AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31006

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31006.t1 MTR_3g095480 97.396 192 3 1 1 190 1 192 7.31e-139 385
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31006.t1 AT3G18800 66.667 198 57 3 1 190 1 197 3.56e-89 260

Find 35 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAATTGGGCTCTTCATTT+TGG 0.160115 3.3:-79174505 MS.gene31006:CDS
GAACCTCCTGAGAGTTATTT+TGG 0.184497 3.3:-79174538 MS.gene31006:CDS
CAGACTCTTAGATGTATTAA+TGG 0.240810 3.3:-79174697 MS.gene31006:CDS
TTGGTAAGTTTAAGAGAAAT+TGG 0.241730 3.3:-79174519 MS.gene31006:CDS
AGAGTTTGAGATTCATTATC+AGG 0.276876 3.3:-79174560 MS.gene31006:CDS
GGGTTCTTGATCTTGATCTA+TGG 0.279818 3.3:-79174484 MS.gene31006:CDS
GTCTTCAATGTCGCCATTGT+TGG 0.363130 3.3:-79174774 MS.gene31006:CDS
TGAGGAAGATGAAGAAGATT+TGG 0.365817 3.3:+79174830 None:intergenic
GTTTGGCTACTGAGAAGCTT+AGG 0.366128 3.3:-79174636 MS.gene31006:CDS
TCATAAGCTTACACTTGGTT+TGG 0.408278 3.3:-79174653 MS.gene31006:CDS
TGGTAAGTTTAAGAGAAATT+GGG 0.438263 3.3:-79174518 MS.gene31006:CDS
GTTGTTGTTGTTGATGGTTG+TGG 0.489653 3.3:+79174974 None:intergenic
TTTGGCTACTGAGAAGCTTA+GGG 0.491256 3.3:-79174635 MS.gene31006:CDS
GGTGGTGATTATGATACTAT+TGG 0.492628 3.3:-79174589 MS.gene31006:CDS
CTATGGCACGTTTCTTCTCG+AGG 0.504585 3.3:+79174884 None:intergenic
CCCAATCACACTTCTCTCCA+TGG 0.514078 3.3:-79174749 MS.gene31006:CDS
GGATGATGGTGTTCAATGCT+TGG 0.519310 3.3:+79174926 None:intergenic
GCCATGGAGAGAAGTGTGAT+TGG 0.521665 3.3:+79174748 None:intergenic
CTCGAAATGGAGCTGGATGA+TGG 0.524313 3.3:+79174912 None:intergenic
TATGGCACGTTTCTTCTCGA+GGG 0.531684 3.3:+79174885 None:intergenic
AACTTACCAAAATAACTCTC+AGG 0.534886 3.3:+79174532 None:intergenic
TGCCATAGACCTTCAAAAGA+AGG 0.542520 3.3:-79174869 MS.gene31006:CDS
AGCTTAGGGATATGAAGATG+AGG 0.544927 3.3:-79174621 MS.gene31006:CDS
AAGATGAGGTTGAGTGGTGG+TGG 0.558791 3.3:-79174607 MS.gene31006:CDS
CCATGGAGAGAAGTGTGATT+GGG 0.569183 3.3:+79174749 None:intergenic
AGGTGTCATAAGCTTACACT+TGG 0.582162 3.3:-79174658 MS.gene31006:CDS
GTTGTTGTTGATGGTTGTGG+TGG 0.583547 3.3:+79174977 None:intergenic
CAATGGCGACATTGAAGACG+TGG 0.610640 3.3:+79174778 None:intergenic
ATAGAAGATGAGATGAGCCA+TGG 0.626380 3.3:+79174732 None:intergenic
ATGGATTCAAGTATCAGAGA+AGG 0.640872 3.3:-79174678 MS.gene31006:CDS
GTGTGATTGGGATCCAACAA+TGG 0.648346 3.3:+79174761 None:intergenic
TTACCAAAATAACTCTCAGG+AGG 0.660707 3.3:+79174535 None:intergenic
GTGCCATGAAAACTAAGCTG+AGG 0.663846 3.3:+79174812 None:intergenic
GATATGAAGATGAGGTTGAG+TGG 0.697448 3.3:-79174613 MS.gene31006:CDS
ATGAAGATGAGGTTGAGTGG+TGG 0.722579 3.3:-79174610 MS.gene31006:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGGTAAGTTTAAGAGAAATT+GGG - chr3.3:79174920-79174939 MS.gene31006:CDS 25.0%
! TTGGTAAGTTTAAGAGAAAT+TGG - chr3.3:79174919-79174938 MS.gene31006:CDS 25.0%
AACTTACCAAAATAACTCTC+AGG + chr3.3:79174909-79174928 None:intergenic 30.0%
CAGACTCTTAGATGTATTAA+TGG - chr3.3:79174741-79174760 MS.gene31006:CDS 30.0%
! AGAGTTTGAGATTCATTATC+AGG - chr3.3:79174878-79174897 MS.gene31006:CDS 30.0%
ATGGATTCAAGTATCAGAGA+AGG - chr3.3:79174760-79174779 MS.gene31006:CDS 35.0%
GGTGGTGATTATGATACTAT+TGG - chr3.3:79174849-79174868 MS.gene31006:CDS 35.0%
TCATAAGCTTACACTTGGTT+TGG - chr3.3:79174785-79174804 MS.gene31006:CDS 35.0%
TGAGGAAGATGAAGAAGATT+TGG + chr3.3:79174611-79174630 None:intergenic 35.0%
TTACCAAAATAACTCTCAGG+AGG + chr3.3:79174906-79174925 None:intergenic 35.0%
! AGAAATTGGGCTCTTCATTT+TGG - chr3.3:79174933-79174952 MS.gene31006:CDS 35.0%
! GAAATTGGGCTCTTCATTTT+GGG - chr3.3:79174934-79174953 MS.gene31006:CDS 35.0%
! TGTGAAGTTCCTTCTTTTGA+AGG + chr3.3:79174581-79174600 None:intergenic 35.0%
!! CTACTTGTTGTTGTTGTTGA+TGG + chr3.3:79174473-79174492 None:intergenic 35.0%
!! TTCCTTCTTTTGAAGGTCTA+TGG + chr3.3:79174574-79174593 None:intergenic 35.0%
AGCTTAGGGATATGAAGATG+AGG - chr3.3:79174817-79174836 MS.gene31006:CDS 40.0%
ATAGAAGATGAGATGAGCCA+TGG + chr3.3:79174709-79174728 None:intergenic 40.0%
GATATGAAGATGAGGTTGAG+TGG - chr3.3:79174825-79174844 MS.gene31006:CDS 40.0%
GGGTTCTTGATCTTGATCTA+TGG - chr3.3:79174954-79174973 MS.gene31006:CDS 40.0%
TGCCATAGACCTTCAAAAGA+AGG - chr3.3:79174569-79174588 MS.gene31006:CDS 40.0%
TTTGGCTACTGAGAAGCTTA+GGG - chr3.3:79174803-79174822 MS.gene31006:CDS 40.0%
! AGGTGTCATAAGCTTACACT+TGG - chr3.3:79174780-79174799 MS.gene31006:CDS 40.0%
! GAACCTCCTGAGAGTTATTT+TGG - chr3.3:79174900-79174919 MS.gene31006:CDS 40.0%
!! CTTCCTCAGCTTAGTTTTCA+TGG - chr3.3:79174623-79174642 MS.gene31006:CDS 40.0%
!! GTTGTTGTTGTTGATGGTTG+TGG + chr3.3:79174467-79174486 None:intergenic 40.0%
ATGAAGATGAGGTTGAGTGG+TGG - chr3.3:79174828-79174847 MS.gene31006:CDS 45.0%
GTCTTCAATGTCGCCATTGT+TGG - chr3.3:79174664-79174683 MS.gene31006:CDS 45.0%
GTGCCATGAAAACTAAGCTG+AGG + chr3.3:79174629-79174648 None:intergenic 45.0%
GTGTGATTGGGATCCAACAA+TGG + chr3.3:79174680-79174699 None:intergenic 45.0%
GTTTGGCTACTGAGAAGCTT+AGG - chr3.3:79174802-79174821 MS.gene31006:CDS 45.0%
TATGGCACGTTTCTTCTCGA+GGG + chr3.3:79174556-79174575 None:intergenic 45.0%
! CCATGGAGAGAAGTGTGATT+GGG + chr3.3:79174692-79174711 None:intergenic 45.0%
! GGATGATGGTGTTCAATGCT+TGG + chr3.3:79174515-79174534 None:intergenic 45.0%
! TCTCGAGGGTTTTCTCGAAA+TGG + chr3.3:79174542-79174561 None:intergenic 45.0%
!! GTTGTTGTTGATGGTTGTGG+TGG + chr3.3:79174464-79174483 None:intergenic 45.0%
AAGATGAGGTTGAGTGGTGG+TGG - chr3.3:79174831-79174850 MS.gene31006:CDS 50.0%
CAATGGCGACATTGAAGACG+TGG + chr3.3:79174663-79174682 None:intergenic 50.0%
CCCAATCACACTTCTCTCCA+TGG - chr3.3:79174689-79174708 MS.gene31006:CDS 50.0%
CTATGGCACGTTTCTTCTCG+AGG + chr3.3:79174557-79174576 None:intergenic 50.0%
CTCGAAATGGAGCTGGATGA+TGG + chr3.3:79174529-79174548 None:intergenic 50.0%
! GCCATGGAGAGAAGTGTGAT+TGG + chr3.3:79174693-79174712 None:intergenic 50.0%
! GGGTTTTCTCGAAATGGAGC+TGG + chr3.3:79174536-79174555 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 79174444 79175016 79174444 ID=MS.gene31006
chr3.3 mRNA 79174444 79175016 79174444 ID=MS.gene31006.t1;Parent=MS.gene31006
chr3.3 exon 79174444 79175016 79174444 ID=MS.gene31006.t1.exon1;Parent=MS.gene31006.t1
chr3.3 CDS 79174444 79175016 79174444 ID=cds.MS.gene31006.t1;Parent=MS.gene31006.t1
Gene Sequence

>MS.gene31006

ATGGCAGACTACGAAAACCACCACAACCATCAACAACAACAACAAGTAGTTTCTCGTGAAACAGCTTTCCAAGCATTGAACACCATCATCCAGCTCCATTTCGAGAAAACCCTCGAGAAGAAACGTGCCATAGACCTTCAAAAGAAGGAACTTCACAAGCTTTTCCAAATCTTCTTCATCTTCCTCAGCTTAGTTTTCATGGCACAATCAATGTCACCACGTCTTCAATGTCGCCATTGTTGGATCCCAATCACACTTCTCTCCATGGCTCATCTCATCTTCTATGTGTCTGTAGCACAGACTCTTAGATGTATTAATGGATTCAAGTATCAGAGAAGGTGTCATAAGCTTACACTTGGTTTGGCTACTGAGAAGCTTAGGGATATGAAGATGAGGTTGAGTGGTGGTGGTGATTATGATACTATTGGTGATGAAGAGTTTGAGATTCATTATCAGGAACCTCCTGAGAGTTATTTTGGTAAGTTTAAGAGAAATTGGGCTCTTCATTTTGGGTTCTTGATCTTGATCTATGGTTTCATGATCTCTTCTTCTGTTGTTCTTCTATGTTTTTGA
Protein sequence

>MS.gene31006.t1

MADYENHHNHQQQQQVVSRETAFQALNTIIQLHFEKTLEKKRAIDLQKKELHKLFQIFFIFLSLVFMAQSMSPRLQCRHCWIPITLLSMAHLIFYVSVAQTLRCINGFKYQRRCHKLTLGLATEKLRDMKMRLSGGGDYDTIGDEEFEIHYQEPPESYFGKFKRNWALHFGFLILIYGFMISSSVVLLCF