AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene015239

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015239.t1 MTR_5g015850 97.810 137 2 1 1 136 1 137 6.36e-97 275
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene015239.t1 AT1G07830 71.528 144 33 3 1 136 1 144 4.39e-67 199

Find 25 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGAATTGCGTCTGAAATCT+TGG 0.295639 5.4:-9381858 MS.gene015239:CDS
CCCTCTTCCGGAGTTCTTTG+AGG 0.397007 5.4:-9382073 MS.gene015239:CDS
GAGATGAAGAAAATGATAAA+TGG 0.401349 5.4:-9381401 MS.gene015239:CDS
TTAGGTAAGCGCTCCGGGTT+AGG 0.401390 5.4:+9381742 None:intergenic
GTTGTGGTATGTGTTGTTAA+AGG 0.420053 5.4:-9381821 MS.gene015239:CDS
AACGAGACACCAGTTGTCTA+TGG 0.421926 5.4:-9382039 MS.gene015239:intron
TGAATTGCGTCTGAAATCTT+GGG 0.436291 5.4:-9381857 MS.gene015239:CDS
TGCTGTTAGAAACCCTCTTC+CGG 0.440920 5.4:-9382085 MS.gene015239:CDS
TCAGCAGACCTCCTTGCGTC+TGG 0.463615 5.4:+9381422 None:intergenic
ATACCTTAGGTAAGCGCTCC+GGG 0.470522 5.4:+9381737 None:intergenic
GAACTTGCGCTTTCCTAACC+CGG 0.481233 5.4:-9381755 MS.gene015239:CDS
GCCTCAAAGAACTCCGGAAG+AGG 0.493349 5.4:+9382072 None:intergenic
TATTTCATACCATAGACAAC+TGG 0.503485 5.4:+9382030 None:intergenic
AATACCTTAGGTAAGCGCTC+CGG 0.514447 5.4:+9381736 None:intergenic
AAACAGTATTCCACTACAGC+TGG 0.543067 5.4:-9382108 MS.gene015239:CDS
ACACATACCACAACTTATGA+AGG 0.545630 5.4:+9381830 None:intergenic
TTTGTTAGGTCGGAGTTGGA+AGG 0.551769 5.4:-9381884 MS.gene015239:intron
GGGATGACCTTCATAAGTTG+TGG 0.556409 5.4:-9381837 MS.gene015239:CDS
TCTAACAGCACCAGCTGTAG+TGG 0.557909 5.4:+9382098 None:intergenic
TAACCCGGAGCGCTTACCTA+AGG 0.570629 5.4:-9381740 MS.gene015239:intron
CTGTCTGCCTCAAAGAACTC+CGG 0.578032 5.4:+9382066 None:intergenic
CCTCAAAGAACTCCGGAAGA+GGG 0.599992 5.4:+9382073 None:intergenic
CGATTGAAGAACCAGACGCA+AGG 0.611981 5.4:-9381433 MS.gene015239:CDS
CAGTAAGCACATGCTTGATG+CGG 0.642610 5.4:+9381462 None:intergenic
TTGAAGAACCAGACGCAAGG+AGG 0.691763 5.4:-9381430 MS.gene015239:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAATGTTAAATTTTGTAT+GGG - chr5.4:9381993-9382012 MS.gene015239:intron 10.0%
!!! GTAAAATGTTAAATTTTGTA+TGG - chr5.4:9381992-9382011 MS.gene015239:intron 15.0%
!!! ATAGTTTTACCATTTTTGTT+AGG - chr5.4:9381658-9381677 MS.gene015239:intron 20.0%
!!! GATTTAATTTATGTGAAATC+AGG - chr5.4:9382055-9382074 MS.gene015239:CDS 20.0%
! AAAAAGTGAAGAAATACCTT+AGG + chr5.4:9381835-9381854 None:intergenic 25.0%
! GAGATGAAGAAAATGATAAA+TGG - chr5.4:9382155-9382174 MS.gene015239:CDS 25.0%
! TATAAGAAAACAAAGTGATG+AGG + chr5.4:9381641-9381660 None:intergenic 25.0%
!! ATGTTAAATTTTGTATGGGT+TGG - chr5.4:9381997-9382016 MS.gene015239:intron 25.0%
!! TGTTAAATTTTGTATGGGTT+GGG - chr5.4:9381998-9382017 MS.gene015239:intron 25.0%
!!! ATTTTTTTGTACCTAATGTG+TGG + chr5.4:9381609-9381628 None:intergenic 25.0%
!!! TTTTACCATTTTTGTTAGGT+CGG - chr5.4:9381662-9381681 MS.gene015239:intron 25.0%
AGTTATGTGGACATTGATAT+AGG - chr5.4:9381895-9381914 MS.gene015239:intron 30.0%
ATCAATGTCCACATAACTAA+GGG + chr5.4:9381893-9381912 None:intergenic 30.0%
CCTATTCTATTGAAAAGAAG+AGG + chr5.4:9381556-9381575 None:intergenic 30.0%
TATCAATGTCCACATAACTA+AGG + chr5.4:9381894-9381913 None:intergenic 30.0%
TATTTCATACCATAGACAAC+TGG + chr5.4:9381529-9381548 None:intergenic 30.0%
TTTCATTATAGCCACACATT+AGG - chr5.4:9381595-9381614 MS.gene015239:intron 30.0%
! CCTCTTCTTTTCAATAGAAT+AGG - chr5.4:9381553-9381572 MS.gene015239:intron 30.0%
! TTTTGTTACCCTTAGTTATG+TGG - chr5.4:9381882-9381901 MS.gene015239:intron 30.0%
!! GTTAAATTTTGTATGGGTTG+GGG - chr5.4:9381999-9382018 MS.gene015239:intron 30.0%
!!! ATTTCTTCACTTTTTACACC+TGG - chr5.4:9381840-9381859 MS.gene015239:CDS 30.0%
!!! TTAAATTTTGTATGGGTTGG+GGG - chr5.4:9382000-9382019 MS.gene015239:intron 30.0%
ACACATACCACAACTTATGA+AGG + chr5.4:9381729-9381748 None:intergenic 35.0%
ATTGATATAGGAAATCGCAG+TGG - chr5.4:9381907-9381926 MS.gene015239:intron 35.0%
! GTTGTGGTATGTGTTGTTAA+AGG - chr5.4:9381735-9381754 MS.gene015239:intron 35.0%
! TGAATTGCGTCTGAAATCTT+GGG - chr5.4:9381699-9381718 MS.gene015239:intron 35.0%
!!! AGTGGAATACTGTTTTGATC+TGG + chr5.4:9381443-9381462 None:intergenic 35.0%
!!! TAAATTTTGTATGGGTTGGG+GGG - chr5.4:9382001-9382020 MS.gene015239:intron 35.0%
AAACAGTATTCCACTACAGC+TGG - chr5.4:9381448-9381467 MS.gene015239:CDS 40.0%
CAACTCCGACCTAACAAAAA+TGG + chr5.4:9381670-9381689 None:intergenic 40.0%
! CATTTTTGTTAGGTCGGAGT+TGG - chr5.4:9381668-9381687 MS.gene015239:intron 40.0%
! CTGAATTGCGTCTGAAATCT+TGG - chr5.4:9381698-9381717 MS.gene015239:intron 40.0%
! GTGGTGCTTTTATCAACGTT+TGG - chr5.4:9381929-9381948 MS.gene015239:intron 40.0%
AACGAGACACCAGTTGTCTA+TGG - chr5.4:9381517-9381536 MS.gene015239:intron 45.0%
AATACCTTAGGTAAGCGCTC+CGG + chr5.4:9381823-9381842 None:intergenic 45.0%
CAGTAAGCACATGCTTGATG+CGG + chr5.4:9382097-9382116 None:intergenic 45.0%
GATATAGGAAATCGCAGTGG+TGG - chr5.4:9381910-9381929 MS.gene015239:intron 45.0%
GGGATGACCTTCATAAGTTG+TGG - chr5.4:9381719-9381738 MS.gene015239:intron 45.0%
TGCTGTTAGAAACCCTCTTC+CGG - chr5.4:9381471-9381490 MS.gene015239:CDS 45.0%
TTTGTTAGGTCGGAGTTGGA+AGG - chr5.4:9381672-9381691 MS.gene015239:intron 45.0%
ATACCTTAGGTAAGCGCTCC+GGG + chr5.4:9381822-9381841 None:intergenic 50.0%
CAACACGCGTAAATCAGACC+AGG + chr5.4:9381861-9381880 None:intergenic 50.0%
CCTCAAAGAACTCCGGAAGA+GGG + chr5.4:9381486-9381505 None:intergenic 50.0%
CGATTGAAGAACCAGACGCA+AGG - chr5.4:9382123-9382142 MS.gene015239:CDS 50.0%
CTGTCTGCCTCAAAGAACTC+CGG + chr5.4:9381493-9381512 None:intergenic 50.0%
GAACTTGCGCTTTCCTAACC+CGG - chr5.4:9381801-9381820 MS.gene015239:CDS 50.0%
TCTAACAGCACCAGCTGTAG+TGG + chr5.4:9381461-9381480 None:intergenic 50.0%
TTGAAGAACCAGACGCAAGG+AGG - chr5.4:9382126-9382145 MS.gene015239:CDS 50.0%
CCCTCTTCCGGAGTTCTTTG+AGG - chr5.4:9381483-9381502 MS.gene015239:intron 55.0%
GCCTCAAAGAACTCCGGAAG+AGG + chr5.4:9381487-9381506 None:intergenic 55.0%
GGTTGGGGGGAAACTGTTCA+CGG - chr5.4:9382014-9382033 MS.gene015239:intron 55.0%
TTAGGTAAGCGCTCCGGGTT+AGG + chr5.4:9381817-9381836 None:intergenic 55.0%
! TAACCCGGAGCGCTTACCTA+AGG - chr5.4:9381816-9381835 MS.gene015239:CDS 55.0%
TCAGCAGACCTCCTTGCGTC+TGG + chr5.4:9382137-9382156 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 9381394 9382184 9381394 ID=MS.gene015239
chr5.4 mRNA 9381394 9382184 9381394 ID=MS.gene015239.t1;Parent=MS.gene015239
chr5.4 exon 9382040 9382184 9382040 ID=MS.gene015239.t1.exon1;Parent=MS.gene015239.t1
chr5.4 CDS 9382040 9382184 9382040 ID=cds.MS.gene015239.t1;Parent=MS.gene015239.t1
chr5.4 exon 9381741 9381898 9381741 ID=MS.gene015239.t1.exon2;Parent=MS.gene015239.t1
chr5.4 CDS 9381741 9381898 9381741 ID=cds.MS.gene015239.t1;Parent=MS.gene015239.t1
chr5.4 exon 9381394 9381501 9381394 ID=MS.gene015239.t1.exon3;Parent=MS.gene015239.t1
chr5.4 CDS 9381394 9381501 9381394 ID=cds.MS.gene015239.t1;Parent=MS.gene015239.t1
Gene Sequence

>MS.gene015239

ATGTTTTTGGCAAGAGCATTTCGACAATCATTCTTTGCTGCTGCTGCCAGATCAAAACAGTATTCCACTACAGCTGGTGCTGTTAGAAACCCTCTTCCGGAGTTCTTTGAGGCAGACAGAGATAACGAGACACCAGTTGTCTATGGTATGAAATATGCACCTCTTCTTTTCAATAGAATAGGAATTAAAAATCTCACTGATTTTCATTATAGCCACACATTAGGTACAAAAAAATTATAATTTTCCTCATCACTTTGTTTTCTTATAGTTTTACCATTTTTGTTAGGTCGGAGTTGGAAGGCTTCTGAATTGCGTCTGAAATCTTGGGATGACCTTCATAAGTTGTGGTATGTGTTGTTAAAGGAAAAGAATATGTTGATGACTCAACGACAAATGCTTCAAGCTCAGAACTTGCGCTTTCCTAACCCGGAGCGCTTACCTAAGGTATTTCTTCACTTTTTACACCTGGTCTGATTTACGCGTGTTGTTTTTGTTACCCTTAGTTATGTGGACATTGATATAGGAAATCGCAGTGGTGGTGCTTTTATCAACGTTTGGTGAACACTTTTTGTTTTAGAACATACGAGAGAAATTGAATGTAAAATGTTAAATTTTGTATGGGTTGGGGGGAAACTGTTCACGGTTAACAATGATTTTTGTTGATTTAATTTATGTGAAATCAGGTGAGAAAGTCAATGTGCCGCATCAAGCATGTGCTTACTGAGAGAGCGATTGAAGAACCAGACGCAAGGAGGTCTGCTGAGATGAAGAAAATGATAAATGGTCTTTGA
Protein sequence

>MS.gene015239.t1

MFLARAFRQSFFAAAARSKQYSTTAGAVRNPLPEFFEADRDNETPVVYGRSWKASELRLKSWDDLHKLWYVLLKEKNMLMTQRQMLQAQNLRFPNPERLPKVRKSMCRIKHVLTERAIEEPDARRSAEMKKMINGL