AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1214750

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1214750 MtrunA17_Chr4g0063791 91.061 179 2 5 1 168 1 176 4.43e-111 313
Msa1214750 MtrunA17_Chr2g0333051 38.889 144 65 4 28 163 5 133 6.45e-19 78.2
Msa1214750 MtrunA17_Chr4g0003391 38.356 146 61 8 28 168 5 126 2.57e-14 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1214750 AT3G15760.1 39.568 139 68 5 31 167 9 133 3.19e-16 71.6
Msa1214750 AT1G52565.1 40.741 135 57 5 28 160 8 121 4.74e-15 68.2

Find 36 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGATCTACTATATTATTT+TGG 0.176418 8_1:-75522970 None:intergenic
GATTGGCTTATTGTTGAATT+TGG 0.199091 8_1:+75522578 Msa1214750:exon
CTATTCTGTTAAGGTGAATT+AGG 0.229252 8_1:+75522770 Msa1214750:three_prime_UTR
TACAAAGCTGCTCTGTTTGC+AGG 0.285163 8_1:-75522523 None:intergenic
AACAGAGCAGCTTTGTATAA+TGG 0.334899 8_1:+75522529 Msa1214750:CDS
TCTCTTCATAACTCTAATAA+AGG 0.367080 8_1:+75522879 Msa1214750:three_prime_UTR
TTATTACCTCTATTCTGTTA+AGG 0.389886 8_1:+75522761 Msa1214750:three_prime_UTR
AAACATGGTGAAGAGAGAAT+TGG 0.390105 8_1:-75522153 None:intergenic
AACATGGTGAAGAGAGAATT+GGG 0.400815 8_1:-75522152 None:intergenic
CTACGTTCTTGTTTATCCTC+TGG 0.413516 8_1:+75522208 Msa1214750:CDS
GATAAACAAGAACGTAGAAT+AGG 0.433110 8_1:-75522202 None:intergenic
CCGAACTAAAATTTGAACAT+TGG 0.462032 8_1:-75522918 None:intergenic
TGAAGAAAAGAAGAAAGGAT+TGG 0.472608 8_1:-75522031 None:intergenic
TTTGATGAAAAGTGAGAAAG+TGG 0.480831 8_1:-75522006 None:intergenic
GAAATTGAATTCAAGATCAA+AGG 0.482344 8_1:+75522459 Msa1214750:CDS
TCTAGAAGTACAGTAAAAGT+AGG 0.512331 8_1:+75522694 Msa1214750:three_prime_UTR
AAGGTTCAAAAGAATTGTAA+TGG 0.522701 8_1:+75522478 Msa1214750:CDS
GTTGTGGATTCATGTAAAGA+TGG 0.540155 8_1:+75522373 Msa1214750:CDS
AATTCACCTTAACAGAATAG+AGG 0.541511 8_1:-75522767 None:intergenic
GCAACCGCCATGGCTGTCTC+CGG 0.543566 8_1:+75522094 Msa1214750:CDS
AGATCGTGTGAATCAACGAT+TGG 0.545757 8_1:+75522561 Msa1214750:CDS
CATATTAGAAGCAGCCAACA+AGG 0.553674 8_1:-75521975 None:intergenic
GTTCAAAAGAATTGTAATGG+TGG 0.561934 8_1:+75522481 Msa1214750:CDS
TGCTGTCTTTGCAACCGCCA+TGG 0.563392 8_1:+75522084 Msa1214750:CDS
AGCAAGGATGATGACTGTGC+CGG 0.571426 8_1:-75522113 None:intergenic
TAGGAAATAGAAGTTGATGA+AGG 0.571660 8_1:+75522713 Msa1214750:three_prime_UTR
ATTTCTGAAGACGGAGAGCA+AGG 0.583155 8_1:-75522129 None:intergenic
AGAATTGGGATTTCTGAAGA+CGG 0.611480 8_1:-75522138 None:intergenic
GACTGTGCCGGAGACAGCCA+TGG 0.611754 8_1:-75522101 None:intergenic
TGCAAAGACAGCACCTTGTG+AGG 0.629596 8_1:-75522074 None:intergenic
CTCTAATAAAGGAAATTATG+CGG 0.638575 8_1:+75522890 Msa1214750:three_prime_UTR
TCTTCAATGATTACCTCACA+AGG 0.650992 8_1:+75522061 Msa1214750:CDS
ATATTAGAAGCAGCCAACAA+GGG 0.667558 8_1:-75521974 None:intergenic
AATGGTGGAAACGAGAACAG+AGG 0.717333 8_1:+75522496 Msa1214750:CDS
GAGTACAGAAAACAACAACA+TGG 0.720965 8_1:+75522400 Msa1214750:CDS
TGTGCCGGAGACAGCCATGG+CGG 0.736789 8_1:-75522098 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTGTTAACATAATTCT+TGG + chr8_1:75522289-75522308 Msa1214750:intron 15.0%
!!! ATAATTTTGTTCATAGTTTT+AGG + chr8_1:75522805-75522824 Msa1214750:three_prime_UTR 15.0%
!!! TAATCTTGTTCATATTTTTT+AGG + chr8_1:75522829-75522848 Msa1214750:three_prime_UTR 15.0%
!!! AATCTTGTTCATATTTTTTA+GGG + chr8_1:75522830-75522849 Msa1214750:three_prime_UTR 15.0%
!!! TTTTTTGTTAACATAATTCT+TGG + chr8_1:75522289-75522308 Msa1214750:intron 15.0%
!!! ATAATTTTGTTCATAGTTTT+AGG + chr8_1:75522805-75522824 Msa1214750:three_prime_UTR 15.0%
!!! TAATCTTGTTCATATTTTTT+AGG + chr8_1:75522829-75522848 Msa1214750:three_prime_UTR 15.0%
!!! AATCTTGTTCATATTTTTTA+GGG + chr8_1:75522830-75522849 Msa1214750:three_prime_UTR 15.0%
!!! TGTTTTGAAGAAAAGAAGAA+AGG - chr8_1:75522039-75522058 None:intergenic 25.0%
!! AACAAGGTTTTTCTCTTTTT+AGG + chr8_1:75522261-75522280 Msa1214750:intron 25.0%
!! ACAAGGTTTTTCTCTTTTTA+GGG + chr8_1:75522262-75522281 Msa1214750:intron 25.0%
!!! TTCTTTGTTTTCTTTTCATC+TGG - chr8_1:75522322-75522341 None:intergenic 25.0%
! GAAATTGAATTCAAGATCAA+AGG + chr8_1:75522459-75522478 Msa1214750:CDS 25.0%
! AAGGTTCAAAAGAATTGTAA+TGG + chr8_1:75522478-75522497 Msa1214750:CDS 25.0%
! TTATTACCTCTATTCTGTTA+AGG + chr8_1:75522761-75522780 Msa1214750:three_prime_UTR 25.0%
!!! TTAGGGTAATTTTGTTATGT+TGG + chr8_1:75522847-75522866 Msa1214750:three_prime_UTR 25.0%
! TCTCTTCATAACTCTAATAA+AGG + chr8_1:75522879-75522898 Msa1214750:three_prime_UTR 25.0%
! CTCTAATAAAGGAAATTATG+CGG + chr8_1:75522890-75522909 Msa1214750:three_prime_UTR 25.0%
!!! CCAATGTTCAAATTTTAGTT+CGG + chr8_1:75522918-75522937 Msa1214750:three_prime_UTR 25.0%
!!! TGTTTTGAAGAAAAGAAGAA+AGG - chr8_1:75522039-75522058 None:intergenic 25.0%
!! AACAAGGTTTTTCTCTTTTT+AGG + chr8_1:75522261-75522280 Msa1214750:intron 25.0%
!! ACAAGGTTTTTCTCTTTTTA+GGG + chr8_1:75522262-75522281 Msa1214750:intron 25.0%
!!! TTCTTTGTTTTCTTTTCATC+TGG - chr8_1:75522322-75522341 None:intergenic 25.0%
! GAAATTGAATTCAAGATCAA+AGG + chr8_1:75522459-75522478 Msa1214750:CDS 25.0%
! AAGGTTCAAAAGAATTGTAA+TGG + chr8_1:75522478-75522497 Msa1214750:CDS 25.0%
! TTATTACCTCTATTCTGTTA+AGG + chr8_1:75522761-75522780 Msa1214750:three_prime_UTR 25.0%
!!! TTAGGGTAATTTTGTTATGT+TGG + chr8_1:75522847-75522866 Msa1214750:three_prime_UTR 25.0%
! TCTCTTCATAACTCTAATAA+AGG + chr8_1:75522879-75522898 Msa1214750:three_prime_UTR 25.0%
! CTCTAATAAAGGAAATTATG+CGG + chr8_1:75522890-75522909 Msa1214750:three_prime_UTR 25.0%
!!! CCAATGTTCAAATTTTAGTT+CGG + chr8_1:75522918-75522937 Msa1214750:three_prime_UTR 25.0%
TTTGATGAAAAGTGAGAAAG+TGG - chr8_1:75522009-75522028 None:intergenic 30.0%
TGAAGAAAAGAAGAAAGGAT+TGG - chr8_1:75522034-75522053 None:intergenic 30.0%
AAGAAGAAGAAGAAGAAACA+TGG - chr8_1:75522171-75522190 None:intergenic 30.0%
GATAAACAAGAACGTAGAAT+AGG - chr8_1:75522205-75522224 None:intergenic 30.0%
AGTAAAAAGTAACTTACCAG+AGG - chr8_1:75522227-75522246 None:intergenic 30.0%
!!! GAAAAGAGTTAGTTTTGCTA+AGG + chr8_1:75522348-75522367 Msa1214750:CDS 30.0%
GTTCAAAAGAATTGTAATGG+TGG + chr8_1:75522481-75522500 Msa1214750:CDS 30.0%
!! GATTGGCTTATTGTTGAATT+TGG + chr8_1:75522578-75522597 Msa1214750:exon 30.0%
! TCTAGAAGTACAGTAAAAGT+AGG + chr8_1:75522694-75522713 Msa1214750:three_prime_UTR 30.0%
!! TAGGAAATAGAAGTTGATGA+AGG + chr8_1:75522713-75522732 Msa1214750:three_prime_UTR 30.0%
!! TAACTGCAACTATGTTTTTG+TGG - chr8_1:75522744-75522763 None:intergenic 30.0%
AATTCACCTTAACAGAATAG+AGG - chr8_1:75522770-75522789 None:intergenic 30.0%
CTATTCTGTTAAGGTGAATT+AGG + chr8_1:75522770-75522789 Msa1214750:three_prime_UTR 30.0%
CCGAACTAAAATTTGAACAT+TGG - chr8_1:75522921-75522940 None:intergenic 30.0%
TTTGATGAAAAGTGAGAAAG+TGG - chr8_1:75522009-75522028 None:intergenic 30.0%
TGAAGAAAAGAAGAAAGGAT+TGG - chr8_1:75522034-75522053 None:intergenic 30.0%
AAGAAGAAGAAGAAGAAACA+TGG - chr8_1:75522171-75522190 None:intergenic 30.0%
GATAAACAAGAACGTAGAAT+AGG - chr8_1:75522205-75522224 None:intergenic 30.0%
AGTAAAAAGTAACTTACCAG+AGG - chr8_1:75522227-75522246 None:intergenic 30.0%
!!! GAAAAGAGTTAGTTTTGCTA+AGG + chr8_1:75522348-75522367 Msa1214750:CDS 30.0%
GTTCAAAAGAATTGTAATGG+TGG + chr8_1:75522481-75522500 Msa1214750:CDS 30.0%
!! GATTGGCTTATTGTTGAATT+TGG + chr8_1:75522578-75522597 Msa1214750:exon 30.0%
! TCTAGAAGTACAGTAAAAGT+AGG + chr8_1:75522694-75522713 Msa1214750:three_prime_UTR 30.0%
!! TAGGAAATAGAAGTTGATGA+AGG + chr8_1:75522713-75522732 Msa1214750:three_prime_UTR 30.0%
!! TAACTGCAACTATGTTTTTG+TGG - chr8_1:75522744-75522763 None:intergenic 30.0%
AATTCACCTTAACAGAATAG+AGG - chr8_1:75522770-75522789 None:intergenic 30.0%
CTATTCTGTTAAGGTGAATT+AGG + chr8_1:75522770-75522789 Msa1214750:three_prime_UTR 30.0%
CCGAACTAAAATTTGAACAT+TGG - chr8_1:75522921-75522940 None:intergenic 30.0%
TCTTCAATGATTACCTCACA+AGG + chr8_1:75522061-75522080 Msa1214750:CDS 35.0%
! AGAATTGGGATTTCTGAAGA+CGG - chr8_1:75522141-75522160 None:intergenic 35.0%
AACATGGTGAAGAGAGAATT+GGG - chr8_1:75522155-75522174 None:intergenic 35.0%
AAACATGGTGAAGAGAGAAT+TGG - chr8_1:75522156-75522175 None:intergenic 35.0%
CTACACACATTGAACAAACA+AGG + chr8_1:75522245-75522264 Msa1214750:intron 35.0%
!! TAGTTTTGCTAAGGATGTTG+TGG + chr8_1:75522357-75522376 Msa1214750:CDS 35.0%
GTTGTGGATTCATGTAAAGA+TGG + chr8_1:75522373-75522392 Msa1214750:CDS 35.0%
GAGTACAGAAAACAACAACA+TGG + chr8_1:75522400-75522419 Msa1214750:CDS 35.0%
! AACAGAGCAGCTTTGTATAA+TGG + chr8_1:75522529-75522548 Msa1214750:CDS 35.0%
!! TGCAACTATGTTTTTGTGGT+GGG - chr8_1:75522740-75522759 None:intergenic 35.0%
TCTTCAATGATTACCTCACA+AGG + chr8_1:75522061-75522080 Msa1214750:CDS 35.0%
! AGAATTGGGATTTCTGAAGA+CGG - chr8_1:75522141-75522160 None:intergenic 35.0%
AACATGGTGAAGAGAGAATT+GGG - chr8_1:75522155-75522174 None:intergenic 35.0%
AAACATGGTGAAGAGAGAAT+TGG - chr8_1:75522156-75522175 None:intergenic 35.0%
CTACACACATTGAACAAACA+AGG + chr8_1:75522245-75522264 Msa1214750:intron 35.0%
!! TAGTTTTGCTAAGGATGTTG+TGG + chr8_1:75522357-75522376 Msa1214750:CDS 35.0%
GTTGTGGATTCATGTAAAGA+TGG + chr8_1:75522373-75522392 Msa1214750:CDS 35.0%
GAGTACAGAAAACAACAACA+TGG + chr8_1:75522400-75522419 Msa1214750:CDS 35.0%
! AACAGAGCAGCTTTGTATAA+TGG + chr8_1:75522529-75522548 Msa1214750:CDS 35.0%
!! TGCAACTATGTTTTTGTGGT+GGG - chr8_1:75522740-75522759 None:intergenic 35.0%
! CTACGTTCTTGTTTATCCTC+TGG + chr8_1:75522208-75522227 Msa1214750:CDS 40.0%
AGATCGTGTGAATCAACGAT+TGG + chr8_1:75522561-75522580 Msa1214750:CDS 40.0%
!! CTGCAACTATGTTTTTGTGG+TGG - chr8_1:75522741-75522760 None:intergenic 40.0%
CATATTAGAAGCAGCCAACA+AGG - chr8_1:75521978-75521997 None:intergenic 40.0%
! CTACGTTCTTGTTTATCCTC+TGG + chr8_1:75522208-75522227 Msa1214750:CDS 40.0%
AGATCGTGTGAATCAACGAT+TGG + chr8_1:75522561-75522580 Msa1214750:CDS 40.0%
!! CTGCAACTATGTTTTTGTGG+TGG - chr8_1:75522741-75522760 None:intergenic 40.0%
! ATTTCTGAAGACGGAGAGCA+AGG - chr8_1:75522132-75522151 None:intergenic 45.0%
! AATGGTGGAAACGAGAACAG+AGG + chr8_1:75522496-75522515 Msa1214750:CDS 45.0%
TACAAAGCTGCTCTGTTTGC+AGG - chr8_1:75522526-75522545 None:intergenic 45.0%
! ATTTCTGAAGACGGAGAGCA+AGG - chr8_1:75522132-75522151 None:intergenic 45.0%
! AATGGTGGAAACGAGAACAG+AGG + chr8_1:75522496-75522515 Msa1214750:CDS 45.0%
TACAAAGCTGCTCTGTTTGC+AGG - chr8_1:75522526-75522545 None:intergenic 45.0%
TGCAAAGACAGCACCTTGTG+AGG - chr8_1:75522077-75522096 None:intergenic 50.0%
AGCAAGGATGATGACTGTGC+CGG - chr8_1:75522116-75522135 None:intergenic 50.0%
TGCAAAGACAGCACCTTGTG+AGG - chr8_1:75522077-75522096 None:intergenic 50.0%
AGCAAGGATGATGACTGTGC+CGG - chr8_1:75522116-75522135 None:intergenic 50.0%
TGCTGTCTTTGCAACCGCCA+TGG + chr8_1:75522084-75522103 Msa1214750:CDS 55.0%
TGCTGTCTTTGCAACCGCCA+TGG + chr8_1:75522084-75522103 Msa1214750:CDS 55.0%
GCAACCGCCATGGCTGTCTC+CGG + chr8_1:75522094-75522113 Msa1214750:CDS 65.0%
TGTGCCGGAGACAGCCATGG+CGG - chr8_1:75522101-75522120 None:intergenic 65.0%
GACTGTGCCGGAGACAGCCA+TGG - chr8_1:75522104-75522123 None:intergenic 65.0%
GCAACCGCCATGGCTGTCTC+CGG + chr8_1:75522094-75522113 Msa1214750:CDS 65.0%
TGTGCCGGAGACAGCCATGG+CGG - chr8_1:75522101-75522120 None:intergenic 65.0%
GACTGTGCCGGAGACAGCCA+TGG - chr8_1:75522104-75522123 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 75521976 75522989 75521976 ID=Msa1214750;Name=Msa1214750
chr8_1 mRNA 75521976 75522989 75521976 ID=Msa1214750-mRNA-1;Parent=Msa1214750;Name=Msa1214750-mRNA-1;_AED=0.05;_eAED=0.05;_QI=19|1|1|1|1|1|2|395|168
chr8_1 exon 75521976 75522229 75521976 ID=Msa1214750-mRNA-1:exon:25940;Parent=Msa1214750-mRNA-1
chr8_1 exon 75522323 75522989 75522323 ID=Msa1214750-mRNA-1:exon:25941;Parent=Msa1214750-mRNA-1
chr8_1 five_prime_UTR 75521976 75521994 75521976 ID=Msa1214750-mRNA-1:five_prime_utr;Parent=Msa1214750-mRNA-1
chr8_1 CDS 75521995 75522229 75521995 ID=Msa1214750-mRNA-1:cds;Parent=Msa1214750-mRNA-1
chr8_1 CDS 75522323 75522594 75522323 ID=Msa1214750-mRNA-1:cds;Parent=Msa1214750-mRNA-1
chr8_1 three_prime_UTR 75522595 75522989 75522595 ID=Msa1214750-mRNA-1:three_prime_utr;Parent=Msa1214750-mRNA-1
Gene Sequence

>Msa1214750

ATGAGACTATACCACTTTCTCACTTTTCATCAAAGACCAATCCTTTCTTCTTTTCTTCAAAACATGTCTTCAATGATTACCTCACAAGGTGCTGTCTTTGCAACCGCCATGGCTGTCTCCGGCACAGTCATCATCCTTGCTCTCCGTCTTCAGAAATCCCAATTCTCTCTTCACCATGTTTCTTCTTCTTCTTCTTCTTCTTCAACTCCTATTCTACGTTCTTGTTTATCCTCTGATGAAAAGAAAACAAAGAAACTGAAGAAAAGAGTTAGTTTTGCTAAGGATGTTGTGGATTCATGTAAAGATGGAGAAGAGTACAGAAAACAACAACATGGTACTAGTACTATGAATAATACTACTAAACATTCTTTGAAATTGAATTCAAGATCAAAGGTTCAAAAGAATTGTAATGGTGGAAACGAGAACAGAGGAATGCCTGCAAACAGAGCAGCTTTGTATAATGGAATTCTTAGAGATCGTGTGAATCAACGATTGGCTTATTGTTGA
Protein sequence

>Msa1214750

MRLYHFLTFHQRPILSSFLQNMSSMITSQGAVFATAMAVSGTVIILALRLQKSQFSLHHVSSSSSSSSTPILRSCLSSDEKKTKKLKKRVSFAKDVVDSCKDGEEYRKQQHGTSTMNNTTKHSLKLNSRSKVQKNCNGGNENRGMPANRAALYNGILRDRVNQRLAYC*