AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0440220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0440220 MtrunA17_Chr3g0087871 96.281 242 7 1 1 240 1 242 2.51e-171 471
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0440220 AT3G63540.1 78.261 138 30 0 102 239 3 140 4.83e-82 242

Find 48 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATATCTAACTTTCCTTTC+TGG 0.121727 3_3:-7072050 Msa0440220:CDS
TCTTTCTCTGTTCTCTTCTT+TGG 0.152693 3_3:+7072071 None:intergenic
GGTGGCGGAGGAGGAGAAAA+TGG 0.261123 3_3:+7072424 None:intergenic
AAACGTTCCTTCCAACCTTC+TGG 0.272048 3_3:+7072146 None:intergenic
AATATCTAACTTTCCTTTCT+GGG 0.289515 3_3:-7072049 Msa0440220:CDS
TTAATATCAAAAGTTGAAAA+AGG 0.291067 3_3:-7072125 Msa0440220:CDS
TTCTGCTGAGTCTTTCTTGT+TGG 0.307382 3_3:+7072184 None:intergenic
GGTGGTGGTTGTGGTGGTGC+TGG 0.309152 3_3:+7072403 None:intergenic
GGTGGTTGTGGTGGTGGTTG+TGG 0.314639 3_3:+7072394 None:intergenic
TATGGTGGTGGTTGTGGTGG+TGG 0.368688 3_3:+7072388 None:intergenic
TATTATGTTTATGAGATTGA+TGG 0.386671 3_3:-7071897 Msa0440220:CDS
TATAGCTGCTGCTGCTGTTA+AGG 0.390254 3_3:+7072319 None:intergenic
GGTGGTGCTGGTGGCGGAGG+AGG 0.407598 3_3:+7072415 None:intergenic
TGTGGTGGTGCTGGTGGCGG+AGG 0.415764 3_3:+7072412 None:intergenic
GCTGTTAAGGTGGTGGTTAG+AGG 0.417250 3_3:+7072332 None:intergenic
TTGTTCAAAACAGCATCTTT+TGG 0.423752 3_3:+7072011 None:intergenic
GGTTGTGGTGGTGCTGGTGG+CGG 0.427977 3_3:+7072409 None:intergenic
GGTTGTGGTGGTGGTTGTGG+TGG 0.436083 3_3:+7072397 None:intergenic
TGATATGGTGGTGGTTGTGG+TGG 0.462996 3_3:+7072385 None:intergenic
AGGAGATGATTCTGCTGCTA+TGG 0.480110 3_3:+7072268 None:intergenic
GAAGAAGTGAAAGATGATAA+AGG 0.482410 3_3:-7071927 Msa0440220:CDS
TCTTTATTCCACTCAGGAGT+AGG 0.485770 3_3:+7071804 None:intergenic
GTGCCGTAGTAGAGATTGTA+AGG 0.489374 3_3:+7072248 None:intergenic
GTGGCGGAGGAGGAGAAAAT+GGG 0.492073 3_3:+7072425 None:intergenic
GCAGCAAACTACGGCGGCTA+CGG 0.501712 3_3:-7072215 Msa0440220:CDS
AATTTGCAAGATATTATTAG+TGG 0.515902 3_3:-7071969 Msa0440220:CDS
TGCTGCTGCTGTTAAGGTGG+TGG 0.518372 3_3:+7072325 None:intergenic
TCCTTATCTTTATTCCACTC+AGG 0.519893 3_3:+7071798 None:intergenic
TTGTGTTTGAATGAGATAAG+AGG 0.520933 3_3:+7072359 None:intergenic
GCGGAGGAGGAGAAAATGGG+TGG 0.522990 3_3:+7072428 None:intergenic
TCCTGAGTGGAATAAAGATA+AGG 0.526998 3_3:-7071799 Msa0440220:CDS
GGTGGTTGTGGTGGTGCTGG+TGG 0.546258 3_3:+7072406 None:intergenic
AGGTGGTGATGTTGTCAGAA+TGG 0.556486 3_3:+7072292 None:intergenic
GCAGCAAGTGCAGCAAACTA+CGG 0.563093 3_3:-7072224 Msa0440220:CDS
TCTACGACGTTCCAGAAGGT+TGG 0.565732 3_3:-7072157 Msa0440220:CDS
AGCTGCTGCTGCTGTTAAGG+TGG 0.570466 3_3:+7072322 None:intergenic
GCAAACTACGGCGGCTACGG+CGG 0.573351 3_3:-7072212 Msa0440220:CDS
TCTCCTTACAATCTCTACTA+CGG 0.578619 3_3:-7072251 Msa0440220:CDS
GAGGAGGAGAAAATGGGTGG+TGG 0.579804 3_3:+7072431 None:intergenic
CGACGTTCCAGAAGGTTGGA+AGG 0.585452 3_3:-7072153 Msa0440220:CDS
GATGATTCTGCTGCTATGGA+AGG 0.605999 3_3:+7072272 None:intergenic
GCAAGTGCAGCAAACTACGG+CGG 0.619443 3_3:-7072221 Msa0440220:CDS
TACATCTACGACGTTCCAGA+AGG 0.628307 3_3:-7072161 Msa0440220:CDS
CTAACTGACGAAACCCAGAA+AGG 0.634618 3_3:+7072036 None:intergenic
TTAATGCTCCTACTCCTGAG+TGG 0.644053 3_3:-7071812 Msa0440220:CDS
GATTCTGCTGCTATGGAAGG+TGG 0.667537 3_3:+7072275 None:intergenic
TGGTGATGATGAGAAAATTG+TGG 0.687506 3_3:+7072451 None:intergenic
TGGTGATGTTGTCAGAATGG+TGG 0.721157 3_3:+7072295 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATATCAAAAGTTGAAAA+AGG - chr3_3:7072085-7072104 Msa0440220:CDS 15.0%
!! AATTTGCAAGATATTATTAG+TGG - chr3_3:7072241-7072260 Msa0440220:CDS 20.0%
!! TATTATGTTTATGAGATTGA+TGG - chr3_3:7072313-7072332 Msa0440220:CDS 20.0%
!! AAAGTTGAAAAAGGTACAAA+TGG - chr3_3:7072094-7072113 Msa0440220:CDS 25.0%
! AATATCTAACTTTCCTTTCT+GGG - chr3_3:7072161-7072180 Msa0440220:CDS 25.0%
!! TGAGATAAGAGGTTTTGATA+TGG + chr3_3:7071843-7071862 None:intergenic 30.0%
TTGTGTTTGAATGAGATAAG+AGG + chr3_3:7071854-7071873 None:intergenic 30.0%
GAATATCTAACTTTCCTTTC+TGG - chr3_3:7072160-7072179 Msa0440220:CDS 30.0%
! TTGTTCAAAACAGCATCTTT+TGG + chr3_3:7072202-7072221 None:intergenic 30.0%
GAAGAAGTGAAAGATGATAA+AGG - chr3_3:7072283-7072302 Msa0440220:CDS 30.0%
! TGGTGATGATGAGAAAATTG+TGG + chr3_3:7071762-7071781 None:intergenic 35.0%
!! GATAAGAGGTTTTGATATGG+TGG + chr3_3:7071840-7071859 None:intergenic 35.0%
TCTCCTTACAATCTCTACTA+CGG - chr3_3:7071959-7071978 Msa0440220:CDS 35.0%
TCTTTCTCTGTTCTCTTCTT+TGG + chr3_3:7072142-7072161 None:intergenic 35.0%
!!! AGATGCTGTTTTGAACAACT+TGG - chr3_3:7072204-7072223 Msa0440220:CDS 35.0%
TCCTGAGTGGAATAAAGATA+AGG - chr3_3:7072411-7072430 Msa0440220:CDS 35.0%
TCCTTATCTTTATTCCACTC+AGG + chr3_3:7072415-7072434 None:intergenic 35.0%
!!! TTTTGATATGGTGGTGGTTG+TGG + chr3_3:7071831-7071850 None:intergenic 40.0%
!! AAGAGGTTTTGATATGGTGG+TGG + chr3_3:7071837-7071856 None:intergenic 40.0%
TTCTGCTGAGTCTTTCTTGT+TGG + chr3_3:7072029-7072048 None:intergenic 40.0%
TCTTTATTCCACTCAGGAGT+AGG + chr3_3:7072409-7072428 None:intergenic 40.0%
TATAGCTGCTGCTGCTGTTA+AGG + chr3_3:7071894-7071913 None:intergenic 45.0%
! TGGTGATGTTGTCAGAATGG+TGG + chr3_3:7071918-7071937 None:intergenic 45.0%
! AGGTGGTGATGTTGTCAGAA+TGG + chr3_3:7071921-7071940 None:intergenic 45.0%
GATGATTCTGCTGCTATGGA+AGG + chr3_3:7071941-7071960 None:intergenic 45.0%
AGGAGATGATTCTGCTGCTA+TGG + chr3_3:7071945-7071964 None:intergenic 45.0%
GTGCCGTAGTAGAGATTGTA+AGG + chr3_3:7071965-7071984 None:intergenic 45.0%
TACATCTACGACGTTCCAGA+AGG - chr3_3:7072049-7072068 Msa0440220:CDS 45.0%
AAACGTTCCTTCCAACCTTC+TGG + chr3_3:7072067-7072086 None:intergenic 45.0%
CTAACTGACGAAACCCAGAA+AGG + chr3_3:7072177-7072196 None:intergenic 45.0%
TTAATGCTCCTACTCCTGAG+TGG - chr3_3:7072398-7072417 Msa0440220:CDS 45.0%
!! TGATATGGTGGTGGTTGTGG+TGG + chr3_3:7071828-7071847 None:intergenic 50.0%
! GCTGTTAAGGTGGTGGTTAG+AGG + chr3_3:7071881-7071900 None:intergenic 50.0%
GATTCTGCTGCTATGGAAGG+TGG + chr3_3:7071938-7071957 None:intergenic 50.0%
GCAGCAAGTGCAGCAAACTA+CGG - chr3_3:7071986-7072005 Msa0440220:CDS 50.0%
TCTACGACGTTCCAGAAGGT+TGG - chr3_3:7072053-7072072 Msa0440220:CDS 50.0%
GAGGAGGAGAAAATGGGTGG+TGG + chr3_3:7071782-7071801 None:intergenic 55.0%
! GTGGCGGAGGAGGAGAAAAT+GGG + chr3_3:7071788-7071807 None:intergenic 55.0%
!! TATGGTGGTGGTTGTGGTGG+TGG + chr3_3:7071825-7071844 None:intergenic 55.0%
TGCTGCTGCTGTTAAGGTGG+TGG + chr3_3:7071888-7071907 None:intergenic 55.0%
AGCTGCTGCTGCTGTTAAGG+TGG + chr3_3:7071891-7071910 None:intergenic 55.0%
GCAAGTGCAGCAAACTACGG+CGG - chr3_3:7071989-7072008 Msa0440220:CDS 55.0%
CGACGTTCCAGAAGGTTGGA+AGG - chr3_3:7072057-7072076 Msa0440220:CDS 55.0%
GCGGAGGAGGAGAAAATGGG+TGG + chr3_3:7071785-7071804 None:intergenic 60.0%
!! GGTGGCGGAGGAGGAGAAAA+TGG + chr3_3:7071789-7071808 None:intergenic 60.0%
!! GGTTGTGGTGGTGGTTGTGG+TGG + chr3_3:7071816-7071835 None:intergenic 60.0%
!! GGTGGTTGTGGTGGTGGTTG+TGG + chr3_3:7071819-7071838 None:intergenic 60.0%
GCAGCAAACTACGGCGGCTA+CGG - chr3_3:7071995-7072014 Msa0440220:CDS 60.0%
!! GGTTGTGGTGGTGCTGGTGG+CGG + chr3_3:7071804-7071823 None:intergenic 65.0%
! GGTGGTTGTGGTGGTGCTGG+TGG + chr3_3:7071807-7071826 None:intergenic 65.0%
! GGTGGTGGTTGTGGTGGTGC+TGG + chr3_3:7071810-7071829 None:intergenic 65.0%
GCAAACTACGGCGGCTACGG+CGG - chr3_3:7071998-7072017 Msa0440220:CDS 65.0%
!! TGTGGTGGTGCTGGTGGCGG+AGG + chr3_3:7071801-7071820 None:intergenic 70.0%
!! GGTGGTGCTGGTGGCGGAGG+AGG + chr3_3:7071798-7071817 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 7071755 7072477 7071755 ID=Msa0440220;Name=Msa0440220
chr3_3 mRNA 7071755 7072477 7071755 ID=Msa0440220-mRNA-1;Parent=Msa0440220;Name=Msa0440220-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|240
chr3_3 exon 7071755 7072477 7071755 ID=Msa0440220-mRNA-1:exon:1485;Parent=Msa0440220-mRNA-1
chr3_3 CDS 7071755 7072477 7071755 ID=Msa0440220-mRNA-1:cds;Parent=Msa0440220-mRNA-1
Gene Sequence

>Msa0440220

ATGGCCACAATTTTCTCATCATCACCACCACCCATTTTCTCCTCCTCCGCCACCAGCACCACCACAACCACCACCACAACCACCACCATATCAAAACCTCTTATCTCATTCAAACACAAACAACCTCTAACCACCACCTTAACAGCAGCAGCAGCTATAGCCACCATTCTGACAACATCACCACCTTCCATAGCAGCAGAATCATCTCCTTACAATCTCTACTACGGCACAGCAGCAAGTGCAGCAAACTACGGCGGCTACGGCGGAAACTCCAACAAGAAAGACTCAGCAGAATACATCTACGACGTTCCAGAAGGTTGGAAGGAACGTTTAATATCAAAAGTTGAAAAAGGTACAAATGGAACAGACAGTGAATTCTACAATCCAAAGAAGAGAACAGAGAAAGAATATCTAACTTTCCTTTCTGGGTTTCGTCAGTTAGCACCAAAAGATGCTGTTTTGAACAACTTGGCACTTTCTGATGTGAATTTGCAAGATATTATTAGTGGTGCTGATAATGTGAGTTCTGAAGAAGTGAAAGATGATAAAGGTCAAGTTTATTATGTTTATGAGATTGATGGCGTTGCTTATCATAGCTTGATTTCTGTTACTTGTGCTAATAATAAGCTTTATGCTCATTTTGTTAATGCTCCTACTCCTGAGTGGAATAAAGATAAGGATCTTCTCACTCATGTTCATAAGTCTTTTAAGACTATTGTATAA

Protein sequence

>Msa0440220

MATIFSSSPPPIFSSSATSTTTTTTTTTTISKPLISFKHKQPLTTTLTAAAAIATILTTSPPSIAAESSPYNLYYGTAASAANYGGYGGNSNKKDSAEYIYDVPEGWKERLISKVEKGTNGTDSEFYNPKKRTEKEYLTFLSGFRQLAPKDAVLNNLALSDVNLQDIISGADNVSSEEVKDDKGQVYYVYEIDGVAYHSLISVTCANNKLYAHFVNAPTPEWNKDKDLLTHVHKSFKTIV*