AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0852450

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 32 sgRNAs with CRISPR-Local

Find 135 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAAAATATTCAAGGATTTA+AGG 0.167891 5_4:+43499251 Msa0852450:five_prime_UTR
GCAGGTTCTGTTTGCTGTTT+AGG 0.261987 5_4:+43499853 Msa0852450:intron
TTGCATCAGTCACTTACTTT+AGG 0.286519 5_4:+43500077 Msa0852450:CDS
TCAGCACGTGTTGGTGTGCT+TGG 0.313885 5_4:+43499966 Msa0852450:CDS
CAGCACGTGTTGGTGTGCTT+GGG 0.323057 5_4:+43499967 Msa0852450:CDS
GGTGGGTGCTGCCTTCTGTT+AGG 0.346591 5_4:+43499874 Msa0852450:CDS
GATATATTTGGGTCAAATAA+TGG 0.350737 5_4:-43499365 None:intergenic
TCAGAGTCACAAAATATTCA+AGG 0.415475 5_4:+43499243 Msa0852450:five_prime_UTR
TTGATGCGGCGTTATGCGTA+GGG 0.417919 5_4:+43499998 Msa0852450:CDS
TTTGATGCGGCGTTATGCGT+AGG 0.426567 5_4:+43499997 Msa0852450:CDS
GCTGCTGCCAGCAGCTTCTG+TGG 0.448517 5_4:+43499937 Msa0852450:CDS
ATGTCGTTGCTGATTGTGAT+TGG 0.451751 5_4:+43499205 Msa0852450:five_prime_UTR
TGTGTGCACCTGCTGTCAGC+TGG 0.454209 5_4:+43499909 Msa0852450:CDS
TTGGGTCAAATAATGGCAAC+AGG 0.463519 5_4:-43499358 None:intergenic
AGCAAACACCAGCTGACAGC+AGG 0.467010 5_4:-43499917 None:intergenic
GTTCTGTTTGCTGTTTAGGT+GGG 0.496688 5_4:+43499857 Msa0852450:CDS
AGCACGTGTTGGTGTGCTTG+GGG 0.499493 5_4:+43499968 Msa0852450:CDS
TGAAGAGCATGGTAATGCAT+TGG 0.500687 5_4:+43499328 Msa0852450:five_prime_UTR
AACCGCACCACAGAAGCTGC+TGG 0.515986 5_4:-43499944 None:intergenic
CAGCAGCCGCACCTAACAGA+AGG 0.531418 5_4:-43499885 None:intergenic
TGCCAGCAGCTTCTGTGGTG+CGG 0.535911 5_4:+43499942 Msa0852450:CDS
GGTTCTGTTTGCTGTTTAGG+TGG 0.539650 5_4:+43499856 Msa0852450:intron
AAACTATCCGAAAAGGCAGC+CGG 0.564569 5_4:-43500036 None:intergenic
AAGGTCATCATGAAGCTGAA+AGG 0.589756 5_4:+43499433 Msa0852450:exon
AAAGTAAGTGACTGATGCAA+AGG 0.593512 5_4:-43500074 None:intergenic
GTCAAATAATGGCAACAGGT+AGG 0.603205 5_4:-43499354 None:intergenic
TTATTGTTTCTTGAAGAGCA+TGG 0.609910 5_4:+43499317 Msa0852450:five_prime_UTR
GCACGTGTTGGTGTGCTTGG+GGG 0.617916 5_4:+43499969 Msa0852450:CDS
GATGCGGCGTTATGCGTAGG+GGG 0.628335 5_4:+43500000 Msa0852450:CDS
TGATGCGGCGTTATGCGTAG+GGG 0.646615 5_4:+43499999 Msa0852450:CDS
TGGTGCGGTTCAGCACGTGT+TGG 0.649916 5_4:+43499957 Msa0852450:CDS
GTGCTGCCTTCTGTTAGGTG+CGG 0.686941 5_4:+43499879 Msa0852450:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAATTGACAAAGATTTA+AGG + chr5_4:43499414-43499433 Msa0852450:five_prime_UTR 15.0%
!! AAAAAATTGACAAAGATTTA+AGG + chr5_4:43499414-43499433 Msa0852450:five_prime_UTR 15.0%
!! ACAAAATATTCAAGGATTTA+AGG + chr5_4:43499251-43499270 Msa0852450:five_prime_UTR 20.0%
!! ATATATGAATATGCATACAA+AGG + chr5_4:43499766-43499785 Msa0852450:intron 20.0%
!! ACAAAATATTCAAGGATTTA+AGG + chr5_4:43499251-43499270 Msa0852450:five_prime_UTR 20.0%
!! ATATATGAATATGCATACAA+AGG + chr5_4:43499766-43499785 Msa0852450:intron 20.0%
! GATATATTTGGGTCAAATAA+TGG - chr5_4:43499368-43499387 None:intergenic 25.0%
!!! CATTTTTGGGAGATATATTT+GGG - chr5_4:43499379-43499398 None:intergenic 25.0%
!!! ACATTTTTGGGAGATATATT+TGG - chr5_4:43499380-43499399 None:intergenic 25.0%
! AAATATATCTCCCAAAAATG+TGG + chr5_4:43499379-43499398 Msa0852450:five_prime_UTR 25.0%
!! GCAATTATAACCACATTTTT+GGG - chr5_4:43499392-43499411 None:intergenic 25.0%
!! TGCAATTATAACCACATTTT+TGG - chr5_4:43499393-43499412 None:intergenic 25.0%
! AAGGAAAATGAATTAGGTAT+GGG - chr5_4:43499500-43499519 None:intergenic 25.0%
! ACATTCAAGGAAAATGAATT+AGG - chr5_4:43499506-43499525 None:intergenic 25.0%
!!! TCACTTTTGATAAATTTGTG+TGG + chr5_4:43499644-43499663 Msa0852450:intron 25.0%
! GATATATTTGGGTCAAATAA+TGG - chr5_4:43499368-43499387 None:intergenic 25.0%
!!! CATTTTTGGGAGATATATTT+GGG - chr5_4:43499379-43499398 None:intergenic 25.0%
!!! ACATTTTTGGGAGATATATT+TGG - chr5_4:43499380-43499399 None:intergenic 25.0%
! AAATATATCTCCCAAAAATG+TGG + chr5_4:43499379-43499398 Msa0852450:five_prime_UTR 25.0%
!! GCAATTATAACCACATTTTT+GGG - chr5_4:43499392-43499411 None:intergenic 25.0%
!! TGCAATTATAACCACATTTT+TGG - chr5_4:43499393-43499412 None:intergenic 25.0%
! AAGGAAAATGAATTAGGTAT+GGG - chr5_4:43499500-43499519 None:intergenic 25.0%
! ACATTCAAGGAAAATGAATT+AGG - chr5_4:43499506-43499525 None:intergenic 25.0%
!!! TCACTTTTGATAAATTTGTG+TGG + chr5_4:43499644-43499663 Msa0852450:intron 25.0%
TCAGAGTCACAAAATATTCA+AGG + chr5_4:43499243-43499262 Msa0852450:five_prime_UTR 30.0%
! TTATTGTTTCTTGAAGAGCA+TGG + chr5_4:43499317-43499336 Msa0852450:five_prime_UTR 30.0%
CAAGGAAAATGAATTAGGTA+TGG - chr5_4:43499501-43499520 None:intergenic 30.0%
ATGAAGGAAAAGAACATTCA+AGG - chr5_4:43499519-43499538 None:intergenic 30.0%
ATGCAACAACATAACAATGA+AGG - chr5_4:43499535-43499554 None:intergenic 30.0%
!!! TAAGTCTATGGTTTTGAGAA+AGG + chr5_4:43499611-43499630 Msa0852450:intron 30.0%
TCAGAGTCACAAAATATTCA+AGG + chr5_4:43499243-43499262 Msa0852450:five_prime_UTR 30.0%
! TTATTGTTTCTTGAAGAGCA+TGG + chr5_4:43499317-43499336 Msa0852450:five_prime_UTR 30.0%
CAAGGAAAATGAATTAGGTA+TGG - chr5_4:43499501-43499520 None:intergenic 30.0%
ATGAAGGAAAAGAACATTCA+AGG - chr5_4:43499519-43499538 None:intergenic 30.0%
ATGCAACAACATAACAATGA+AGG - chr5_4:43499535-43499554 None:intergenic 30.0%
!!! TAAGTCTATGGTTTTGAGAA+AGG + chr5_4:43499611-43499630 Msa0852450:intron 30.0%
TCAAACACAACTTCTTGAAG+GGG - chr5_4:43499579-43499598 None:intergenic 35.0%
GTCAAACACAACTTCTTGAA+GGG - chr5_4:43499580-43499599 None:intergenic 35.0%
AGTCAAACACAACTTCTTGA+AGG - chr5_4:43499581-43499600 None:intergenic 35.0%
CTAGAGACTGTATAAGTCTA+TGG + chr5_4:43499599-43499618 Msa0852450:intron 35.0%
!!! CTATGGTTTTGAGAAAGGTA+TGG + chr5_4:43499616-43499635 Msa0852450:intron 35.0%
TCTCGTATCTAACAAACTGA+AGG - chr5_4:43499686-43499705 None:intergenic 35.0%
! TGCCTTTTCGGATAGTTTTT+GGG + chr5_4:43500041-43500060 Msa0852450:CDS 35.0%
AAAGTAAGTGACTGATGCAA+AGG - chr5_4:43500077-43500096 None:intergenic 35.0%
TCAAACACAACTTCTTGAAG+GGG - chr5_4:43499579-43499598 None:intergenic 35.0%
GTCAAACACAACTTCTTGAA+GGG - chr5_4:43499580-43499599 None:intergenic 35.0%
AGTCAAACACAACTTCTTGA+AGG - chr5_4:43499581-43499600 None:intergenic 35.0%
CTAGAGACTGTATAAGTCTA+TGG + chr5_4:43499599-43499618 Msa0852450:intron 35.0%
!!! CTATGGTTTTGAGAAAGGTA+TGG + chr5_4:43499616-43499635 Msa0852450:intron 35.0%
TCTCGTATCTAACAAACTGA+AGG - chr5_4:43499686-43499705 None:intergenic 35.0%
! TGCCTTTTCGGATAGTTTTT+GGG + chr5_4:43500041-43500060 Msa0852450:CDS 35.0%
AAAGTAAGTGACTGATGCAA+AGG - chr5_4:43500077-43500096 None:intergenic 35.0%
! ATGTCGTTGCTGATTGTGAT+TGG + chr5_4:43499205-43499224 Msa0852450:five_prime_UTR 40.0%
! TGAAGAGCATGGTAATGCAT+TGG + chr5_4:43499328-43499347 Msa0852450:five_prime_UTR 40.0%
GTCAAATAATGGCAACAGGT+AGG - chr5_4:43499357-43499376 None:intergenic 40.0%
TTGGGTCAAATAATGGCAAC+AGG - chr5_4:43499361-43499380 None:intergenic 40.0%
AAGGTCATCATGAAGCTGAA+AGG + chr5_4:43499433-43499452 Msa0852450:exon 40.0%
ATACACATAAGTGATGCACG+TGG - chr5_4:43499471-43499490 None:intergenic 40.0%
CAAACACAACTTCTTGAAGG+GGG - chr5_4:43499578-43499597 None:intergenic 40.0%
!!! GGTTTTTTTGTGTTGTTCGC+AGG + chr5_4:43499835-43499854 Msa0852450:intron 40.0%
!! GTTCTGTTTGCTGTTTAGGT+GGG + chr5_4:43499857-43499876 Msa0852450:CDS 40.0%
! CTGCCTTTTCGGATAGTTTT+TGG + chr5_4:43500040-43500059 Msa0852450:CDS 40.0%
GACCCAAAAACTATCCGAAA+AGG - chr5_4:43500046-43500065 None:intergenic 40.0%
GCATCAGTCACTTACTTTAG+AGG + chr5_4:43500079-43500098 Msa0852450:CDS 40.0%
! ATGTCGTTGCTGATTGTGAT+TGG + chr5_4:43499205-43499224 Msa0852450:five_prime_UTR 40.0%
! TGAAGAGCATGGTAATGCAT+TGG + chr5_4:43499328-43499347 Msa0852450:five_prime_UTR 40.0%
GTCAAATAATGGCAACAGGT+AGG - chr5_4:43499357-43499376 None:intergenic 40.0%
TTGGGTCAAATAATGGCAAC+AGG - chr5_4:43499361-43499380 None:intergenic 40.0%
AAGGTCATCATGAAGCTGAA+AGG + chr5_4:43499433-43499452 Msa0852450:exon 40.0%
ATACACATAAGTGATGCACG+TGG - chr5_4:43499471-43499490 None:intergenic 40.0%
CAAACACAACTTCTTGAAGG+GGG - chr5_4:43499578-43499597 None:intergenic 40.0%
!!! GGTTTTTTTGTGTTGTTCGC+AGG + chr5_4:43499835-43499854 Msa0852450:intron 40.0%
!! GTTCTGTTTGCTGTTTAGGT+GGG + chr5_4:43499857-43499876 Msa0852450:CDS 40.0%
! CTGCCTTTTCGGATAGTTTT+TGG + chr5_4:43500040-43500059 Msa0852450:CDS 40.0%
GACCCAAAAACTATCCGAAA+AGG - chr5_4:43500046-43500065 None:intergenic 40.0%
! ACTCATTTGCTGCTGTCATG+CGG + chr5_4:43499796-43499815 Msa0852450:intron 45.0%
!! GCAGGTTCTGTTTGCTGTTT+AGG + chr5_4:43499853-43499872 Msa0852450:intron 45.0%
!! GGTTCTGTTTGCTGTTTAGG+TGG + chr5_4:43499856-43499875 Msa0852450:intron 45.0%
AAACTATCCGAAAAGGCAGC+CGG - chr5_4:43500039-43500058 None:intergenic 45.0%
! ACTCATTTGCTGCTGTCATG+CGG + chr5_4:43499796-43499815 Msa0852450:intron 45.0%
!! GCAGGTTCTGTTTGCTGTTT+AGG + chr5_4:43499853-43499872 Msa0852450:intron 45.0%
!! GGTTCTGTTTGCTGTTTAGG+TGG + chr5_4:43499856-43499875 Msa0852450:intron 45.0%
AAACTATCCGAAAAGGCAGC+CGG - chr5_4:43500039-43500058 None:intergenic 45.0%
! CAACTTCTTGAAGGGGGTGT+TGG - chr5_4:43499572-43499591 None:intergenic 50.0%
CCTGCTAGCTGCTCAACATA+AGG - chr5_4:43499742-43499761 None:intergenic 50.0%
CCTTATGTTGAGCAGCTAGC+AGG + chr5_4:43499739-43499758 Msa0852450:intron 50.0%
TTTGATGCGGCGTTATGCGT+AGG + chr5_4:43499997-43500016 Msa0852450:CDS 50.0%
TTGATGCGGCGTTATGCGTA+GGG + chr5_4:43499998-43500017 Msa0852450:CDS 50.0%
AGGGGGTCATTGTTCTTGTC+CGG + chr5_4:43500017-43500036 Msa0852450:CDS 50.0%
! TTCTTGTCCGGCTGCCTTTT+CGG + chr5_4:43500029-43500048 Msa0852450:CDS 50.0%
! CAACTTCTTGAAGGGGGTGT+TGG - chr5_4:43499572-43499591 None:intergenic 50.0%
CCTGCTAGCTGCTCAACATA+AGG - chr5_4:43499742-43499761 None:intergenic 50.0%
CCTTATGTTGAGCAGCTAGC+AGG + chr5_4:43499739-43499758 Msa0852450:intron 50.0%
TTTGATGCGGCGTTATGCGT+AGG + chr5_4:43499997-43500016 Msa0852450:CDS 50.0%
TTGATGCGGCGTTATGCGTA+GGG + chr5_4:43499998-43500017 Msa0852450:CDS 50.0%
AGGGGGTCATTGTTCTTGTC+CGG + chr5_4:43500017-43500036 Msa0852450:CDS 50.0%
! TTCTTGTCCGGCTGCCTTTT+CGG + chr5_4:43500029-43500048 Msa0852450:CDS 50.0%
TGCGGTTATGTCTGCTGTGC+TGG + chr5_4:43499814-43499833 Msa0852450:intron 55.0%
GTGCTGCCTTCTGTTAGGTG+CGG + chr5_4:43499879-43499898 Msa0852450:CDS 55.0%
AGCAAACACCAGCTGACAGC+AGG - chr5_4:43499920-43499939 None:intergenic 55.0%
! TCAGCACGTGTTGGTGTGCT+TGG + chr5_4:43499966-43499985 Msa0852450:CDS 55.0%
! CAGCACGTGTTGGTGTGCTT+GGG + chr5_4:43499967-43499986 Msa0852450:CDS 55.0%
! AGCACGTGTTGGTGTGCTTG+GGG + chr5_4:43499968-43499987 Msa0852450:CDS 55.0%
TGATGCGGCGTTATGCGTAG+GGG + chr5_4:43499999-43500018 Msa0852450:CDS 55.0%
TGCGGTTATGTCTGCTGTGC+TGG + chr5_4:43499814-43499833 Msa0852450:intron 55.0%
GTGCTGCCTTCTGTTAGGTG+CGG + chr5_4:43499879-43499898 Msa0852450:CDS 55.0%
AGCAAACACCAGCTGACAGC+AGG - chr5_4:43499920-43499939 None:intergenic 55.0%
! TCAGCACGTGTTGGTGTGCT+TGG + chr5_4:43499966-43499985 Msa0852450:CDS 55.0%
! CAGCACGTGTTGGTGTGCTT+GGG + chr5_4:43499967-43499986 Msa0852450:CDS 55.0%
! AGCACGTGTTGGTGTGCTTG+GGG + chr5_4:43499968-43499987 Msa0852450:CDS 55.0%
TGATGCGGCGTTATGCGTAG+GGG + chr5_4:43499999-43500018 Msa0852450:CDS 55.0%
! GGTGGGTGCTGCCTTCTGTT+AGG + chr5_4:43499874-43499893 Msa0852450:CDS 60.0%
CAGCAGCCGCACCTAACAGA+AGG - chr5_4:43499888-43499907 None:intergenic 60.0%
TGTGTGCACCTGCTGTCAGC+TGG + chr5_4:43499909-43499928 Msa0852450:CDS 60.0%
TGCCAGCAGCTTCTGTGGTG+CGG + chr5_4:43499942-43499961 Msa0852450:CDS 60.0%
AACCGCACCACAGAAGCTGC+TGG - chr5_4:43499947-43499966 None:intergenic 60.0%
TGGTGCGGTTCAGCACGTGT+TGG + chr5_4:43499957-43499976 Msa0852450:CDS 60.0%
! GCACGTGTTGGTGTGCTTGG+GGG + chr5_4:43499969-43499988 Msa0852450:CDS 60.0%
TGTTGGTGTGCTTGGGGGCT+GGG + chr5_4:43499974-43499993 Msa0852450:CDS 60.0%
CTTGGGGGCTGGGTTTGATG+CGG + chr5_4:43499984-43500003 Msa0852450:CDS 60.0%
GATGCGGCGTTATGCGTAGG+GGG + chr5_4:43500000-43500019 Msa0852450:CDS 60.0%
! GGTGGGTGCTGCCTTCTGTT+AGG + chr5_4:43499874-43499893 Msa0852450:CDS 60.0%
CAGCAGCCGCACCTAACAGA+AGG - chr5_4:43499888-43499907 None:intergenic 60.0%
TGTGTGCACCTGCTGTCAGC+TGG + chr5_4:43499909-43499928 Msa0852450:CDS 60.0%
TGCCAGCAGCTTCTGTGGTG+CGG + chr5_4:43499942-43499961 Msa0852450:CDS 60.0%
AACCGCACCACAGAAGCTGC+TGG - chr5_4:43499947-43499966 None:intergenic 60.0%
TGGTGCGGTTCAGCACGTGT+TGG + chr5_4:43499957-43499976 Msa0852450:CDS 60.0%
! GCACGTGTTGGTGTGCTTGG+GGG + chr5_4:43499969-43499988 Msa0852450:CDS 60.0%
TGTTGGTGTGCTTGGGGGCT+GGG + chr5_4:43499974-43499993 Msa0852450:CDS 60.0%
CTTGGGGGCTGGGTTTGATG+CGG + chr5_4:43499984-43500003 Msa0852450:CDS 60.0%
GATGCGGCGTTATGCGTAGG+GGG + chr5_4:43500000-43500019 Msa0852450:CDS 60.0%
GCTGCTGCCAGCAGCTTCTG+TGG + chr5_4:43499937-43499956 Msa0852450:CDS 65.0%
! GTGTTGGTGTGCTTGGGGGC+TGG + chr5_4:43499973-43499992 Msa0852450:CDS 65.0%
GCTGCTGCCAGCAGCTTCTG+TGG + chr5_4:43499937-43499956 Msa0852450:CDS 65.0%
! GTGTTGGTGTGCTTGGGGGC+TGG + chr5_4:43499973-43499992 Msa0852450:CDS 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 43499194 43500098 43499194 ID=Msa0852450;Name=Msa0852450
chr5_4 mRNA 43499194 43500098 43499194 ID=Msa0852450-mRNA-1;Parent=Msa0852450;Name=Msa0852450-mRNA-1;_AED=0.24;_eAED=0.60;_QI=248|0|0.5|1|1|1|2|0|84
chr5_4 exon 43499194 43499454 43499194 ID=Msa0852450-mRNA-1:exon:13789;Parent=Msa0852450-mRNA-1
chr5_4 exon 43499857 43500098 43499857 ID=Msa0852450-mRNA-1:exon:13790;Parent=Msa0852450-mRNA-1
chr5_4 five_prime_UTR 43499194 43499441 43499194 ID=Msa0852450-mRNA-1:five_prime_utr;Parent=Msa0852450-mRNA-1
chr5_4 CDS 43499442 43499454 43499442 ID=Msa0852450-mRNA-1:cds;Parent=Msa0852450-mRNA-1
chr5_4 CDS 43499857 43500098 43499857 ID=Msa0852450-mRNA-1:cds;Parent=Msa0852450-mRNA-1
Gene Sequence

>Msa0852450

ATGAAGCTGAAAGGTTCTGTTTGCTGTTTAGGTGGGTGCTGCCTTCTGTTAGGTGCGGCTGCTGCTGTGTGCACCTGCTGTCAGCTGGTGTTTGCTGCTGCCAGCAGCTTCTGTGGTGCGGTTCAGCACGTGTTGGTGTGCTTGGGGGCTGGGTTTGATGCGGCGTTATGCGTAGGGGGTCATTGTTCTTGTCCGGCTGCCTTTTCGGATAGTTTTTGGGTCTTTGTATACCTTTGCATCAGTCACTTACTTTAG
Protein sequence

>Msa0852450

MKLKGSVCCLGGCCLLLGAAAAVCTCCQLVFAAASSFCGAVQHVLVCLGAGFDAALCVGGHCSCPAAFSDSFWVFVYLCISHLL*