AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1076130

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1076130 MtrunA17_Chr7g0259971 96.923 65 2 0 1 65 1 65 1.52e-41 129
Msa1076130 MtrunA17_Chr5g0394401 72.131 61 16 1 1 61 1 60 1.14e-26 91.7
Msa1076130 MtrunA17_Chr1g0205521 72.581 62 16 1 1 62 1 61 2.51e-26 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAAGTATTATATTCTTTC+TGG 0.087702 7_2:-74541407 None:intergenic
GGATTTGAATTATCTATCTT+TGG 0.233172 7_2:+74541137 Msa1076130:three_prime_UTR
TGGTGAAGTGCTACTACTTT+TGG 0.272794 7_2:-74540664 None:intergenic
GGATTGAAGCCACCCCATTT+TGG 0.303345 7_2:-74540684 None:intergenic
CCATCAAAATATACACGTTA+AGG 0.316896 7_2:+74541115 Msa1076130:CDS
GTAGTAGCACTTCACCAAAA+TGG 0.326072 7_2:+74540670 Msa1076130:exon
TCTACCCATTGAAGAAGCTT+TGG 0.346676 7_2:+74540711 Msa1076130:CDS
TAGTAGCACTTCACCAAAAT+GGG 0.356184 7_2:+74540671 Msa1076130:exon
GATTTGAATTATCTATCTTT+GGG 0.371999 7_2:+74541138 Msa1076130:three_prime_UTR
CTACCCATTGAAGAAGCTTT+GGG 0.376258 7_2:+74540712 Msa1076130:CDS
TGGGTGAGTTTCGACAAATA+TGG 0.383460 7_2:+74541157 Msa1076130:three_prime_UTR
ACAAGTATTATATTCTTTCT+GGG 0.397148 7_2:-74541406 None:intergenic
GGGTGAGTTTCGACAAATAT+GGG 0.397445 7_2:+74541158 Msa1076130:three_prime_UTR
CATCAAAATATACACGTTAA+GGG 0.412552 7_2:+74541116 Msa1076130:CDS
AAGAGATGAGAGAGATAGAA+AGG 0.423561 7_2:+74541213 Msa1076130:three_prime_UTR
TGGTCAATCCTGGTCGAGTC+GGG 0.436022 7_2:+74541076 Msa1076130:CDS
CATTGAAGAAGCTTTGGGTT+CGG 0.445914 7_2:+74540717 Msa1076130:CDS
CTGGTCAATCCTGGTCGAGT+CGG 0.460174 7_2:+74541075 Msa1076130:CDS
AAACTTTACAAGTATTTGAA+AGG 0.476738 7_2:-74541313 None:intergenic
GCTTCTTCAATGGGTAGAGT+AGG 0.487680 7_2:-74540706 None:intergenic
GCAAGTTCTCTGGTCAATCC+TGG 0.497290 7_2:+74541066 Msa1076130:CDS
CGAACCCAAAGCTTCTTCAA+TGG 0.503333 7_2:-74540716 None:intergenic
GTGAAGATGTGCAAGTTCTC+TGG 0.505261 7_2:+74541056 Msa1076130:CDS
GAACCCAAAGCTTCTTCAAT+GGG 0.506226 7_2:-74540715 None:intergenic
CTTCTTCAATGGGTAGAGTA+GGG 0.513099 7_2:-74540705 None:intergenic
AACTTTACAAGTATTTGAAA+GGG 0.516791 7_2:-74541312 None:intergenic
TGTATATACTAGTCTTGATG+TGG 0.538227 7_2:-74541260 None:intergenic
GTATATACTAGTCTTGATGT+GGG 0.554173 7_2:-74541259 None:intergenic
AGGCGGCACCCGACTCGACC+AGG 0.560698 7_2:-74541084 None:intergenic
ATATACTAGTCTTGATGTGG+GGG 0.612239 7_2:-74541257 None:intergenic
TATATACTAGTCTTGATGTG+GGG 0.621823 7_2:-74541258 None:intergenic
AGGATTATACATCTTATACA+AGG 0.638133 7_2:+74541015 Msa1076130:CDS
AGAACTTGCACATCTTCACA+CGG 0.663889 7_2:-74541052 None:intergenic
AGCACTTCACCAAAATGGGG+TGG 0.674042 7_2:+74540675 Msa1076130:exon
GAACTTGCACATCTTCACAC+GGG 0.699833 7_2:-74541051 None:intergenic
AGTAGCACTTCACCAAAATG+GGG 0.708319 7_2:+74540672 Msa1076130:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACTTTACAATTATTTTTTT+AGG - chr7_2:74541340-74541359 None:intergenic 10.0%
!!! AACTTTACAATTATTTTTTT+AGG - chr7_2:74541340-74541359 None:intergenic 10.0%
!! ATATATGAACATGAATTATA+TGG - chr7_2:74540912-74540931 None:intergenic 15.0%
!! CATAAGAAACAAAAATTAAT+CGG - chr7_2:74540983-74541002 None:intergenic 15.0%
!!! TTTTGTTTCTTATGTAAAAT+AGG + chr7_2:74540989-74541008 Msa1076130:intron 15.0%
!! TTGAAAAAAAAAAAATATGG+AGG + chr7_2:74541190-74541209 Msa1076130:three_prime_UTR 15.0%
!! ATATATGAACATGAATTATA+TGG - chr7_2:74540912-74540931 None:intergenic 15.0%
!! CATAAGAAACAAAAATTAAT+CGG - chr7_2:74540983-74541002 None:intergenic 15.0%
!!! TTTTGTTTCTTATGTAAAAT+AGG + chr7_2:74540989-74541008 Msa1076130:intron 15.0%
!! TTGAAAAAAAAAAAATATGG+AGG + chr7_2:74541190-74541209 Msa1076130:three_prime_UTR 15.0%
!!! ATCATTGTTTTGTATAAAGT+AGG - chr7_2:74540944-74540963 None:intergenic 20.0%
!! GATTTGAATTATCTATCTTT+GGG + chr7_2:74541138-74541157 Msa1076130:three_prime_UTR 20.0%
!! AACTTTACAAGTATTTGAAA+GGG - chr7_2:74541315-74541334 None:intergenic 20.0%
!! AAACTTTACAAGTATTTGAA+AGG - chr7_2:74541316-74541335 None:intergenic 20.0%
!! ACAAGTATTATATTCTTTCT+GGG - chr7_2:74541409-74541428 None:intergenic 20.0%
!! TACAAGTATTATATTCTTTC+TGG - chr7_2:74541410-74541429 None:intergenic 20.0%
!!! ATCATTGTTTTGTATAAAGT+AGG - chr7_2:74540944-74540963 None:intergenic 20.0%
!! GATTTGAATTATCTATCTTT+GGG + chr7_2:74541138-74541157 Msa1076130:three_prime_UTR 20.0%
!! AACTTTACAAGTATTTGAAA+GGG - chr7_2:74541315-74541334 None:intergenic 20.0%
!! AAACTTTACAAGTATTTGAA+AGG - chr7_2:74541316-74541335 None:intergenic 20.0%
!! ACAAGTATTATATTCTTTCT+GGG - chr7_2:74541409-74541428 None:intergenic 20.0%
!! TACAAGTATTATATTCTTTC+TGG - chr7_2:74541410-74541429 None:intergenic 20.0%
! AAAGATGGAATCATATTGTA+TGG - chr7_2:74540805-74540824 None:intergenic 25.0%
! TACAATTGCATAATCAAAGA+TGG - chr7_2:74540820-74540839 None:intergenic 25.0%
!! TTATATGGATTGTACAAGAA+TGG - chr7_2:74540897-74540916 None:intergenic 25.0%
! TTCTTATGTAAAATAGGTAG+AGG + chr7_2:74540995-74541014 Msa1076130:intron 25.0%
! AGGATTATACATCTTATACA+AGG + chr7_2:74541015-74541034 Msa1076130:CDS 25.0%
! CATCAAAATATACACGTTAA+GGG + chr7_2:74541116-74541135 Msa1076130:CDS 25.0%
! GGATTTGAATTATCTATCTT+TGG + chr7_2:74541137-74541156 Msa1076130:three_prime_UTR 25.0%
! AAAGATGGAATCATATTGTA+TGG - chr7_2:74540805-74540824 None:intergenic 25.0%
! TACAATTGCATAATCAAAGA+TGG - chr7_2:74540820-74540839 None:intergenic 25.0%
!! TTATATGGATTGTACAAGAA+TGG - chr7_2:74540897-74540916 None:intergenic 25.0%
! TTCTTATGTAAAATAGGTAG+AGG + chr7_2:74540995-74541014 Msa1076130:intron 25.0%
! AGGATTATACATCTTATACA+AGG + chr7_2:74541015-74541034 Msa1076130:CDS 25.0%
! CATCAAAATATACACGTTAA+GGG + chr7_2:74541116-74541135 Msa1076130:CDS 25.0%
! GGATTTGAATTATCTATCTT+TGG + chr7_2:74541137-74541156 Msa1076130:three_prime_UTR 25.0%
!! TACGTCTTTTATTGGTTGAA+TGG - chr7_2:74540745-74540764 None:intergenic 30.0%
! TGCTAACTTACGTCTTTTAT+TGG - chr7_2:74540753-74540772 None:intergenic 30.0%
TACAAGAATGGTCTAAGAAA+AGG - chr7_2:74540885-74540904 None:intergenic 30.0%
!!! ATATTTTGATGGCAAAGTAG+AGG - chr7_2:74541107-74541126 None:intergenic 30.0%
!! CCTTAACGTGTATATTTTGA+TGG - chr7_2:74541118-74541137 None:intergenic 30.0%
CCATCAAAATATACACGTTA+AGG + chr7_2:74541115-74541134 Msa1076130:CDS 30.0%
!! TATATACTAGTCTTGATGTG+GGG - chr7_2:74541261-74541280 None:intergenic 30.0%
!! GTATATACTAGTCTTGATGT+GGG - chr7_2:74541262-74541281 None:intergenic 30.0%
!! TGTATATACTAGTCTTGATG+TGG - chr7_2:74541263-74541282 None:intergenic 30.0%
!!! CATTTTTATGTGCTGATTTC+TGG + chr7_2:74541443-74541462 Msa1076130:three_prime_UTR 30.0%
!! TACGTCTTTTATTGGTTGAA+TGG - chr7_2:74540745-74540764 None:intergenic 30.0%
! TGCTAACTTACGTCTTTTAT+TGG - chr7_2:74540753-74540772 None:intergenic 30.0%
TACAAGAATGGTCTAAGAAA+AGG - chr7_2:74540885-74540904 None:intergenic 30.0%
!!! ATATTTTGATGGCAAAGTAG+AGG - chr7_2:74541107-74541126 None:intergenic 30.0%
!! CCTTAACGTGTATATTTTGA+TGG - chr7_2:74541118-74541137 None:intergenic 30.0%
CCATCAAAATATACACGTTA+AGG + chr7_2:74541115-74541134 Msa1076130:CDS 30.0%
!! TATATACTAGTCTTGATGTG+GGG - chr7_2:74541261-74541280 None:intergenic 30.0%
!! GTATATACTAGTCTTGATGT+GGG - chr7_2:74541262-74541281 None:intergenic 30.0%
!! TGTATATACTAGTCTTGATG+TGG - chr7_2:74541263-74541282 None:intergenic 30.0%
!!! CATTTTTATGTGCTGATTTC+TGG + chr7_2:74541443-74541462 Msa1076130:three_prime_UTR 30.0%
TAGTAGCACTTCACCAAAAT+GGG + chr7_2:74540671-74540690 Msa1076130:exon 35.0%
AAGAGATGAGAGAGATAGAA+AGG + chr7_2:74541213-74541232 Msa1076130:three_prime_UTR 35.0%
!! ATATACTAGTCTTGATGTGG+GGG - chr7_2:74541260-74541279 None:intergenic 35.0%
!!! TTTTATGTGCTGATTTCTGG+TGG + chr7_2:74541446-74541465 Msa1076130:three_prime_UTR 35.0%
TAGTAGCACTTCACCAAAAT+GGG + chr7_2:74540671-74540690 Msa1076130:exon 35.0%
AAGAGATGAGAGAGATAGAA+AGG + chr7_2:74541213-74541232 Msa1076130:three_prime_UTR 35.0%
!! ATATACTAGTCTTGATGTGG+GGG - chr7_2:74541260-74541279 None:intergenic 35.0%
!!! TTTTATGTGCTGATTTCTGG+TGG + chr7_2:74541446-74541465 Msa1076130:three_prime_UTR 35.0%
!! TGGTGAAGTGCTACTACTTT+TGG - chr7_2:74540667-74540686 None:intergenic 40.0%
GTAGTAGCACTTCACCAAAA+TGG + chr7_2:74540670-74540689 Msa1076130:exon 40.0%
AGTAGCACTTCACCAAAATG+GGG + chr7_2:74540672-74540691 Msa1076130:exon 40.0%
CTTCTTCAATGGGTAGAGTA+GGG - chr7_2:74540708-74540727 None:intergenic 40.0%
TCTACCCATTGAAGAAGCTT+TGG + chr7_2:74540711-74540730 Msa1076130:CDS 40.0%
CTACCCATTGAAGAAGCTTT+GGG + chr7_2:74540712-74540731 Msa1076130:CDS 40.0%
GAACCCAAAGCTTCTTCAAT+GGG - chr7_2:74540718-74540737 None:intergenic 40.0%
!! CATTGAAGAAGCTTTGGGTT+CGG + chr7_2:74540717-74540736 Msa1076130:CDS 40.0%
AGAACTTGCACATCTTCACA+CGG - chr7_2:74541055-74541074 None:intergenic 40.0%
!! TTTTGATGGCAAAGTAGAGG+CGG - chr7_2:74541104-74541123 None:intergenic 40.0%
TGGGTGAGTTTCGACAAATA+TGG + chr7_2:74541157-74541176 Msa1076130:three_prime_UTR 40.0%
GGGTGAGTTTCGACAAATAT+GGG + chr7_2:74541158-74541177 Msa1076130:three_prime_UTR 40.0%
!! TGGTGAAGTGCTACTACTTT+TGG - chr7_2:74540667-74540686 None:intergenic 40.0%
GTAGTAGCACTTCACCAAAA+TGG + chr7_2:74540670-74540689 Msa1076130:exon 40.0%
AGTAGCACTTCACCAAAATG+GGG + chr7_2:74540672-74540691 Msa1076130:exon 40.0%
CTTCTTCAATGGGTAGAGTA+GGG - chr7_2:74540708-74540727 None:intergenic 40.0%
TCTACCCATTGAAGAAGCTT+TGG + chr7_2:74540711-74540730 Msa1076130:CDS 40.0%
CTACCCATTGAAGAAGCTTT+GGG + chr7_2:74540712-74540731 Msa1076130:CDS 40.0%
GAACCCAAAGCTTCTTCAAT+GGG - chr7_2:74540718-74540737 None:intergenic 40.0%
!! CATTGAAGAAGCTTTGGGTT+CGG + chr7_2:74540717-74540736 Msa1076130:CDS 40.0%
AGAACTTGCACATCTTCACA+CGG - chr7_2:74541055-74541074 None:intergenic 40.0%
!! TTTTGATGGCAAAGTAGAGG+CGG - chr7_2:74541104-74541123 None:intergenic 40.0%
TGGGTGAGTTTCGACAAATA+TGG + chr7_2:74541157-74541176 Msa1076130:three_prime_UTR 40.0%
GGGTGAGTTTCGACAAATAT+GGG + chr7_2:74541158-74541177 Msa1076130:three_prime_UTR 40.0%
GCTTCTTCAATGGGTAGAGT+AGG - chr7_2:74540709-74540728 None:intergenic 45.0%
CGAACCCAAAGCTTCTTCAA+TGG - chr7_2:74540719-74540738 None:intergenic 45.0%
GAACTTGCACATCTTCACAC+GGG - chr7_2:74541054-74541073 None:intergenic 45.0%
GTGAAGATGTGCAAGTTCTC+TGG + chr7_2:74541056-74541075 Msa1076130:CDS 45.0%
GCTTCTTCAATGGGTAGAGT+AGG - chr7_2:74540709-74540728 None:intergenic 45.0%
CGAACCCAAAGCTTCTTCAA+TGG - chr7_2:74540719-74540738 None:intergenic 45.0%
GAACTTGCACATCTTCACAC+GGG - chr7_2:74541054-74541073 None:intergenic 45.0%
GTGAAGATGTGCAAGTTCTC+TGG + chr7_2:74541056-74541075 Msa1076130:CDS 45.0%
!! AATTTGAAAAAAAAAAAATA+TGG + chr7_2:74541187-74541206 Msa1076130:three_prime_UTR 5.0%
!! AATTTGAAAAAAAAAAAATA+TGG + chr7_2:74541187-74541206 Msa1076130:three_prime_UTR 5.0%
AGCACTTCACCAAAATGGGG+TGG + chr7_2:74540675-74540694 Msa1076130:exon 50.0%
! GGATTGAAGCCACCCCATTT+TGG - chr7_2:74540687-74540706 None:intergenic 50.0%
GCAAGTTCTCTGGTCAATCC+TGG + chr7_2:74541066-74541085 Msa1076130:CDS 50.0%
AGCACTTCACCAAAATGGGG+TGG + chr7_2:74540675-74540694 Msa1076130:exon 50.0%
! GGATTGAAGCCACCCCATTT+TGG - chr7_2:74540687-74540706 None:intergenic 50.0%
GCAAGTTCTCTGGTCAATCC+TGG + chr7_2:74541066-74541085 Msa1076130:CDS 50.0%
CTGGTCAATCCTGGTCGAGT+CGG + chr7_2:74541075-74541094 Msa1076130:CDS 55.0%
TGGTCAATCCTGGTCGAGTC+GGG + chr7_2:74541076-74541095 Msa1076130:CDS 55.0%
CTGGTCAATCCTGGTCGAGT+CGG + chr7_2:74541075-74541094 Msa1076130:CDS 55.0%
TGGTCAATCCTGGTCGAGTC+GGG + chr7_2:74541076-74541095 Msa1076130:CDS 55.0%
! AGGCGGCACCCGACTCGACC+AGG - chr7_2:74541087-74541106 None:intergenic 75.0%
! AGGCGGCACCCGACTCGACC+AGG - chr7_2:74541087-74541106 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 74540663 74541475 74540663 ID=Msa1076130;Name=Msa1076130
chr7_2 mRNA 74540663 74541475 74540663 ID=Msa1076130-mRNA-1;Parent=Msa1076130;Name=Msa1076130-mRNA-1;_AED=0.01;_eAED=0.01;_QI=26|1|1|1|0|0|2|340|65
chr7_2 exon 74540663 74540761 74540663 ID=Msa1076130-mRNA-1:exon:17572;Parent=Msa1076130-mRNA-1
chr7_2 exon 74541011 74541475 74541011 ID=Msa1076130-mRNA-1:exon:17573;Parent=Msa1076130-mRNA-1
chr7_2 five_prime_UTR 74540663 74540688 74540663 ID=Msa1076130-mRNA-1:five_prime_utr;Parent=Msa1076130-mRNA-1
chr7_2 CDS 74540689 74540761 74540689 ID=Msa1076130-mRNA-1:cds;Parent=Msa1076130-mRNA-1
chr7_2 CDS 74541011 74541135 74541011 ID=Msa1076130-mRNA-1:cds;Parent=Msa1076130-mRNA-1
chr7_2 three_prime_UTR 74541136 74541475 74541136 ID=Msa1076130-mRNA-1:three_prime_utr;Parent=Msa1076130-mRNA-1
Gene Sequence

>Msa1076130

ATGGGGTGGCTTCAATCCCTACTCTACCCATTGAAGAAGCTTTGGGTTCGGATCCATTCAACCAATAAAAGACGTAGAGGATTATACATCTTATACAAGGATGTTAAGTCATGCCCGTGTGAAGATGTGCAAGTTCTCTGGTCAATCCTGGTCGAGTCGGGTGCCGCCTCTACTTTGCCATCAAAATATACACGTTAA
Protein sequence

>Msa1076130

MGWLQSLLYPLKKLWVRIHSTNKRRRGLYILYKDVKSCPCEDVQVLWSILVESGAASTLPSKYTR*