AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0048950


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0048950 MtrunA17_Chr1g0159001 95.161 62 3 0 1 62 1 62 5.53e-29 97.4
Msa0048950 MtrunA17_Chr3g0126341 77.966 59 11 1 4 62 7 63 7.24e-25 87.0
Msa0048950 MtrunA17_Chr6g0485341 40.000 60 36 0 3 62 4 63 3.71e-12 55.1
Msa0048950 MtrunA17_Chr6g0485321 40.000 60 36 0 3 62 4 63 1.49e-11 53.5
Msa0048950 MtrunA17_Chr6g0485351 41.667 60 35 0 3 62 5 64 2.17e-11 53.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0048950 AT2G46330.1 66.000 50 15 1 13 62 15 62 6.66e-16 65.1
Msa0048950 AT3G61640.1 57.143 56 22 1 7 62 9 62 1.75e-15 63.9
Msa0048950 AT5G53250.1 76.923 39 9 0 24 62 25 63 1.00e-14 61.6

Find 11 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGCAAGGCCACCAGCATT+AGG 0.444107 1_2:-2046010 None:intergenic
TCACTTGTGGGAGCAGGAGC+AGG 0.473725 1_2:-2045151 None:intergenic
TTCTTCACAGTCTGTTGCTC+CGG 0.477404 1_2:+2045126 Msa0048950:CDS
GTGGGAGCAGGAGCAGGAGC+CGG 0.500195 1_2:-2045145 None:intergenic
TTAGGACATATGCTATTGCT+TGG 0.507960 1_2:-2045992 None:intergenic
TTACCATCACTTGTGGGAGC+AGG 0.532408 1_2:-2045157 None:intergenic
GCTCCTGCTCCCACAAGTGA+TGG 0.550760 1_2:+2045154 Msa0048950:CDS
AATAGCATATGTCCTAATGC+TGG 0.576700 1_2:+2045998 Msa0048950:CDS
AGCATATGTCCTAATGCTGG+TGG 0.610729 1_2:+2046001 Msa0048950:CDS
AAGATGCGTAAATAAGACCA+AGG 0.685667 1_2:-2045090 None:intergenic
AATGATGTAAGTGAGAAGCA+AGG 0.690125 1_2:-2046024 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAGATTATGATTTTAACAT+AGG + chr1_2:2045188-2045207 Msa0048950:intron 15.0%
!! TCAATCAAAAACTTTAAATA+AGG + chr1_2:2045431-2045450 Msa0048950:intron 15.0%
!! TAATAAATCTAGACTATATT+GGG + chr1_2:2045630-2045649 Msa0048950:intron 15.0%
!!! TTTGGTTTTTTTTTTTTCAA+CGG + chr1_2:2045758-2045777 Msa0048950:intron 15.0%
!! TGTTATTATTAACTGATAAT+AGG - chr1_2:2045785-2045804 None:intergenic 15.0%
!!! TAAGATTATGATTTTAACAT+AGG + chr1_2:2045188-2045207 Msa0048950:intron 15.0%
!! TCAATCAAAAACTTTAAATA+AGG + chr1_2:2045431-2045450 Msa0048950:intron 15.0%
!! TAATAAATCTAGACTATATT+GGG + chr1_2:2045630-2045649 Msa0048950:intron 15.0%
!!! TTTGGTTTTTTTTTTTTCAA+CGG + chr1_2:2045758-2045777 Msa0048950:intron 15.0%
!! TGTTATTATTAACTGATAAT+AGG - chr1_2:2045785-2045804 None:intergenic 15.0%
!! TCAAGAAAAATAACACAATT+AGG - chr1_2:2045285-2045304 None:intergenic 20.0%
!! CAATATAGTCTAGATTTATT+AGG - chr1_2:2045631-2045650 None:intergenic 20.0%
!! CTAATAAATCTAGACTATAT+TGG + chr1_2:2045629-2045648 Msa0048950:intron 20.0%
!!! GCCACAATTTAATTATTTTT+CGG + chr1_2:2045728-2045747 Msa0048950:intron 20.0%
!! ACCGAAAAATAATTAAATTG+TGG - chr1_2:2045732-2045751 None:intergenic 20.0%
!! CATTTGATACAATATAACTA+TGG - chr1_2:2045901-2045920 None:intergenic 20.0%
!!! AATTTTAATTATTAGCCATG+CGG - chr1_2:2045942-2045961 None:intergenic 20.0%
!!! AAATTGTTCTTAAATTTTGC+AGG + chr1_2:2045957-2045976 Msa0048950:intron 20.0%
!! TCAAGAAAAATAACACAATT+AGG - chr1_2:2045285-2045304 None:intergenic 20.0%
!! CAATATAGTCTAGATTTATT+AGG - chr1_2:2045631-2045650 None:intergenic 20.0%
!! CTAATAAATCTAGACTATAT+TGG + chr1_2:2045629-2045648 Msa0048950:intron 20.0%
!!! GCCACAATTTAATTATTTTT+CGG + chr1_2:2045728-2045747 Msa0048950:intron 20.0%
!! ACCGAAAAATAATTAAATTG+TGG - chr1_2:2045732-2045751 None:intergenic 20.0%
!! CATTTGATACAATATAACTA+TGG - chr1_2:2045901-2045920 None:intergenic 20.0%
!!! AATTTTAATTATTAGCCATG+CGG - chr1_2:2045942-2045961 None:intergenic 20.0%
!!! AAATTGTTCTTAAATTTTGC+AGG + chr1_2:2045957-2045976 Msa0048950:intron 20.0%
! TGTTTGTGAATTGTTAATCA+TGG - chr1_2:2045680-2045699 None:intergenic 25.0%
! TGATATAGTTCGATTCAAAA+AGG + chr1_2:2045808-2045827 Msa0048950:intron 25.0%
! ATACAATATAACTATGGAGT+GGG - chr1_2:2045895-2045914 None:intergenic 25.0%
! TTGTATCAAATGTAGTTGTA+TGG + chr1_2:2045909-2045928 Msa0048950:intron 25.0%
! TGTTTGTGAATTGTTAATCA+TGG - chr1_2:2045680-2045699 None:intergenic 25.0%
! TGATATAGTTCGATTCAAAA+AGG + chr1_2:2045808-2045827 Msa0048950:intron 25.0%
! ATACAATATAACTATGGAGT+GGG - chr1_2:2045895-2045914 None:intergenic 25.0%
! TTGTATCAAATGTAGTTGTA+TGG + chr1_2:2045909-2045928 Msa0048950:intron 25.0%
AAAAACTTACCATCACTTGT+GGG - chr1_2:2045166-2045185 None:intergenic 30.0%
TAAAAACTTACCATCACTTG+TGG - chr1_2:2045167-2045186 None:intergenic 30.0%
AATCCATGAACCATATAAGA+TGG - chr1_2:2045257-2045276 None:intergenic 30.0%
AAAAAGAGTTTCTCAACATG+AGG - chr1_2:2045394-2045413 None:intergenic 30.0%
!! TTATTTTTCGGTGTGACTTT+TGG + chr1_2:2045740-2045759 Msa0048950:intron 30.0%
TACAGTTCAACTTTCAGATA+TGG + chr1_2:2045831-2045850 Msa0048950:intron 30.0%
GATACAATATAACTATGGAG+TGG - chr1_2:2045896-2045915 None:intergenic 30.0%
AAAAACTTACCATCACTTGT+GGG - chr1_2:2045166-2045185 None:intergenic 30.0%
TAAAAACTTACCATCACTTG+TGG - chr1_2:2045167-2045186 None:intergenic 30.0%
AATCCATGAACCATATAAGA+TGG - chr1_2:2045257-2045276 None:intergenic 30.0%
AAAAAGAGTTTCTCAACATG+AGG - chr1_2:2045394-2045413 None:intergenic 30.0%
!! TTATTTTTCGGTGTGACTTT+TGG + chr1_2:2045740-2045759 Msa0048950:intron 30.0%
TACAGTTCAACTTTCAGATA+TGG + chr1_2:2045831-2045850 Msa0048950:intron 30.0%
GATACAATATAACTATGGAG+TGG - chr1_2:2045896-2045915 None:intergenic 30.0%
AAGATGCGTAAATAAGACCA+AGG - chr1_2:2045093-2045112 None:intergenic 35.0%
GTTGATCTCACCATCTTATA+TGG + chr1_2:2045244-2045263 Msa0048950:intron 35.0%
TCACCATCTTATATGGTTCA+TGG + chr1_2:2045251-2045270 Msa0048950:intron 35.0%
GCAATTTAGACTACAACATC+TGG + chr1_2:2045463-2045482 Msa0048950:intron 35.0%
GAATCACAGCTATACATGAT+TGG - chr1_2:2045535-2045554 None:intergenic 35.0%
AATCATGGTTCCATTCTCAT+CGG - chr1_2:2045665-2045684 None:intergenic 35.0%
TTAGGACATATGCTATTGCT+TGG - chr1_2:2045995-2046014 None:intergenic 35.0%
AATAGCATATGTCCTAATGC+TGG + chr1_2:2045998-2046017 Msa0048950:CDS 35.0%
AATGATGTAAGTGAGAAGCA+AGG - chr1_2:2046027-2046046 None:intergenic 35.0%
AAGATGCGTAAATAAGACCA+AGG - chr1_2:2045093-2045112 None:intergenic 35.0%
GTTGATCTCACCATCTTATA+TGG + chr1_2:2045244-2045263 Msa0048950:intron 35.0%
TCACCATCTTATATGGTTCA+TGG + chr1_2:2045251-2045270 Msa0048950:intron 35.0%
GCAATTTAGACTACAACATC+TGG + chr1_2:2045463-2045482 Msa0048950:intron 35.0%
GAATCACAGCTATACATGAT+TGG - chr1_2:2045535-2045554 None:intergenic 35.0%
AATCATGGTTCCATTCTCAT+CGG - chr1_2:2045665-2045684 None:intergenic 35.0%
TTAGGACATATGCTATTGCT+TGG - chr1_2:2045995-2046014 None:intergenic 35.0%
AATAGCATATGTCCTAATGC+TGG + chr1_2:2045998-2046017 Msa0048950:CDS 35.0%
AATGATGTAAGTGAGAAGCA+AGG - chr1_2:2046027-2046046 None:intergenic 35.0%
! TTACGCATCTTTTGCGTCAA+TGG + chr1_2:2045102-2045121 Msa0048950:CDS 40.0%
CTTCAACCAGAATCACATTG+TGG - chr1_2:2045507-2045526 None:intergenic 40.0%
! CAGATATGGATGCCTTTTGT+AGG + chr1_2:2045845-2045864 Msa0048950:intron 40.0%
! ATATGGATGCCTTTTGTAGG+AGG + chr1_2:2045848-2045867 Msa0048950:intron 40.0%
! TATGGATGCCTTTTGTAGGA+GGG + chr1_2:2045849-2045868 Msa0048950:intron 40.0%
TTGTATGGTTTCAAACCGCA+TGG + chr1_2:2045924-2045943 Msa0048950:intron 40.0%
! TTACGCATCTTTTGCGTCAA+TGG + chr1_2:2045102-2045121 Msa0048950:CDS 40.0%
CTTCAACCAGAATCACATTG+TGG - chr1_2:2045507-2045526 None:intergenic 40.0%
! CAGATATGGATGCCTTTTGT+AGG + chr1_2:2045845-2045864 Msa0048950:intron 40.0%
! ATATGGATGCCTTTTGTAGG+AGG + chr1_2:2045848-2045867 Msa0048950:intron 40.0%
! TATGGATGCCTTTTGTAGGA+GGG + chr1_2:2045849-2045868 Msa0048950:intron 40.0%
TTGTATGGTTTCAAACCGCA+TGG + chr1_2:2045924-2045943 Msa0048950:intron 40.0%
TTCTTCACAGTCTGTTGCTC+CGG + chr1_2:2045126-2045145 Msa0048950:CDS 45.0%
GATGGTGAGATCAACATCGA+AGG - chr1_2:2045239-2045258 None:intergenic 45.0%
CAGTGACCACAATGTGATTC+TGG + chr1_2:2045498-2045517 Msa0048950:intron 45.0%
! GTTTCATGCACCGATGAGAA+TGG + chr1_2:2045652-2045671 Msa0048950:intron 45.0%
! ATGGATGCCTTTTGTAGGAG+GGG + chr1_2:2045850-2045869 Msa0048950:intron 45.0%
AGCATATGTCCTAATGCTGG+TGG + chr1_2:2046001-2046020 Msa0048950:CDS 45.0%
TTCTTCACAGTCTGTTGCTC+CGG + chr1_2:2045126-2045145 Msa0048950:CDS 45.0%
GATGGTGAGATCAACATCGA+AGG - chr1_2:2045239-2045258 None:intergenic 45.0%
CAGTGACCACAATGTGATTC+TGG + chr1_2:2045498-2045517 Msa0048950:intron 45.0%
! GTTTCATGCACCGATGAGAA+TGG + chr1_2:2045652-2045671 Msa0048950:intron 45.0%
! ATGGATGCCTTTTGTAGGAG+GGG + chr1_2:2045850-2045869 Msa0048950:intron 45.0%
AGCATATGTCCTAATGCTGG+TGG + chr1_2:2046001-2046020 Msa0048950:CDS 45.0%
!! TTTTGGGTGGTCGTGTTCCT+TGG + chr1_2:2045073-2045092 Msa0048950:CDS 50.0%
TTACCATCACTTGTGGGAGC+AGG - chr1_2:2045160-2045179 None:intergenic 50.0%
!! TTTTGGGTGGTCGTGTTCCT+TGG + chr1_2:2045073-2045092 Msa0048950:CDS 50.0%
TTACCATCACTTGTGGGAGC+AGG - chr1_2:2045160-2045179 None:intergenic 50.0%
GTGAGCTCCCCTCCTACAAA+AGG - chr1_2:2045860-2045879 None:intergenic 55.0%
GAAGCAAGGCCACCAGCATT+AGG - chr1_2:2046013-2046032 None:intergenic 55.0%
GTGAGCTCCCCTCCTACAAA+AGG - chr1_2:2045860-2045879 None:intergenic 55.0%
GAAGCAAGGCCACCAGCATT+AGG - chr1_2:2046013-2046032 None:intergenic 55.0%
TCACTTGTGGGAGCAGGAGC+AGG - chr1_2:2045154-2045173 None:intergenic 60.0%
GCTCCTGCTCCCACAAGTGA+TGG + chr1_2:2045154-2045173 Msa0048950:CDS 60.0%
TCACTTGTGGGAGCAGGAGC+AGG - chr1_2:2045154-2045173 None:intergenic 60.0%
GCTCCTGCTCCCACAAGTGA+TGG + chr1_2:2045154-2045173 Msa0048950:CDS 60.0%
GTGGGAGCAGGAGCAGGAGC+CGG - chr1_2:2045148-2045167 None:intergenic 70.0%
GTGGGAGCAGGAGCAGGAGC+CGG - chr1_2:2045148-2045167 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 2045061 2046052 2045061 ID=Msa0048950;Name=Msa0048950
chr1_2 mRNA 2045061 2046052 2045061 ID=Msa0048950-mRNA-1;Parent=Msa0048950;Name=Msa0048950-mRNA-1;_AED=0.20;_eAED=0.20;_QI=0|0|0|0.5|1|1|2|0|62
chr1_2 exon 2045061 2045175 2045061 ID=Msa0048950-mRNA-1:exon:377;Parent=Msa0048950-mRNA-1
chr1_2 exon 2045979 2046052 2045979 ID=Msa0048950-mRNA-1:exon:378;Parent=Msa0048950-mRNA-1
chr1_2 CDS 2045061 2045175 2045061 ID=Msa0048950-mRNA-1:cds;Parent=Msa0048950-mRNA-1
chr1_2 CDS 2045979 2046052 2045979 ID=Msa0048950-mRNA-1:cds;Parent=Msa0048950-mRNA-1
Gene Sequence

>Msa0048950

ATGGCAGTTTCATTTTGGGTGGTCGTGTTCCTTGGTCTTATTTACGCATCTTTTGCGTCAATGGCTTCTTCACAGTCTGTTGCTCCGGCTCCTGCTCCTGCTCCCACAAGTGATGGAACATCAATTGACCAAGCAATAGCATATGTCCTAATGCTGGTGGCCTTGCTTCTCACTTACATCATTCATTAA

Protein sequence

>Msa0048950

MAVSFWVVVFLGLIYASFASMASSQSVAPAPAPAPTSDGTSIDQAIAYVLMLVALLLTYIIH*