AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0679550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0679550 MtrunA17_Chr4g0003391 96.063 127 5 0 1 127 1 127 1.07e-77 225
Msa0679550 MtrunA17_Chr2g0333051 52.555 137 48 5 1 123 1 134 4.27e-35 117
Msa0679550 MtrunA17_Chr4g0063791 40.411 146 59 6 5 126 35 176 4.91e-17 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0679550 AT1G52565.1 43.571 140 52 5 1 127 4 129 3.42e-18 75.1
Msa0679550 AT3G15760.1 40.580 138 60 6 1 123 1 131 4.83e-15 67.0

Find 32 sgRNAs with CRISPR-Local

Find 101 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAATATTTGAAGTCCTAA+TGG 0.333607 4_4:+37364586 Msa0679550:three_prime_UTR
GTCATTGATCATCTTGGTTA+TGG 0.365817 4_4:+37364397 Msa0679550:exon
AGAGATAGAGTTCAAAGAAT+GGG 0.376812 4_4:+37364369 Msa0679550:CDS
TACAAAGCAACTCTATTTGC+TGG 0.381833 4_4:-37364333 None:intergenic
TAGAACAAGAAGAAATTAGA+TGG 0.398648 4_4:+37364481 Msa0679550:three_prime_UTR
TTTCTGAATTGGGTGTTTCA+TGG 0.405044 4_4:-37363849 None:intergenic
CTCTTAAAATTGCCAAGAGT+TGG 0.419774 4_4:-37364722 None:intergenic
GCTTGTAGAGGAAAAGAAGA+AGG 0.443148 4_4:+37364176 Msa0679550:intron
TATAAACAAGATCGTAGAAT+AGG 0.444103 4_4:-37363877 None:intergenic
AAAAGGTTGTGAATTTATGA+TGG 0.447654 4_4:+37364615 Msa0679550:three_prime_UTR
AAGAGATAGAGTTCAAAGAA+TGG 0.465347 4_4:+37364368 Msa0679550:CDS
GGTGTTTCATGGAATTGAAA+TGG 0.466904 4_4:-37363838 None:intergenic
GGTGTTGTCATTGATCATCT+TGG 0.482671 4_4:+37364391 Msa0679550:exon
AATAGAGTTGCTTTGTACAA+TGG 0.493962 4_4:+37364339 Msa0679550:CDS
GCTTGACTATGTCCAACTCT+TGG 0.517400 4_4:+37364710 Msa0679550:three_prime_UTR
GTGAATTTATGATGGAAGGG+TGG 0.540534 4_4:+37364623 Msa0679550:three_prime_UTR
TGAATTTATGATGGAAGGGT+GGG 0.559563 4_4:+37364624 Msa0679550:three_prime_UTR
CTACGATCTTGTTTATACAC+AGG 0.560268 4_4:+37363883 Msa0679550:CDS
GGTTGTGAATTTATGATGGA+AGG 0.562242 4_4:+37364619 Msa0679550:three_prime_UTR
AGTTGAAACAACCATGGCTG+TGG 0.569166 4_4:-37363773 None:intergenic
GAGATAGAGTTCAAAGAATG+GGG 0.570523 4_4:+37364370 Msa0679550:CDS
GTGAGATTGAAGTCATGTTG+TGG 0.573467 4_4:-37363735 None:intergenic
AAGGGTGGGTATTCTTGTGA+AGG 0.586206 4_4:+37364638 Msa0679550:three_prime_UTR
TGGTTATGGAAGTTAGAACA+TGG 0.589490 4_4:+37364411 Msa0679550:three_prime_UTR
GTTGTGAATTTATGATGGAA+GGG 0.606258 4_4:+37364620 Msa0679550:three_prime_UTR
TTAGAACATGGTATAGAACA+TGG 0.610591 4_4:+37364453 Msa0679550:three_prime_UTR
GGTTATGGAAGTTAGAACAT+GGG 0.634893 4_4:+37364412 Msa0679550:three_prime_UTR
TAGAACATGGTATAGAACAT+GGG 0.653391 4_4:+37364454 Msa0679550:three_prime_UTR
AACAGTAGTTGAAACAACCA+TGG 0.660669 4_4:-37363779 None:intergenic
AACATGACTTCAATCTCACA+AGG 0.670440 4_4:+37363739 Msa0679550:exon
AAACAGAGTAAAGAAAACAG+AGG 0.672838 4_4:-37363708 None:intergenic
AAAGATCTAATGTATTCTTG+TGG 0.676296 4_4:+37364675 Msa0679550:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTATTTTATTTTTAGGT+GGG + chr4_4:37364554-37364573 Msa0679550:three_prime_UTR 10.0%
!!! ATTTTATTTTATTTTTAGGT+GGG + chr4_4:37364554-37364573 Msa0679550:three_prime_UTR 10.0%
!!! GATTTTATTTTATTTTTAGG+TGG + chr4_4:37364553-37364572 Msa0679550:three_prime_UTR 15.0%
!!! GATTTTATTTTATTTTTAGG+TGG + chr4_4:37364553-37364572 Msa0679550:three_prime_UTR 15.0%
!!! TTTTTCAGATACTATTCTAT+AGG + chr4_4:37363967-37363986 Msa0679550:intron 20.0%
!! ATGTTTCATACAAAATATTC+AGG - chr4_4:37364125-37364144 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG + chr4_4:37364249-37364268 Msa0679550:CDS 20.0%
!!! TTTTTCAGATACTATTCTAT+AGG + chr4_4:37363967-37363986 Msa0679550:intron 20.0%
!! ATGTTTCATACAAAATATTC+AGG - chr4_4:37364125-37364144 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG + chr4_4:37364249-37364268 Msa0679550:CDS 20.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG - chr4_4:37363862-37363881 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG - chr4_4:37363863-37363882 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG - chr4_4:37363880-37363899 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG + chr4_4:37364224-37364243 Msa0679550:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG + chr4_4:37364248-37364267 Msa0679550:CDS 25.0%
! AAGAATTTAGAGAAAAACAG+GGG + chr4_4:37364250-37364269 Msa0679550:CDS 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG + chr4_4:37364441-37364460 Msa0679550:three_prime_UTR 25.0%
! TAGAACAAGAAGAAATTAGA+TGG + chr4_4:37364481-37364500 Msa0679550:three_prime_UTR 25.0%
!! AACAATATTTGAAGTCCTAA+TGG + chr4_4:37364586-37364605 Msa0679550:three_prime_UTR 25.0%
! AAAAGGTTGTGAATTTATGA+TGG + chr4_4:37364615-37364634 Msa0679550:three_prime_UTR 25.0%
! AAAGATCTAATGTATTCTTG+TGG + chr4_4:37364675-37364694 Msa0679550:three_prime_UTR 25.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG - chr4_4:37363862-37363881 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG - chr4_4:37363863-37363882 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG - chr4_4:37363880-37363899 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG + chr4_4:37364224-37364243 Msa0679550:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG + chr4_4:37364248-37364267 Msa0679550:CDS 25.0%
! AAGAATTTAGAGAAAAACAG+GGG + chr4_4:37364250-37364269 Msa0679550:CDS 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG + chr4_4:37364441-37364460 Msa0679550:three_prime_UTR 25.0%
! TAGAACAAGAAGAAATTAGA+TGG + chr4_4:37364481-37364500 Msa0679550:three_prime_UTR 25.0%
!! AACAATATTTGAAGTCCTAA+TGG + chr4_4:37364586-37364605 Msa0679550:three_prime_UTR 25.0%
! AAAAGGTTGTGAATTTATGA+TGG + chr4_4:37364615-37364634 Msa0679550:three_prime_UTR 25.0%
! AAAGATCTAATGTATTCTTG+TGG + chr4_4:37364675-37364694 Msa0679550:three_prime_UTR 25.0%
AAACAGAGTAAAGAAAACAG+AGG - chr4_4:37363711-37363730 None:intergenic 30.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG + chr4_4:37364164-37364183 Msa0679550:intron 30.0%
! AATAGAGTTGCTTTGTACAA+TGG + chr4_4:37364339-37364358 Msa0679550:CDS 30.0%
AAGAGATAGAGTTCAAAGAA+TGG + chr4_4:37364368-37364387 Msa0679550:CDS 30.0%
AGAGATAGAGTTCAAAGAAT+GGG + chr4_4:37364369-37364388 Msa0679550:CDS 30.0%
TTAGAACATGGTATAGAACA+TGG + chr4_4:37364453-37364472 Msa0679550:three_prime_UTR 30.0%
TAGAACATGGTATAGAACAT+GGG + chr4_4:37364454-37364473 Msa0679550:three_prime_UTR 30.0%
! AGTCCTAATGGATCAAAAAA+AGG + chr4_4:37364598-37364617 Msa0679550:three_prime_UTR 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG - chr4_4:37364604-37364623 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG + chr4_4:37364620-37364639 Msa0679550:three_prime_UTR 30.0%
AAACAGAGTAAAGAAAACAG+AGG - chr4_4:37363711-37363730 None:intergenic 30.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG + chr4_4:37364164-37364183 Msa0679550:intron 30.0%
! AATAGAGTTGCTTTGTACAA+TGG + chr4_4:37364339-37364358 Msa0679550:CDS 30.0%
AAGAGATAGAGTTCAAAGAA+TGG + chr4_4:37364368-37364387 Msa0679550:CDS 30.0%
AGAGATAGAGTTCAAAGAAT+GGG + chr4_4:37364369-37364388 Msa0679550:CDS 30.0%
TTAGAACATGGTATAGAACA+TGG + chr4_4:37364453-37364472 Msa0679550:three_prime_UTR 30.0%
TAGAACATGGTATAGAACAT+GGG + chr4_4:37364454-37364473 Msa0679550:three_prime_UTR 30.0%
! AGTCCTAATGGATCAAAAAA+AGG + chr4_4:37364598-37364617 Msa0679550:three_prime_UTR 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG - chr4_4:37364604-37364623 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG + chr4_4:37364620-37364639 Msa0679550:three_prime_UTR 30.0%
AACATGACTTCAATCTCACA+AGG + chr4_4:37363739-37363758 Msa0679550:exon 35.0%
AACAGTAGTTGAAACAACCA+TGG - chr4_4:37363782-37363801 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG - chr4_4:37363841-37363860 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG - chr4_4:37363852-37363871 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG + chr4_4:37363883-37363902 Msa0679550:CDS 35.0%
TACAAAGCAACTCTATTTGC+TGG - chr4_4:37364336-37364355 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG + chr4_4:37364370-37364389 Msa0679550:CDS 35.0%
GTCATTGATCATCTTGGTTA+TGG + chr4_4:37364397-37364416 Msa0679550:exon 35.0%
TGGTTATGGAAGTTAGAACA+TGG + chr4_4:37364411-37364430 Msa0679550:three_prime_UTR 35.0%
GGTTATGGAAGTTAGAACAT+GGG + chr4_4:37364412-37364431 Msa0679550:three_prime_UTR 35.0%
!!! TTATTTTTAGGTGGGTGTGT+TGG + chr4_4:37364562-37364581 Msa0679550:three_prime_UTR 35.0%
! GGTTGTGAATTTATGATGGA+AGG + chr4_4:37364619-37364638 Msa0679550:three_prime_UTR 35.0%
! TGAATTTATGATGGAAGGGT+GGG + chr4_4:37364624-37364643 Msa0679550:three_prime_UTR 35.0%
CTCTTAAAATTGCCAAGAGT+TGG - chr4_4:37364725-37364744 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG + chr4_4:37363739-37363758 Msa0679550:exon 35.0%
AACAGTAGTTGAAACAACCA+TGG - chr4_4:37363782-37363801 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG - chr4_4:37363841-37363860 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG - chr4_4:37363852-37363871 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG + chr4_4:37363883-37363902 Msa0679550:CDS 35.0%
TACAAAGCAACTCTATTTGC+TGG - chr4_4:37364336-37364355 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG + chr4_4:37364370-37364389 Msa0679550:CDS 35.0%
GTCATTGATCATCTTGGTTA+TGG + chr4_4:37364397-37364416 Msa0679550:exon 35.0%
TGGTTATGGAAGTTAGAACA+TGG + chr4_4:37364411-37364430 Msa0679550:three_prime_UTR 35.0%
GGTTATGGAAGTTAGAACAT+GGG + chr4_4:37364412-37364431 Msa0679550:three_prime_UTR 35.0%
!!! TTATTTTTAGGTGGGTGTGT+TGG + chr4_4:37364562-37364581 Msa0679550:three_prime_UTR 35.0%
! GGTTGTGAATTTATGATGGA+AGG + chr4_4:37364619-37364638 Msa0679550:three_prime_UTR 35.0%
! TGAATTTATGATGGAAGGGT+GGG + chr4_4:37364624-37364643 Msa0679550:three_prime_UTR 35.0%
CTCTTAAAATTGCCAAGAGT+TGG - chr4_4:37364725-37364744 None:intergenic 35.0%
GTGAGATTGAAGTCATGTTG+TGG - chr4_4:37363738-37363757 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG + chr4_4:37363762-37363781 Msa0679550:CDS 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG + chr4_4:37364176-37364195 Msa0679550:intron 40.0%
! GGTGTTGTCATTGATCATCT+TGG + chr4_4:37364391-37364410 Msa0679550:exon 40.0%
! GTGAATTTATGATGGAAGGG+TGG + chr4_4:37364623-37364642 Msa0679550:three_prime_UTR 40.0%
AACAACGTTGTCTTGTGTTG+TGG - chr4_4:37363671-37363690 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG - chr4_4:37363738-37363757 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG + chr4_4:37363762-37363781 Msa0679550:CDS 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG + chr4_4:37364176-37364195 Msa0679550:intron 40.0%
! GGTGTTGTCATTGATCATCT+TGG + chr4_4:37364391-37364410 Msa0679550:exon 40.0%
! GTGAATTTATGATGGAAGGG+TGG + chr4_4:37364623-37364642 Msa0679550:three_prime_UTR 40.0%
AGTTGAAACAACCATGGCTG+TGG - chr4_4:37363776-37363795 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG - chr4_4:37364318-37364337 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG + chr4_4:37364638-37364657 Msa0679550:three_prime_UTR 45.0%
GCTTGACTATGTCCAACTCT+TGG + chr4_4:37364710-37364729 Msa0679550:three_prime_UTR 45.0%
AGTTGAAACAACCATGGCTG+TGG - chr4_4:37363776-37363795 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG - chr4_4:37364318-37364337 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG + chr4_4:37364638-37364657 Msa0679550:three_prime_UTR 45.0%
GCTTGACTATGTCCAACTCT+TGG + chr4_4:37364710-37364729 Msa0679550:three_prime_UTR 45.0%
!!! TTAGATTTTATTTTATTTTT+AGG + chr4_4:37364550-37364569 Msa0679550:three_prime_UTR 5.0%
!!! TTAGATTTTATTTTATTTTT+AGG + chr4_4:37364550-37364569 Msa0679550:three_prime_UTR 5.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 37363669 37364761 37363669 ID=Msa0679550;Name=Msa0679550
chr4_4 mRNA 37363669 37364761 37363669 ID=Msa0679550-mRNA-1;Parent=Msa0679550;Name=Msa0679550-mRNA-1;_AED=0.05;_eAED=0.05;_QI=73|1|1|1|1|1|2|357|127
chr4_4 exon 37363669 37363904 37363669 ID=Msa0679550-mRNA-1:exon:8816;Parent=Msa0679550-mRNA-1
chr4_4 exon 37364184 37364761 37364184 ID=Msa0679550-mRNA-1:exon:8817;Parent=Msa0679550-mRNA-1
chr4_4 five_prime_UTR 37363669 37363741 37363669 ID=Msa0679550-mRNA-1:five_prime_utr;Parent=Msa0679550-mRNA-1
chr4_4 CDS 37363742 37363904 37363742 ID=Msa0679550-mRNA-1:cds;Parent=Msa0679550-mRNA-1
chr4_4 CDS 37364184 37364404 37364184 ID=Msa0679550-mRNA-1:cds;Parent=Msa0679550-mRNA-1
chr4_4 three_prime_UTR 37364405 37364761 37364405 ID=Msa0679550-mRNA-1:three_prime_utr;Parent=Msa0679550-mRNA-1
Gene Sequence

>Msa0679550

ATGACTTCAATCTCACAAGGTCTTGTTTTAACCACAGCCATGGTTGTTTCAACTACTGTTCTTTATCTTACTTTCTGTAAACAAAAAAACTCATCACCATTTCAATTCCATGAAACACCCAATTCAGAAAACAAACCTATTCTACGATCTTGTTTATACACAGAGGAAAAGAAGAAGGAAAAATTAAGAAAGAAGAAGAAAGTGAAATTTTCAGAAAATGTGATGGTGAAAGAATTTAGAGAAAAACAGGGGAAGAAAAACAGAGTATCAATTAATGAATGCAGAAATGAAATTCCAGAAACAAAAGCAATGCCAGCAAATAGAGTTGCTTTGTACAATGGAATTTTAAGAGATAGAGTTCAAAGAATGGGGTGTTGTCATTGA

Protein sequence

>Msa0679550

MTSISQGLVLTTAMVVSTTVLYLTFCKQKNSSPFQFHETPNSENKPILRSCLYTEEKKKEKLRKKKKVKFSENVMVKEFREKQGKKNRVSINECRNEIPETKAMPANRVALYNGILRDRVQRMGCCH*