATTTCCTCTTGAG+AGG - chr4.2:33059550-33059569 MS.gene052302:intron 35.0%
TTGATACTCGTAATCCAGTA+TGG + chr4.2:33060126-33060145 None:intergenic 35.0%
ATGAGAAAGTAAACACGCCA+AGG - chr4.2:33059663-33059682 MS.gene052302:intron 40.0%
CTCGATATAACACTGATGTG+TGG - chr4.2:33060064-33060083 MS.gene052302:intron 40.0%
GACTTAAATTTGGTCCGTTG+AGG - chr4.2:33059804-33059823 MS.gene052302:intron 40.0%
GAGCATTACTGGATTGTCTA+CGG - chr4.2:33060088-33060107 MS.gene052302:CDS 40.0%
GATCTTAATCCCACACTTGA+GGG - chr4.2:33059572-33059591 MS.gene052302:intron 40.0%
GATTCTGAATCAGACAATGG+AGG - chr4.2:33059068-33059087 MS.gene052302:intron 40.0%
TGTACAGTCGATGAAAGAAC+AGG - chr4.2:33059780-33059799 MS.gene052302:intron 40.0%
! CAATTCGCTCTTCCAGTTTT+GGG - chr4.2:33058883-33058902 MS.gene052302:CDS 40.0%
!! CTTCGGGTAACTTTGAGTTT+TGG + chr4.2:33060009-33060028 None:intergenic 40.0%
!!! CATGCAACTATTTTGGTCTC+TGG + chr4.2:33059439-33059458 None:intergenic 40.0%
ACACTTGAGGGTGAGAATGT+CGG - chr4.2:33059584-33059603 MS.gene052302:intron 45.0%
ACATTCTCACCCTCAAGTGT+GGG + chr4.2:33059584-33059603 None:intergenic 45.0%
CGGGGGAGAAAAGTCATTTA+AGG + chr4.2:33059480-33059499 None:intergenic 45.0%
GGATCTTAATCCCACACTTG+AGG - chr4.2:33059571-33059590 MS.gene052302:intron 45.0%
GGGATTAAGATCCTCTCAAG+AGG + chr4.2:33059564-33059583 None:intergenic 45.0%
GGTCATCTTCATCACCATAC+TGG - chr4.2:33060109-33060128 MS.gene052302:CDS 45.0%
TAAATTTGGTCCGTTGAGGC+TGG - chr4.2:33059808-33059827 MS.gene052302:intron 45.0%
! CTACGTCTGTTGCTTATCCT+TGG + chr4.2:33059683-33059702 None:intergenic 45.0%
! GCAATTCGCTCTTCCAGTTT+TGG - chr4.2:33058882-33058901 MS.gene052302:CDS 45.0%
GACATTCTCACCCTCAAGTG+TGG + chr4.2:33059585-33059604 None:intergenic 50.0%
GCTGCAACAATGCCCAAAAC+TGG + chr4.2:33058898-33058917 None:intergenic 50.0%
TGATGTGTGGCGAGCATTAC+TGG - chr4.2:33060077-33060096 MS.gene052302:intron 50.0%
CACTGTCAGACCAGCCTCAA+CGG + chr4.2:33059821-33059840 None:intergenic 55.0%
! GTGAGACTAGTCACTGACCC+TGG + chr4.2:33059402-33059421 None:intergenic 55.0%
!! GTCTTCTAGCTCGCCTCTCT+CGG + chr4.2:33059115-33059134 None:intergenic 55.0%
!! TCTTCTAGCTCGCCTCTCTC+GGG + chr4.2:33059114-33059133 None:intergenic 55.0%
CAACATCCAGCTCCCGAGAG+AGG - chr4.2:33059099-33059118 MS.gene052302:intron 60.0%
CTCTCTCGGGAGCTGGATGT+TGG + chr4.2:33059101-33059120 None:intergenic 60.0%
AGCTCGCCTCTCTCGGGAGC+TGG + chr4.2:33059108-33059127 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 33058871 33060176 33058871 ID=MS.gene052302
chr4.2 mRNA 33058871 33060176 33058871 ID=MS.gene052302.t1;Parent=MS.gene052302
chr4.2 exon 33060084 33060176 33060084 ID=MS.gene052302.t1.exon1;Parent=MS.gene052302.t1
chr4.2 CDS 33060084 33060176 33060084 ID=cds.MS.gene052302.t1;Parent=MS.gene052302.t1
chr4.2 exon 33059907 33060000 33059907 ID=MS.gene052302.t1.exon2;Parent=MS.gene052302.t1
chr4.2 CDS 33059907 33060000 33059907 ID=cds.MS.gene052302.t1;Parent=MS.gene052302.t1
chr4.2 exon 33058871 33058986 33058871 ID=MS.gene052302.t1.exon3;Parent=MS.gene052302.t1
chr4.2 CDS 33058871 33058986 33058871 ID=cds.MS.gene052302.t1;Parent=MS.gene052302.t1
Gene Sequence

>MS.gene052302

ATGGATGCAATGCAATTCGCTCTTCCAGTTTTGGGCATTGTTGCAGCTGCAGCTGTGACCTTCTATGCAGTGAGTTTCAATGAGATTAGAGAGGTAAGTCACTAAGCAGCATCATCAACTATGTAATATATATTACTTGATATCTTTATCAATCTTATAAAATTGAATTATGACAGAAATCACTTCAAGATTGGGATGATTCTGAATCAGACAATGGAGGTTTTAGACCAACATCCAGCTCCCGAGAGAGGCGAGCTAGAAGACAAGCTAGTAAAAATACCAAAAAATAACTTCAACAGCAACGATAATTACTCTCTTTAAATGTTATGTTGTCTTTCATTTCTTTATTTTTGATGCTTGGTTTTATACTAAATAAATAGTAGCAAATTGTTTGTACTAGGTTGAGTGACCTTTTCAATAGTTCTTGTTGGTGCTCGTTGAATAGTGCTCGTGTTCCATTTTCTATTAGAAAAATGTAGAAAATTGTGTATCAAATTTGAGTTAGAAGTCACATTTTTTGTGTTTTCTCCAGGGTCAGTGACTAGTCTCACAACAAGTTGCACATCCAGAGACCAAAATAGTTGCATGTTCATTTTTACATCTCATCCTTAAATGACTTTTCTCCCCCGTTTTCAAATTTCAATGTTATACTCCTTTTATATTTTAATGGTCTAGATTCTCTCATTATTTCCTCTTGAGAGGATCTTAATCCCACACTTGAGGGTGAGAATGTCGGTTAGATTACCTATATGTTTTTCTTTTTGACAGTTGATTACCTAAACTATATTAGCAATGAGAAAGTAAACACGCCAAGGATAAGCAACAGACGTAGAATAGTATTTTTTTTTTTGGTCAAAAAATAGTAGTTTTTTATTACGTCGGTTTTTTTTTGGATAATAATACGTAGGTTGTACAGTCGATGAAAGAACAGGTGACTTAAATTTGGTCCGTTGAGGCTGGTCTGACAGTGTGATCACTAAAAAGTAATATCGGGTGTCTTTTATTGTGCATCACAAATCTGATTTAGTTTTACATTGCTTGTGTTTTGTGTTTTTTTTTTTTAGCTTGTGTTTTGTGTTTTTTTTTTTTAGAAGATATTAGTTTAATCATTCGTATGTCAATTAAATATAAGTCACCAAAACTCAAAGTTACCCGAAGTATTTTCCTTAATTTTGTTGGCTCAACTTCAGATGCTCGATATAACACTGATGTGTGGCGAGCATTACTGGATTGTCTACGGTCATCTTCATCACCATACTGGATTACGAGTATCAATCTCATCCCTTCCCTTGATAATAAAGTTTAA

Protein sequence

>MS.gene052302.t1

MDAMQFALPVLGIVAAAAVTFYAVSFNEIREKSLQDWDDSESDNGGFRPTSSSRERRARRQANARYNTDVWRALLDCLRSSSSPYWITSINLIPSLDNKV