AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1306920


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1306920 MtrunA17_Chr8g0377581 84.322 236 33 2 1 233 1 235 1.55e-133 375
Msa1306920 MtrunA17_Chr1g0151511 47.909 263 85 7 3 218 4 261 6.53e-57 182
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACAAAATTGGAGAAAATTT+TGG 0.213621 8_4:-1877298 None:intergenic
GGAGGCTATGATGTTATTCT+TGG 0.292173 8_4:+1877342 Msa1306920:CDS
TCTGCTGACAATGGTGCTTC+AGG 0.313597 8_4:+1877321 Msa1306920:CDS
AAAGAGTTTCGCAATGTTGA+TGG 0.333069 8_4:+1877486 Msa1306920:CDS
GATTCACAACGACCGGTAAT+CGG 0.388566 8_4:-1877246 None:intergenic
CGAAATTCGATGCCGATTAC+CGG 0.390204 8_4:+1877234 None:intergenic
TGGAGGGCCGATGGGTCCTC+GGG 0.410669 8_4:+1877779 Msa1306920:CDS
GTTTAAGTTCCTTGTGAAGC+TGG 0.424424 8_4:-1877395 None:intergenic
GTCCTCGGGACATAGAAATT+AGG 0.434748 8_4:+1877793 Msa1306920:CDS
AAATTCAATCAAGAAGTTAG+TGG 0.438478 8_4:+1877531 Msa1306920:CDS
GTGGAGGGCCGATGGGTCCT+CGG 0.438544 8_4:+1877778 Msa1306920:CDS
AACTTTATGCTGCGGAGAAA+AGG 0.440522 8_4:+1877850 Msa1306920:CDS
ATTGTCAGCAGAGACAAAAT+TGG 0.442188 8_4:-1877310 None:intergenic
TTAAACTATCAAAATCTCAT+AGG 0.445350 8_4:+1877412 Msa1306920:CDS
GAGAGAATTGAAAGTATGTC+GGG 0.447028 8_4:+1877891 Msa1306920:CDS
CGGAGGGTTAGTTGCTCCTC+GGG 0.449386 8_4:+1877611 Msa1306920:CDS
TATTCTTGGAAAGACTTTCA+AGG 0.486432 8_4:+1877356 Msa1306920:CDS
AGAGAGAATTGAAAGTATGT+CGG 0.498267 8_4:+1877890 Msa1306920:CDS
ACAAACAAGAAACTTGAAGT+AGG 0.507231 8_4:+1877816 Msa1306920:CDS
TTTAGATGATTCACAACGAC+CGG 0.509528 8_4:-1877253 None:intergenic
TGCGAAGAGTGGAGGGCCGA+TGG 0.514612 8_4:+1877770 Msa1306920:CDS
ATTCTTGGAAAGACTTTCAA+GGG 0.523914 8_4:+1877357 Msa1306920:CDS
GGGACAAGAACAACAGAAAG+AGG 0.527695 8_4:+1877725 Msa1306920:CDS
GCGAAGAGTGGAGGGCCGAT+GGG 0.536215 8_4:+1877771 Msa1306920:CDS
CTCCTCGGGATGTAGAAGTC+AGG 0.538589 8_4:+1877625 Msa1306920:CDS
TTTAGAAGTTGAAAATGCGA+AGG 0.547721 8_4:+1877704 Msa1306920:CDS
GCGGAGGGTTAGTTGCTCCT+CGG 0.558909 8_4:+1877610 Msa1306920:CDS
CAAACAAGAAACTTGAAGTA+GGG 0.559654 8_4:+1877817 Msa1306920:CDS
AGCAATGATGCGAAGAGTGG+AGG 0.563241 8_4:+1877762 Msa1306920:CDS
GCAATGATGCGAAGAGTGGA+GGG 0.571141 8_4:+1877763 Msa1306920:CDS
GAATGAAGCCGTGAGTGAGA+AGG 0.573910 8_4:+1877659 Msa1306920:CDS
TAAGAAGAAAATGAAACACT+AGG 0.578476 8_4:+1877923 Msa1306920:CDS
TGAGAAGGAGAAAATGCAAA+GGG 0.591298 8_4:+1877674 Msa1306920:CDS
AAGAAGAAAATGAAACACTA+GGG 0.592449 8_4:+1877924 Msa1306920:CDS
GTCCTAATTTCTATGTCCCG+AGG 0.595550 8_4:-1877795 None:intergenic
TTCTAAGCAACAGAAAGAGA+TGG 0.598515 8_4:+1877554 Msa1306920:CDS
CTAAGCAATGATGCGAAGAG+TGG 0.602938 8_4:+1877759 Msa1306920:CDS
CTTGCTCAACCAGCTTCACA+AGG 0.605167 8_4:+1877386 Msa1306920:CDS
AAAGATAAGTAACAATGCGA+AGG 0.605305 8_4:+1877581 Msa1306920:CDS
TCTATGTCCCGAGGACCCAT+CGG 0.610923 8_4:-1877786 None:intergenic
TTAGAAGTTGAAAATGCGAA+GGG 0.610992 8_4:+1877705 Msa1306920:CDS
GCTGACAATGGTGCTTCAGG+AGG 0.622331 8_4:+1877324 Msa1306920:CDS
GAGAAAAGGAAGAATCAAGA+TGG 0.623121 8_4:+1877864 Msa1306920:CDS
GACCTGACTTCTACATCCCG+AGG 0.639086 8_4:-1877627 None:intergenic
GTGAGAAGGAGAAAATGCAA+AGG 0.641271 8_4:+1877673 Msa1306920:CDS
AATGCGAAGGTTGAAAGCGG+AGG 0.641854 8_4:+1877594 Msa1306920:CDS
ATGCGAAGGTTGAAAGCGGA+GGG 0.642455 8_4:+1877595 Msa1306920:CDS
TGAGAGTAAACTTTATGCTG+CGG 0.645952 8_4:+1877842 Msa1306920:CDS
AACAATGCGAAGGTTGAAAG+CGG 0.662379 8_4:+1877591 Msa1306920:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAACTATCAAAATCTCAT+AGG + chr8_4:1877412-1877431 Msa1306920:CDS 20.0%
!! GACAAAATTGGAGAAAATTT+TGG - chr8_4:1877301-1877320 None:intergenic 25.0%
! AAATTCAATCAAGAAGTTAG+TGG + chr8_4:1877531-1877550 Msa1306920:CDS 25.0%
TATTCTTGGAAAGACTTTCA+AGG + chr8_4:1877356-1877375 Msa1306920:CDS 30.0%
ATTCTTGGAAAGACTTTCAA+GGG + chr8_4:1877357-1877376 Msa1306920:CDS 30.0%
AAAGATAAGTAACAATGCGA+AGG + chr8_4:1877581-1877600 Msa1306920:CDS 30.0%
TTTAGAAGTTGAAAATGCGA+AGG + chr8_4:1877704-1877723 Msa1306920:CDS 30.0%
TTAGAAGTTGAAAATGCGAA+GGG + chr8_4:1877705-1877724 Msa1306920:CDS 30.0%
ACAAACAAGAAACTTGAAGT+AGG + chr8_4:1877816-1877835 Msa1306920:CDS 30.0%
CAAACAAGAAACTTGAAGTA+GGG + chr8_4:1877817-1877836 Msa1306920:CDS 30.0%
! AGAGAGAATTGAAAGTATGT+CGG + chr8_4:1877890-1877909 Msa1306920:CDS 30.0%
TTTAGATGATTCACAACGAC+CGG - chr8_4:1877256-1877275 None:intergenic 35.0%
ATTGTCAGCAGAGACAAAAT+TGG - chr8_4:1877313-1877332 None:intergenic 35.0%
! AATTTTGTCTCTGCTGACAA+TGG + chr8_4:1877312-1877331 Msa1306920:CDS 35.0%
AAAGAGTTTCGCAATGTTGA+TGG + chr8_4:1877486-1877505 Msa1306920:CDS 35.0%
TTCTAAGCAACAGAAAGAGA+TGG + chr8_4:1877554-1877573 Msa1306920:CDS 35.0%
TAGAAGTCAGGTCAAAAAAG+AGG + chr8_4:1877637-1877656 Msa1306920:CDS 35.0%
TGAGAAGGAGAAAATGCAAA+GGG + chr8_4:1877674-1877693 Msa1306920:CDS 35.0%
TGAGAGTAAACTTTATGCTG+CGG + chr8_4:1877842-1877861 Msa1306920:CDS 35.0%
GAGAAAAGGAAGAATCAAGA+TGG + chr8_4:1877864-1877883 Msa1306920:CDS 35.0%
! GAGAGAATTGAAAGTATGTC+GGG + chr8_4:1877891-1877910 Msa1306920:CDS 35.0%
GGAGGCTATGATGTTATTCT+TGG + chr8_4:1877342-1877361 Msa1306920:CDS 40.0%
! GTTTAAGTTCCTTGTGAAGC+TGG - chr8_4:1877398-1877417 None:intergenic 40.0%
AACAATGCGAAGGTTGAAAG+CGG + chr8_4:1877591-1877610 Msa1306920:CDS 40.0%
! CATTTTCTCCTTCTCACTCA+CGG - chr8_4:1877670-1877689 None:intergenic 40.0%
GTGAGAAGGAGAAAATGCAA+AGG + chr8_4:1877673-1877692 Msa1306920:CDS 40.0%
AACTTTATGCTGCGGAGAAA+AGG + chr8_4:1877850-1877869 Msa1306920:CDS 40.0%
GATTCACAACGACCGGTAAT+CGG - chr8_4:1877249-1877268 None:intergenic 45.0%
!! GGAGAAAATTTTGGCAGCTC+TGG - chr8_4:1877292-1877311 None:intergenic 45.0%
GGGACAAGAACAACAGAAAG+AGG + chr8_4:1877725-1877744 Msa1306920:CDS 45.0%
CTAAGCAATGATGCGAAGAG+TGG + chr8_4:1877759-1877778 Msa1306920:CDS 45.0%
GTCCTCGGGACATAGAAATT+AGG + chr8_4:1877793-1877812 Msa1306920:CDS 45.0%
GTCCTAATTTCTATGTCCCG+AGG - chr8_4:1877798-1877817 None:intergenic 45.0%
TCTGCTGACAATGGTGCTTC+AGG + chr8_4:1877321-1877340 Msa1306920:CDS 50.0%
CTTGCTCAACCAGCTTCACA+AGG + chr8_4:1877386-1877405 Msa1306920:CDS 50.0%
AATGCGAAGGTTGAAAGCGG+AGG + chr8_4:1877594-1877613 Msa1306920:CDS 50.0%
ATGCGAAGGTTGAAAGCGGA+GGG + chr8_4:1877595-1877614 Msa1306920:CDS 50.0%
GAATGAAGCCGTGAGTGAGA+AGG + chr8_4:1877659-1877678 Msa1306920:CDS 50.0%
AGCAATGATGCGAAGAGTGG+AGG + chr8_4:1877762-1877781 Msa1306920:CDS 50.0%
GCAATGATGCGAAGAGTGGA+GGG + chr8_4:1877763-1877782 Msa1306920:CDS 50.0%
GCTGACAATGGTGCTTCAGG+AGG + chr8_4:1877324-1877343 Msa1306920:CDS 55.0%
CTCCTCGGGATGTAGAAGTC+AGG + chr8_4:1877625-1877644 Msa1306920:CDS 55.0%
GACCTGACTTCTACATCCCG+AGG - chr8_4:1877630-1877649 None:intergenic 55.0%
TCTATGTCCCGAGGACCCAT+CGG - chr8_4:1877789-1877808 None:intergenic 55.0%
!! GCGGAGGGTTAGTTGCTCCT+CGG + chr8_4:1877610-1877629 Msa1306920:CDS 60.0%
!! CGGAGGGTTAGTTGCTCCTC+GGG + chr8_4:1877611-1877630 Msa1306920:CDS 60.0%
TGCGAAGAGTGGAGGGCCGA+TGG + chr8_4:1877770-1877789 Msa1306920:CDS 65.0%
GCGAAGAGTGGAGGGCCGAT+GGG + chr8_4:1877771-1877790 Msa1306920:CDS 65.0%
GTGGAGGGCCGATGGGTCCT+CGG + chr8_4:1877778-1877797 Msa1306920:CDS 70.0%
TGGAGGGCCGATGGGTCCTC+GGG + chr8_4:1877779-1877798 Msa1306920:CDS 70.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 1877243 1877944 1877243 ID=Msa1306920;Name=Msa1306920
chr8_4 mRNA 1877243 1877944 1877243 ID=Msa1306920-mRNA-1;Parent=Msa1306920;Name=Msa1306920-mRNA-1;_AED=0.12;_eAED=0.13;_QI=0|-1|0|1|-1|1|1|0|233
chr8_4 exon 1877243 1877944 1877243 ID=Msa1306920-mRNA-1:exon:599;Parent=Msa1306920-mRNA-1
chr8_4 CDS 1877243 1877944 1877243 ID=Msa1306920-mRNA-1:cds;Parent=Msa1306920-mRNA-1
Gene Sequence

>Msa1306920

ATGCCGATTACCGGTCGTTGTGAATCATCTAAAGAGATTTCGCTTTCCAGAGCTGCCAAAATTTTCTCCAATTTTGTCTCTGCTGACAATGGTGCTTCAGGAGGCTATGATGTTATTCTTGGAAAGACTTTCAAGGGTTTCAACTTGCTCAACCAGCTTCACAAGGAACTTAAACTATCAAAATCTCATAGGAAGAATCGTCAAAGCTACATAACAGAAGATAGTGTTGATGTGAAATCTGAAAAAGAGTTTCGCAATGTTGATGGAAAGTTGAATCAGAATGATGTTAAATTCAATCAAGAAGTTAGTGGTTCTAAGCAACAGAAAGAGATGGAGAAAAAGATAAGTAACAATGCGAAGGTTGAAAGCGGAGGGTTAGTTGCTCCTCGGGATGTAGAAGTCAGGTCAAAAAAGAGGAATGAAGCCGTGAGTGAGAAGGAGAAAATGCAAAGGGACAAGAATTTAGAAGTTGAAAATGCGAAGGGACAAGAACAACAGAAAGAGGTAGAGAAAAAACTAAGCAATGATGCGAAGAGTGGAGGGCCGATGGGTCCTCGGGACATAGAAATTAGGACAAACAAGAAACTTGAAGTAGGGAGTGAGAGTAAACTTTATGCTGCGGAGAAAAGGAAGAATCAAGATGGTGAAGAGAGAATTGAAAGTATGTCGGGAGAACATTCTAAGAAGAAAATGAAACACTAG

Protein sequence

>Msa1306920

MPITGRCESSKEISLSRAAKIFSNFVSADNGASGGYDVILGKTFKGFNLLNQLHKELKLSKSHRKNRQSYITEDSVDVKSEKEFRNVDGKLNQNDVKFNQEVSGSKQQKEMEKKISNNAKVESGGLVAPRDVEVRSKKRNEAVSEKEKMQRDKNLEVENAKGQEQQKEVEKKLSNDAKSGGPMGPRDIEIRTNKKLEVGSESKLYAAEKRKNQDGEERIESMSGEHSKKKMKH*