AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0230140


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0230140 MtrunA17_Chr3g0137931 96.732 153 2 2 1 153 1 150 3.36e-107 301
Msa0230140 MtrunA17_Chr6g0477991 93.750 96 6 0 58 153 7 102 5.64e-65 193
Msa0230140 MtrunA17_Chr6g0476161 87.879 66 8 0 76 141 10 75 1.65e-38 127
Msa0230140 MtrunA17_Chr3g0138201 61.538 52 20 0 43 94 28 79 4.12e-19 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0230140 AT2G18660.1 37.879 132 68 5 23 151 7 127 1.78e-19 79.3
Msa0230140 AT4G30380.1 33.333 132 68 6 27 152 5 122 4.97e-11 57.0

Find 31 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGGTACTGCTTCTTCTTA+TGG 0.173763 2_2:+1987499 Msa0230140:CDS
CAACATTGATATTTGCATTA+GGG 0.294856 2_2:-1988298 None:intergenic
TGCTCATTTGTTTGAGCAAT+AGG 0.304172 2_2:-1987462 None:intergenic
TCAACATTGATATTTGCATT+AGG 0.306005 2_2:-1988299 None:intergenic
ACTGCCACAAATATATTTCC+TGG 0.404012 2_2:-1988080 None:intergenic
CTACAGCTTGTGATGGGAAT+AGG 0.406360 2_2:+1988042 Msa0230140:CDS
TGGGTGTACTCACGTATATA+TGG 0.432788 2_2:-1987526 None:intergenic
AATGAAGGGTTGTGGGATAA+TGG 0.441192 2_2:+1988104 Msa0230140:CDS
AGCATTATTCTTGCAGATGT+TGG 0.481138 2_2:+1987481 Msa0230140:CDS
TGGCAGTGAATGAAGGGTTG+TGG 0.485625 2_2:+1988096 Msa0230140:CDS
ATATTTGTGGCAGTGAATGA+AGG 0.490865 2_2:+1988089 Msa0230140:CDS
TACAGAGTAAGGTGTGTAAG+TGG 0.500626 2_2:+1988146 Msa0230140:CDS
GGCAGTGAATGAAGGGTTGT+GGG 0.502397 2_2:+1988097 Msa0230140:CDS
ATCAATAAGCCATGCAAAGG+TGG 0.523686 2_2:+1988170 Msa0230140:CDS
TCCACCAGGAAATATATTTG+TGG 0.549161 2_2:+1988076 Msa0230140:CDS
AGTTGACATGTGGAAAGTGT+GGG 0.573051 2_2:-1988249 None:intergenic
CAGTTGACATGTGGAAAGTG+TGG 0.576339 2_2:-1988250 None:intergenic
ATACTACTACCACCTTTGCA+TGG 0.578652 2_2:-1988179 None:intergenic
GTGGAAGGAGATACAGAGTA+AGG 0.582766 2_2:+1988135 Msa0230140:CDS
TGGGATAATGGTGCAGCATG+TGG 0.603337 2_2:+1988116 Msa0230140:CDS
GGAATCAATAAGCCATGCAA+AGG 0.623535 2_2:+1988167 Msa0230140:CDS
TATTTGTGGCAGTGAATGAA+GGG 0.626127 2_2:+1988090 Msa0230140:CDS
TGTGCAGCTACAGCTTGTGA+TGG 0.627923 2_2:+1988035 Msa0230140:intron
GTGCAGCTACAGCTTGTGAT+GGG 0.628864 2_2:+1988036 Msa0230140:intron
GCCACAAATATATTTCCTGG+TGG 0.638508 2_2:-1988077 None:intergenic
CAAATGCTTCAGTTGACATG+TGG 0.644023 2_2:-1988259 None:intergenic
ATAATGGTGCAGCATGTGGA+AGG 0.648736 2_2:+1988120 Msa0230140:CDS
AGGAGACAACAGTTTCCACC+AGG 0.667613 2_2:+1988062 Msa0230140:CDS
GTGTACTCACGTATATATGG+AGG 0.706847 2_2:-1987523 None:intergenic
TTGACATGTGGAAAGTGTGG+GGG 0.720155 2_2:-1988247 None:intergenic
GTTGACATGTGGAAAGTGTG+GGG 0.728941 2_2:-1988248 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAATATTGAATGAATAAA+TGG - chr2_2:1987552-1987571 None:intergenic 15.0%
!! AGAAATATTGAATGAATAAA+TGG - chr2_2:1987552-1987571 None:intergenic 15.0%
!! ATATTGAATGAATAAATGGT+GGG - chr2_2:1987548-1987567 None:intergenic 20.0%
!! AATATTGAATGAATAAATGG+TGG - chr2_2:1987549-1987568 None:intergenic 20.0%
!! TATTTAACGTGGAAAAAAAA+TGG - chr2_2:1987610-1987629 None:intergenic 20.0%
!!! GTTCCAAACATTTTAAAAAT+GGG - chr2_2:1987861-1987880 None:intergenic 20.0%
!! ATTAATATGTGAAATTTGTG+TGG - chr2_2:1987883-1987902 None:intergenic 20.0%
!! ATATTGAATGAATAAATGGT+GGG - chr2_2:1987548-1987567 None:intergenic 20.0%
!! AATATTGAATGAATAAATGG+TGG - chr2_2:1987549-1987568 None:intergenic 20.0%
!! TATTTAACGTGGAAAAAAAA+TGG - chr2_2:1987610-1987629 None:intergenic 20.0%
!!! GTTCCAAACATTTTAAAAAT+GGG - chr2_2:1987861-1987880 None:intergenic 20.0%
!! ATTAATATGTGAAATTTGTG+TGG - chr2_2:1987883-1987902 None:intergenic 20.0%
!!! AACTATGATTTTTTGCTTGA+TGG - chr2_2:1987375-1987394 None:intergenic 25.0%
! TAGCTCAAAAACAAATAATG+AGG + chr2_2:1987410-1987429 Msa0230140:CDS 25.0%
! ATGATATATCATGTATACGT+AGG - chr2_2:1987579-1987598 None:intergenic 25.0%
! AGTGTTAAACTAAATGTTGA+TGG - chr2_2:1987793-1987812 None:intergenic 25.0%
!!! AGTCCCATTTTTAAAATGTT+TGG + chr2_2:1987855-1987874 Msa0230140:intron 25.0%
!!! GGTTCCAAACATTTTAAAAA+TGG - chr2_2:1987862-1987881 None:intergenic 25.0%
! CAACATTGATATTTGCATTA+GGG - chr2_2:1988301-1988320 None:intergenic 25.0%
! TCAACATTGATATTTGCATT+AGG - chr2_2:1988302-1988321 None:intergenic 25.0%
!!! AACTATGATTTTTTGCTTGA+TGG - chr2_2:1987375-1987394 None:intergenic 25.0%
! TAGCTCAAAAACAAATAATG+AGG + chr2_2:1987410-1987429 Msa0230140:CDS 25.0%
! ATGATATATCATGTATACGT+AGG - chr2_2:1987579-1987598 None:intergenic 25.0%
! AGTGTTAAACTAAATGTTGA+TGG - chr2_2:1987793-1987812 None:intergenic 25.0%
!!! AGTCCCATTTTTAAAATGTT+TGG + chr2_2:1987855-1987874 Msa0230140:intron 25.0%
!!! GGTTCCAAACATTTTAAAAA+TGG - chr2_2:1987862-1987881 None:intergenic 25.0%
! CAACATTGATATTTGCATTA+GGG - chr2_2:1988301-1988320 None:intergenic 25.0%
! TCAACATTGATATTTGCATT+AGG - chr2_2:1988302-1988321 None:intergenic 25.0%
!! AAAGAGATTAGTCTCCTATA+AGG - chr2_2:1987663-1987682 None:intergenic 30.0%
AACCAATCGGTATCATTATA+GGG - chr2_2:1987692-1987711 None:intergenic 30.0%
!! AAAGAGATTAGTCTCCTATA+AGG - chr2_2:1987663-1987682 None:intergenic 30.0%
AACCAATCGGTATCATTATA+GGG - chr2_2:1987692-1987711 None:intergenic 30.0%
TGCTCATTTGTTTGAGCAAT+AGG - chr2_2:1987465-1987484 None:intergenic 35.0%
AGCATTATTCTTGCAGATGT+TGG + chr2_2:1987481-1987500 Msa0230140:CDS 35.0%
!! AGAGGTGTTGATATTTAACG+TGG - chr2_2:1987621-1987640 None:intergenic 35.0%
AGTTTAGTGCATCACCTTAT+AGG + chr2_2:1987646-1987665 Msa0230140:intron 35.0%
ACCAATCGGTATCATTATAG+GGG - chr2_2:1987691-1987710 None:intergenic 35.0%
CAACCAATCGGTATCATTAT+AGG - chr2_2:1987693-1987712 None:intergenic 35.0%
! CTATAATGATACCGATTGGT+TGG + chr2_2:1987691-1987710 Msa0230140:intron 35.0%
TCCACCAGGAAATATATTTG+TGG + chr2_2:1988076-1988095 Msa0230140:CDS 35.0%
ACTGCCACAAATATATTTCC+TGG - chr2_2:1988083-1988102 None:intergenic 35.0%
ATATTTGTGGCAGTGAATGA+AGG + chr2_2:1988089-1988108 Msa0230140:CDS 35.0%
TATTTGTGGCAGTGAATGAA+GGG + chr2_2:1988090-1988109 Msa0230140:CDS 35.0%
TGCTCATTTGTTTGAGCAAT+AGG - chr2_2:1987465-1987484 None:intergenic 35.0%
AGCATTATTCTTGCAGATGT+TGG + chr2_2:1987481-1987500 Msa0230140:CDS 35.0%
!! AGAGGTGTTGATATTTAACG+TGG - chr2_2:1987621-1987640 None:intergenic 35.0%
AGTTTAGTGCATCACCTTAT+AGG + chr2_2:1987646-1987665 Msa0230140:intron 35.0%
ACCAATCGGTATCATTATAG+GGG - chr2_2:1987691-1987710 None:intergenic 35.0%
CAACCAATCGGTATCATTAT+AGG - chr2_2:1987693-1987712 None:intergenic 35.0%
! CTATAATGATACCGATTGGT+TGG + chr2_2:1987691-1987710 Msa0230140:intron 35.0%
TCCACCAGGAAATATATTTG+TGG + chr2_2:1988076-1988095 Msa0230140:CDS 35.0%
ACTGCCACAAATATATTTCC+TGG - chr2_2:1988083-1988102 None:intergenic 35.0%
ATATTTGTGGCAGTGAATGA+AGG + chr2_2:1988089-1988108 Msa0230140:CDS 35.0%
TATTTGTGGCAGTGAATGAA+GGG + chr2_2:1988090-1988109 Msa0230140:CDS 35.0%
GTTGGTACTGCTTCTTCTTA+TGG + chr2_2:1987499-1987518 Msa0230140:CDS 40.0%
GTGTACTCACGTATATATGG+AGG - chr2_2:1987526-1987545 None:intergenic 40.0%
TGGGTGTACTCACGTATATA+TGG - chr2_2:1987529-1987548 None:intergenic 40.0%
GATGCACTAAACTACAAGAG+AGG - chr2_2:1987639-1987658 None:intergenic 40.0%
ACCCCTATAATGATACCGAT+TGG + chr2_2:1987687-1987706 Msa0230140:intron 40.0%
! TAATGATACCGATTGGTTGG+AGG + chr2_2:1987694-1987713 Msa0230140:intron 40.0%
! TTTTACCACCTCCAACCAAT+CGG - chr2_2:1987705-1987724 None:intergenic 40.0%
GCCACAAATATATTTCCTGG+TGG - chr2_2:1988080-1988099 None:intergenic 40.0%
AATGAAGGGTTGTGGGATAA+TGG + chr2_2:1988104-1988123 Msa0230140:CDS 40.0%
TACAGAGTAAGGTGTGTAAG+TGG + chr2_2:1988146-1988165 Msa0230140:CDS 40.0%
GGAATCAATAAGCCATGCAA+AGG + chr2_2:1988167-1988186 Msa0230140:CDS 40.0%
ATCAATAAGCCATGCAAAGG+TGG + chr2_2:1988170-1988189 Msa0230140:CDS 40.0%
ATACTACTACCACCTTTGCA+TGG - chr2_2:1988182-1988201 None:intergenic 40.0%
! AGTTGACATGTGGAAAGTGT+GGG - chr2_2:1988252-1988271 None:intergenic 40.0%
CAAATGCTTCAGTTGACATG+TGG - chr2_2:1988262-1988281 None:intergenic 40.0%
GTTGGTACTGCTTCTTCTTA+TGG + chr2_2:1987499-1987518 Msa0230140:CDS 40.0%
GTGTACTCACGTATATATGG+AGG - chr2_2:1987526-1987545 None:intergenic 40.0%
TGGGTGTACTCACGTATATA+TGG - chr2_2:1987529-1987548 None:intergenic 40.0%
GATGCACTAAACTACAAGAG+AGG - chr2_2:1987639-1987658 None:intergenic 40.0%
ACCCCTATAATGATACCGAT+TGG + chr2_2:1987687-1987706 Msa0230140:intron 40.0%
! TAATGATACCGATTGGTTGG+AGG + chr2_2:1987694-1987713 Msa0230140:intron 40.0%
! TTTTACCACCTCCAACCAAT+CGG - chr2_2:1987705-1987724 None:intergenic 40.0%
GCCACAAATATATTTCCTGG+TGG - chr2_2:1988080-1988099 None:intergenic 40.0%
AATGAAGGGTTGTGGGATAA+TGG + chr2_2:1988104-1988123 Msa0230140:CDS 40.0%
TACAGAGTAAGGTGTGTAAG+TGG + chr2_2:1988146-1988165 Msa0230140:CDS 40.0%
GGAATCAATAAGCCATGCAA+AGG + chr2_2:1988167-1988186 Msa0230140:CDS 40.0%
ATCAATAAGCCATGCAAAGG+TGG + chr2_2:1988170-1988189 Msa0230140:CDS 40.0%
ATACTACTACCACCTTTGCA+TGG - chr2_2:1988182-1988201 None:intergenic 40.0%
! AGTTGACATGTGGAAAGTGT+GGG - chr2_2:1988252-1988271 None:intergenic 40.0%
CAAATGCTTCAGTTGACATG+TGG - chr2_2:1988262-1988281 None:intergenic 40.0%
! CTACAGCTTGTGATGGGAAT+AGG + chr2_2:1988042-1988061 Msa0230140:CDS 45.0%
ATAATGGTGCAGCATGTGGA+AGG + chr2_2:1988120-1988139 Msa0230140:CDS 45.0%
GTGGAAGGAGATACAGAGTA+AGG + chr2_2:1988135-1988154 Msa0230140:CDS 45.0%
! TTGACATGTGGAAAGTGTGG+GGG - chr2_2:1988250-1988269 None:intergenic 45.0%
! GTTGACATGTGGAAAGTGTG+GGG - chr2_2:1988251-1988270 None:intergenic 45.0%
CAGTTGACATGTGGAAAGTG+TGG - chr2_2:1988253-1988272 None:intergenic 45.0%
! CTACAGCTTGTGATGGGAAT+AGG + chr2_2:1988042-1988061 Msa0230140:CDS 45.0%
ATAATGGTGCAGCATGTGGA+AGG + chr2_2:1988120-1988139 Msa0230140:CDS 45.0%
GTGGAAGGAGATACAGAGTA+AGG + chr2_2:1988135-1988154 Msa0230140:CDS 45.0%
! TTGACATGTGGAAAGTGTGG+GGG - chr2_2:1988250-1988269 None:intergenic 45.0%
! GTTGACATGTGGAAAGTGTG+GGG - chr2_2:1988251-1988270 None:intergenic 45.0%
CAGTTGACATGTGGAAAGTG+TGG - chr2_2:1988253-1988272 None:intergenic 45.0%
! TGATACCGATTGGTTGGAGG+TGG + chr2_2:1987697-1987716 Msa0230140:intron 50.0%
TGTGCAGCTACAGCTTGTGA+TGG + chr2_2:1988035-1988054 Msa0230140:intron 50.0%
GTGCAGCTACAGCTTGTGAT+GGG + chr2_2:1988036-1988055 Msa0230140:intron 50.0%
AGGAGACAACAGTTTCCACC+AGG + chr2_2:1988062-1988081 Msa0230140:CDS 50.0%
TGGCAGTGAATGAAGGGTTG+TGG + chr2_2:1988096-1988115 Msa0230140:CDS 50.0%
GGCAGTGAATGAAGGGTTGT+GGG + chr2_2:1988097-1988116 Msa0230140:CDS 50.0%
! TGGGATAATGGTGCAGCATG+TGG + chr2_2:1988116-1988135 Msa0230140:CDS 50.0%
! TGATACCGATTGGTTGGAGG+TGG + chr2_2:1987697-1987716 Msa0230140:intron 50.0%
TGTGCAGCTACAGCTTGTGA+TGG + chr2_2:1988035-1988054 Msa0230140:intron 50.0%
GTGCAGCTACAGCTTGTGAT+GGG + chr2_2:1988036-1988055 Msa0230140:intron 50.0%
AGGAGACAACAGTTTCCACC+AGG + chr2_2:1988062-1988081 Msa0230140:CDS 50.0%
TGGCAGTGAATGAAGGGTTG+TGG + chr2_2:1988096-1988115 Msa0230140:CDS 50.0%
GGCAGTGAATGAAGGGTTGT+GGG + chr2_2:1988097-1988116 Msa0230140:CDS 50.0%
! TGGGATAATGGTGCAGCATG+TGG + chr2_2:1988116-1988135 Msa0230140:CDS 50.0%
! GTGGAAAGTGTGGGGGCATG+AGG - chr2_2:1988243-1988262 None:intergenic 60.0%
! GTGGAAAGTGTGGGGGCATG+AGG - chr2_2:1988243-1988262 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 1987367 1988334 1987367 ID=Msa0230140;Name=Msa0230140
chr2_2 mRNA 1987367 1988334 1987367 ID=Msa0230140-mRNA-1;Parent=Msa0230140;Name=Msa0230140-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|153
chr2_2 exon 1987367 1987535 1987367 ID=Msa0230140-mRNA-1:exon:760;Parent=Msa0230140-mRNA-1
chr2_2 exon 1988042 1988334 1988042 ID=Msa0230140-mRNA-1:exon:761;Parent=Msa0230140-mRNA-1
chr2_2 CDS 1987367 1987535 1987367 ID=Msa0230140-mRNA-1:cds;Parent=Msa0230140-mRNA-1
chr2_2 CDS 1988042 1988334 1988042 ID=Msa0230140-mRNA-1:cds;Parent=Msa0230140-mRNA-1
Gene Sequence

>Msa0230140

ATGTACCATCAAGCAAAAAATCATAGTTTGCGTATATCAATCATAGCTCAAAAACAAATAATGAGGTCATTTATGCTTGTTGTAATAATTTCAAGCCTATTGCTCAAACAAATGAGCATTATTCTTGCAGATGTTGGTACTGCTTCTTCTTATGGTCCTCCATATATACCTACAGCTTGTGATGGGAATAGGAGACAACAGTTTCCACCAGGAAATATATTTGTGGCAGTGAATGAAGGGTTGTGGGATAATGGTGCAGCATGTGGAAGGAGATACAGAGTAAGGTGTGTAAGTGGAATCAATAAGCCATGCAAAGGTGGTAGTAGTATTGATGTTAAAGTTGTTGATTCTATTACTTGTACAAGATCCTCATGCCCCCACACTTTCCACATGTCAACTGAAGCATTTGCAGCTATCTCACGCTTCCCTAATGCAAATATCAATGTTGAATACATTCAGTAA

Protein sequence

>Msa0230140

MYHQAKNHSLRISIIAQKQIMRSFMLVVIISSLLLKQMSIILADVGTASSYGPPYIPTACDGNRRQQFPPGNIFVAVNEGLWDNGAACGRRYRVRCVSGINKPCKGGSSIDVKVVDSITCTRSSCPHTFHMSTEAFAAISRFPNANINVEYIQ*