AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1194690

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCACAGGGATGACGGTTT+GGG 0.227588 8_1:+42016236 Msa1194690:five_prime_UTR
TCATTATACCTAACATAAAT+TGG 0.230942 8_1:-42016328 None:intergenic
TTTGCACAGGGATGACGGTT+TGG 0.335779 8_1:+42016235 Msa1194690:five_prime_UTR
TTGAGTTTCTAAGCAAATAA+TGG 0.358465 8_1:+42016636 Msa1194690:three_prime_UTR
AGAAACTATCTAATGTTTCC+AGG 0.375467 8_1:+42016599 Msa1194690:three_prime_UTR
TGTGGCGCAACTCATGAAAT+TGG 0.429611 8_1:+42016298 Msa1194690:CDS
TAGGTTTATGCATACAAATC+AGG 0.431471 8_1:+42016536 Msa1194690:three_prime_UTR
TGCTATTAGCTGGTGTTGGT+TGG 0.471070 8_1:+42016559 Msa1194690:three_prime_UTR
CTTTGATCTTCTTAAGAAGC+TGG 0.474951 8_1:+42016466 Msa1194690:CDS
TCAAGGATATTTAGATGCCC+TGG 0.486759 8_1:-42016617 None:intergenic
TGACAGACTAACATAAAGAA+TGG 0.487712 8_1:-42016680 None:intergenic
AGATCAAAGTTGAGGTTGCA+TGG 0.498263 8_1:-42016452 None:intergenic
GCATTGTCTCTGCCATCATA+TGG 0.506035 8_1:+42016265 Msa1194690:exon
ACAAATCAGGTGCTATTAGC+TGG 0.518107 8_1:+42016549 Msa1194690:three_prime_UTR
GATCTTCTTAAGAAGCTGGC+AGG 0.533432 8_1:+42016470 Msa1194690:CDS
ATTATTTGCTTAGAAACTCA+AGG 0.536924 8_1:-42016634 None:intergenic
CATGAGTTGCGCCACATCAA+AGG 0.541976 8_1:-42016291 None:intergenic
CATCAAAGGCTACCATATGA+TGG 0.567903 8_1:-42016277 None:intergenic
TCTTAAGAAGATCAAAGTTG+AGG 0.571010 8_1:-42016460 None:intergenic
TGCACAGGGATGACGGTTTG+GGG 0.573855 8_1:+42016237 Msa1194690:five_prime_UTR
GAAACTATCTAATGTTTCCA+GGG 0.584202 8_1:+42016600 Msa1194690:three_prime_UTR
AACCTAGTCGTATCTCTCGT+CGG 0.594968 8_1:-42016519 None:intergenic
CAGGTGCTATTAGCTGGTGT+TGG 0.611664 8_1:+42016555 Msa1194690:three_prime_UTR
GGCGCAACTCATGAAATTGG+TGG 0.617859 8_1:+42016301 Msa1194690:CDS
TCATATGGTAGCCTTTGATG+TGG 0.643558 8_1:+42016280 Msa1194690:exon
ATCCGACGAGAGATACGACT+AGG 0.699549 8_1:+42016517 Msa1194690:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAGAAAAAAGATGAAA+TGG + chr8_1:42015859-42015878 Msa1194690:intron 15.0%
!! TAAAAGAAAAAAGATGAAAT+GGG + chr8_1:42015860-42015879 Msa1194690:intron 15.0%
!!! TTAACTTTTCTTCATTATTA+AGG + chr8_1:42015895-42015914 Msa1194690:intron 15.0%
!! TTGTTATAAAGTATAAACAA+AGG + chr8_1:42015926-42015945 Msa1194690:intron 15.0%
!! GATTAAAACAAGTATATAAA+TGG - chr8_1:42016017-42016036 None:intergenic 15.0%
!! TTAAAAGAAAAAAGATGAAA+TGG + chr8_1:42015859-42015878 Msa1194690:intron 15.0%
!! TAAAAGAAAAAAGATGAAAT+GGG + chr8_1:42015860-42015879 Msa1194690:intron 15.0%
!!! TTAACTTTTCTTCATTATTA+AGG + chr8_1:42015895-42015914 Msa1194690:intron 15.0%
!! TTGTTATAAAGTATAAACAA+AGG + chr8_1:42015926-42015945 Msa1194690:intron 15.0%
!! GATTAAAACAAGTATATAAA+TGG - chr8_1:42016017-42016036 None:intergenic 15.0%
!!! TTTTATTTTTGTTTCTAGAC+AGG + chr8_1:42016211-42016230 Msa1194690:intron 20.0%
!! TCATTATACCTAACATAAAT+TGG - chr8_1:42016331-42016350 None:intergenic 20.0%
!!! TTTTGTTTTTATCTCTATGA+TGG + chr8_1:42016414-42016433 Msa1194690:intron 20.0%
!!! TTTTATTTTTGTTTCTAGAC+AGG + chr8_1:42016211-42016230 Msa1194690:intron 20.0%
!! TCATTATACCTAACATAAAT+TGG - chr8_1:42016331-42016350 None:intergenic 20.0%
!!! TTTTGTTTTTATCTCTATGA+TGG + chr8_1:42016414-42016433 Msa1194690:intron 20.0%
! TTTCTTCATTATTAAGGAGT+TGG + chr8_1:42015901-42015920 Msa1194690:intron 25.0%
! CTTTATACACATTCATGAAA+TGG + chr8_1:42016371-42016390 Msa1194690:intron 25.0%
! TGAAATGGACATAGATTTAA+TGG + chr8_1:42016386-42016405 Msa1194690:intron 25.0%
! ATTATTTGCTTAGAAACTCA+AGG - chr8_1:42016637-42016656 None:intergenic 25.0%
! TTGAGTTTCTAAGCAAATAA+TGG + chr8_1:42016636-42016655 Msa1194690:three_prime_UTR 25.0%
! TTTCTTCATTATTAAGGAGT+TGG + chr8_1:42015901-42015920 Msa1194690:intron 25.0%
! CTTTATACACATTCATGAAA+TGG + chr8_1:42016371-42016390 Msa1194690:intron 25.0%
! TGAAATGGACATAGATTTAA+TGG + chr8_1:42016386-42016405 Msa1194690:intron 25.0%
! ATTATTTGCTTAGAAACTCA+AGG - chr8_1:42016637-42016656 None:intergenic 25.0%
! TTGAGTTTCTAAGCAAATAA+TGG + chr8_1:42016636-42016655 Msa1194690:three_prime_UTR 25.0%
AAAAAGTGATTGACATTGGA+AGG + chr8_1:42016101-42016120 Msa1194690:intron 30.0%
TAGAGATGCTTATTAAGACT+AGG + chr8_1:42016125-42016144 Msa1194690:intron 30.0%
AACAAACTACAAACAAGACA+TGG - chr8_1:42016161-42016180 None:intergenic 30.0%
!!! TATGTTTTGATGACTCTTAC+TGG + chr8_1:42016182-42016201 Msa1194690:intron 30.0%
AATGGACATAGATTTAATGG+AGG + chr8_1:42016389-42016408 Msa1194690:intron 30.0%
TCTTAAGAAGATCAAAGTTG+AGG - chr8_1:42016463-42016482 None:intergenic 30.0%
TAGGTTTATGCATACAAATC+AGG + chr8_1:42016536-42016555 Msa1194690:three_prime_UTR 30.0%
AGAAACTATCTAATGTTTCC+AGG + chr8_1:42016599-42016618 Msa1194690:three_prime_UTR 30.0%
GAAACTATCTAATGTTTCCA+GGG + chr8_1:42016600-42016619 Msa1194690:three_prime_UTR 30.0%
TGACAGACTAACATAAAGAA+TGG - chr8_1:42016683-42016702 None:intergenic 30.0%
AAAAAGTGATTGACATTGGA+AGG + chr8_1:42016101-42016120 Msa1194690:intron 30.0%
TAGAGATGCTTATTAAGACT+AGG + chr8_1:42016125-42016144 Msa1194690:intron 30.0%
AACAAACTACAAACAAGACA+TGG - chr8_1:42016161-42016180 None:intergenic 30.0%
!!! TATGTTTTGATGACTCTTAC+TGG + chr8_1:42016182-42016201 Msa1194690:intron 30.0%
AATGGACATAGATTTAATGG+AGG + chr8_1:42016389-42016408 Msa1194690:intron 30.0%
TCTTAAGAAGATCAAAGTTG+AGG - chr8_1:42016463-42016482 None:intergenic 30.0%
TAGGTTTATGCATACAAATC+AGG + chr8_1:42016536-42016555 Msa1194690:three_prime_UTR 30.0%
AGAAACTATCTAATGTTTCC+AGG + chr8_1:42016599-42016618 Msa1194690:three_prime_UTR 30.0%
GAAACTATCTAATGTTTCCA+GGG + chr8_1:42016600-42016619 Msa1194690:three_prime_UTR 30.0%
TGACAGACTAACATAAAGAA+TGG - chr8_1:42016683-42016702 None:intergenic 30.0%
ACATTTGAGCATAGCATATG+AGG - chr8_1:42015976-42015995 None:intergenic 35.0%
! GTTTCTGTTGATTGCTACTA+TGG - chr8_1:42016079-42016098 None:intergenic 35.0%
ACGCAAAAAGTGATTGACAT+TGG + chr8_1:42016097-42016116 Msa1194690:intron 35.0%
TACAAACAAGACATGGTTGA+TGG - chr8_1:42016154-42016173 None:intergenic 35.0%
GTGGATGTCCAATTTATGTT+AGG + chr8_1:42016320-42016339 Msa1194690:intron 35.0%
CTTTGATCTTCTTAAGAAGC+TGG + chr8_1:42016466-42016485 Msa1194690:CDS 35.0%
ACAAAAAGAGAGTCATGTGT+AGG - chr8_1:42016496-42016515 None:intergenic 35.0%
ACATTTGAGCATAGCATATG+AGG - chr8_1:42015976-42015995 None:intergenic 35.0%
! GTTTCTGTTGATTGCTACTA+TGG - chr8_1:42016079-42016098 None:intergenic 35.0%
ACGCAAAAAGTGATTGACAT+TGG + chr8_1:42016097-42016116 Msa1194690:intron 35.0%
TACAAACAAGACATGGTTGA+TGG - chr8_1:42016154-42016173 None:intergenic 35.0%
GTGGATGTCCAATTTATGTT+AGG + chr8_1:42016320-42016339 Msa1194690:intron 35.0%
CTTTGATCTTCTTAAGAAGC+TGG + chr8_1:42016466-42016485 Msa1194690:CDS 35.0%
ACAAAAAGAGAGTCATGTGT+AGG - chr8_1:42016496-42016515 None:intergenic 35.0%
! TTTCTAGACAGGTTTTGCAC+AGG + chr8_1:42016222-42016241 Msa1194690:intron 40.0%
! TTCTAGACAGGTTTTGCACA+GGG + chr8_1:42016223-42016242 Msa1194690:intron 40.0%
CATCAAAGGCTACCATATGA+TGG - chr8_1:42016280-42016299 None:intergenic 40.0%
TCATATGGTAGCCTTTGATG+TGG + chr8_1:42016280-42016299 Msa1194690:exon 40.0%
AGATCAAAGTTGAGGTTGCA+TGG - chr8_1:42016455-42016474 None:intergenic 40.0%
!! ACAAATCAGGTGCTATTAGC+TGG + chr8_1:42016549-42016568 Msa1194690:three_prime_UTR 40.0%
TCAAGGATATTTAGATGCCC+TGG - chr8_1:42016620-42016639 None:intergenic 40.0%
! TTTCTAGACAGGTTTTGCAC+AGG + chr8_1:42016222-42016241 Msa1194690:intron 40.0%
! TTCTAGACAGGTTTTGCACA+GGG + chr8_1:42016223-42016242 Msa1194690:intron 40.0%
CATCAAAGGCTACCATATGA+TGG - chr8_1:42016280-42016299 None:intergenic 40.0%
TCATATGGTAGCCTTTGATG+TGG + chr8_1:42016280-42016299 Msa1194690:exon 40.0%
AGATCAAAGTTGAGGTTGCA+TGG - chr8_1:42016455-42016474 None:intergenic 40.0%
!! ACAAATCAGGTGCTATTAGC+TGG + chr8_1:42016549-42016568 Msa1194690:three_prime_UTR 40.0%
TCAAGGATATTTAGATGCCC+TGG - chr8_1:42016620-42016639 None:intergenic 40.0%
GCATTGTCTCTGCCATCATA+TGG + chr8_1:42016265-42016284 Msa1194690:exon 45.0%
TGTGGCGCAACTCATGAAAT+TGG + chr8_1:42016298-42016317 Msa1194690:CDS 45.0%
GATCTTCTTAAGAAGCTGGC+AGG + chr8_1:42016470-42016489 Msa1194690:CDS 45.0%
AACCTAGTCGTATCTCTCGT+CGG - chr8_1:42016522-42016541 None:intergenic 45.0%
!! TGCTATTAGCTGGTGTTGGT+TGG + chr8_1:42016559-42016578 Msa1194690:three_prime_UTR 45.0%
GCATTGTCTCTGCCATCATA+TGG + chr8_1:42016265-42016284 Msa1194690:exon 45.0%
TGTGGCGCAACTCATGAAAT+TGG + chr8_1:42016298-42016317 Msa1194690:CDS 45.0%
GATCTTCTTAAGAAGCTGGC+AGG + chr8_1:42016470-42016489 Msa1194690:CDS 45.0%
AACCTAGTCGTATCTCTCGT+CGG - chr8_1:42016522-42016541 None:intergenic 45.0%
!! TGCTATTAGCTGGTGTTGGT+TGG + chr8_1:42016559-42016578 Msa1194690:three_prime_UTR 45.0%
! CAGGTTTTGCACAGGGATGA+CGG + chr8_1:42016230-42016249 Msa1194690:intron 50.0%
! TTTGCACAGGGATGACGGTT+TGG + chr8_1:42016235-42016254 Msa1194690:five_prime_UTR 50.0%
! TTGCACAGGGATGACGGTTT+GGG + chr8_1:42016236-42016255 Msa1194690:five_prime_UTR 50.0%
CATGAGTTGCGCCACATCAA+AGG - chr8_1:42016294-42016313 None:intergenic 50.0%
GGCGCAACTCATGAAATTGG+TGG + chr8_1:42016301-42016320 Msa1194690:CDS 50.0%
ATCCGACGAGAGATACGACT+AGG + chr8_1:42016517-42016536 Msa1194690:exon 50.0%
!! CAGGTGCTATTAGCTGGTGT+TGG + chr8_1:42016555-42016574 Msa1194690:three_prime_UTR 50.0%
! CAGGTTTTGCACAGGGATGA+CGG + chr8_1:42016230-42016249 Msa1194690:intron 50.0%
! TTTGCACAGGGATGACGGTT+TGG + chr8_1:42016235-42016254 Msa1194690:five_prime_UTR 50.0%
! TTGCACAGGGATGACGGTTT+GGG + chr8_1:42016236-42016255 Msa1194690:five_prime_UTR 50.0%
CATGAGTTGCGCCACATCAA+AGG - chr8_1:42016294-42016313 None:intergenic 50.0%
GGCGCAACTCATGAAATTGG+TGG + chr8_1:42016301-42016320 Msa1194690:CDS 50.0%
ATCCGACGAGAGATACGACT+AGG + chr8_1:42016517-42016536 Msa1194690:exon 50.0%
!! CAGGTGCTATTAGCTGGTGT+TGG + chr8_1:42016555-42016574 Msa1194690:three_prime_UTR 50.0%
! TGCACAGGGATGACGGTTTG+GGG + chr8_1:42016237-42016256 Msa1194690:five_prime_UTR 55.0%
! TGCACAGGGATGACGGTTTG+GGG + chr8_1:42016237-42016256 Msa1194690:five_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 42015836 42016721 42015836 ID=Msa1194690;Name=Msa1194690
chr8_1 mRNA 42015836 42016721 42015836 ID=Msa1194690-mRNA-1;Parent=Msa1194690;Name=Msa1194690-mRNA-1;_AED=0.08;_eAED=0.33;_QI=65|0|0.25|0.5|1|1|4|204|41
chr8_1 exon 42015836 42015843 42015836 ID=Msa1194690-mRNA-1:exon:13585;Parent=Msa1194690-mRNA-1
chr8_1 exon 42015917 42015922 42015917 ID=Msa1194690-mRNA-1:exon:13586;Parent=Msa1194690-mRNA-1
chr8_1 exon 42016233 42016336 42016233 ID=Msa1194690-mRNA-1:exon:13587;Parent=Msa1194690-mRNA-1
chr8_1 exon 42016445 42016721 42016445 ID=Msa1194690-mRNA-1:exon:13588;Parent=Msa1194690-mRNA-1
chr8_1 five_prime_UTR 42015836 42015843 42015836 ID=Msa1194690-mRNA-1:five_prime_utr;Parent=Msa1194690-mRNA-1
chr8_1 five_prime_UTR 42015917 42015922 42015917 ID=Msa1194690-mRNA-1:five_prime_utr;Parent=Msa1194690-mRNA-1
chr8_1 five_prime_UTR 42016233 42016283 42016233 ID=Msa1194690-mRNA-1:five_prime_utr;Parent=Msa1194690-mRNA-1
chr8_1 CDS 42016284 42016336 42016284 ID=Msa1194690-mRNA-1:cds;Parent=Msa1194690-mRNA-1
chr8_1 CDS 42016445 42016517 42016445 ID=Msa1194690-mRNA-1:cds;Parent=Msa1194690-mRNA-1
chr8_1 three_prime_UTR 42016518 42016721 42016518 ID=Msa1194690-mRNA-1:three_prime_utr;Parent=Msa1194690-mRNA-1
Gene Sequence

>Msa1194690

ATGGTAGCCTTTGATGTGGCGCAACTCATGAAATTGGTGGATGTCCAATTTATTGATAATCCATGCAACCTCAACTTTGATCTTCTTAAGAAGCTGGCAGGCCTACACATGACTCTCTTTTTGTGA
Protein sequence

>Msa1194690

MVAFDVAQLMKLVDVQFIDNPCNLNFDLLKKLAGLHMTLFL*