AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0584850

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584850 MtrunA17_Chr4g0019551 54.386 114 31 1 1 93 1 114 5.80e-31 110
Msa0584850 MtrunA17_Chr4g0019481 48.182 110 36 2 1 89 1 110 1.22e-23 91.3
Msa0584850 MtrunA17_Chr4g0019471 43.548 124 35 2 1 89 1 124 1.33e-21 86.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCGAATCTAATATTAAATT+TGG 0.129441 4_2:-4956096 None:intergenic
AAATAATTTACAAGATGATA+TGG 0.212103 4_2:+4956323 Msa0584850:CDS
GGTGGTTGAGGATGGTTATT+TGG 0.221703 4_2:-4956135 None:intergenic
TGTGGTTGAGGCTGGTTATT+TGG 0.223810 4_2:-4956156 None:intergenic
GCTTTCTGATAAGTGCTTCT+TGG 0.258496 4_2:-4956425 None:intergenic
TGCCATTTCCTCTTGCTTCC+TGG 0.265597 4_2:-4956493 None:intergenic
GGAGGCTGGCTCAAGTTAAT+TGG 0.275027 4_2:-4956225 None:intergenic
AGGTTCAAAGCTCGAACATT+AGG 0.361025 4_2:-4956246 None:intergenic
TGACTCGTATGCACAATAGA+AGG 0.372588 4_2:-4956276 None:intergenic
TATCAGAAAGCAAGAAGCTT+TGG 0.383471 4_2:+4956437 Msa0584850:CDS
GGCTGGTTATTTGGTGGTTG+AGG 0.391961 4_2:-4956147 None:intergenic
GGTTATTTGGTGGTTGAGGA+TGG 0.406136 4_2:-4956143 None:intergenic
TACCAGGAAGCAAGAGGAAA+TGG 0.421313 4_2:+4956491 Msa0584850:CDS
GGATGGTTATTTGGTGGTAG+AGG 0.431093 4_2:-4956126 None:intergenic
AAGTGAAGATGGAGCAGAAA+AGG 0.463976 4_2:+4956391 Msa0584850:CDS
AAGTTAATTGGCTGCACATG+TGG 0.509287 4_2:-4956213 None:intergenic
AATAATTTACAAGATGATAT+GGG 0.509595 4_2:+4956324 Msa0584850:CDS
GTTGCTTCTTCATCATCTCA+AGG 0.532802 4_2:-4956608 None:intergenic
GGTTGAGGCTGGTTATTTGG+TGG 0.533930 4_2:-4956153 None:intergenic
GACTCGTATGCACAATAGAA+GGG 0.537355 4_2:-4956275 None:intergenic
GAGAATGCAACAACAACACT+TGG 0.542875 4_2:+4956464 Msa0584850:CDS
GAGCAATCTAAGACAAATGC+TGG 0.544449 4_2:+4956573 Msa0584850:CDS
AACATGCACTGCTAAAACAT+GGG 0.552835 4_2:-4956058 None:intergenic
AAGCTCGAACATTAGGAGGC+TGG 0.553043 4_2:-4956239 None:intergenic
ACTGCATAAGAATTCTAGCT+TGG 0.557073 4_2:-4956010 None:intergenic
GGTTGAGGATGGTTATTTGG+TGG 0.557091 4_2:-4956132 None:intergenic
TAACATGCACTGCTAAAACA+TGG 0.569150 4_2:-4956059 None:intergenic
TCAACTGTTAGAAGTGAAGA+TGG 0.576254 4_2:+4956380 Msa0584850:CDS
TTCAAAGCTCGAACATTAGG+AGG 0.585789 4_2:-4956243 None:intergenic
ACTGCTAAAACATGGGGAGA+TGG 0.597465 4_2:-4956051 None:intergenic
GGAAACTACCAGGAAGCAAG+AGG 0.631081 4_2:+4956485 Msa0584850:CDS
GAAACAACATGAGGAGACAA+TGG 0.637862 4_2:+4956548 Msa0584850:CDS
AACAACACTTGGAAACTACC+AGG 0.641183 4_2:+4956475 Msa0584850:CDS
ACTCGTATGCACAATAGAAG+GGG 0.645441 4_2:-4956274 None:intergenic
CTCGTATGCACAATAGAAGG+GGG 0.684292 4_2:-4956273 None:intergenic
TTAATTGGCTGCACATGTGG+AGG 0.687081 4_2:-4956210 None:intergenic
ACATGCACTGCTAAAACATG+GGG 0.693010 4_2:-4956057 None:intergenic
AAACATGCAGAAACAACATG+AGG 0.696986 4_2:+4956539 Msa0584850:CDS
TGTGGAGGTGATGCATTGTG+TGG 0.709748 4_2:-4956195 None:intergenic
GCATACGAGTCAAGATCCTG+AGG 0.710797 4_2:+4956287 Msa0584850:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAATTTACAAGATGATA+TGG + chr4_2:4956323-4956342 Msa0584850:CDS 15.0%
!! AATAATTTACAAGATGATAT+GGG + chr4_2:4956324-4956343 Msa0584850:CDS 15.0%
!! CTCGAATCTAATATTAAATT+TGG - chr4_2:4956099-4956118 None:intergenic 20.0%
! TTTTGAACGATAATAACCTC+AGG - chr4_2:4956306-4956325 None:intergenic 30.0%
! ACTGCATAAGAATTCTAGCT+TGG - chr4_2:4956013-4956032 None:intergenic 35.0%
AACATGCACTGCTAAAACAT+GGG - chr4_2:4956061-4956080 None:intergenic 35.0%
TAACATGCACTGCTAAAACA+TGG - chr4_2:4956062-4956081 None:intergenic 35.0%
TCAACTGTTAGAAGTGAAGA+TGG + chr4_2:4956380-4956399 Msa0584850:CDS 35.0%
TATCAGAAAGCAAGAAGCTT+TGG + chr4_2:4956437-4956456 Msa0584850:CDS 35.0%
AAACATGCAGAAACAACATG+AGG + chr4_2:4956539-4956558 Msa0584850:CDS 35.0%
ACATGCACTGCTAAAACATG+GGG - chr4_2:4956060-4956079 None:intergenic 40.0%
! TGTGTTGCATTTTGTGGTTG+AGG - chr4_2:4956171-4956190 None:intergenic 40.0%
AAGTTAATTGGCTGCACATG+TGG - chr4_2:4956216-4956235 None:intergenic 40.0%
TTCAAAGCTCGAACATTAGG+AGG - chr4_2:4956246-4956265 None:intergenic 40.0%
AGGTTCAAAGCTCGAACATT+AGG - chr4_2:4956249-4956268 None:intergenic 40.0%
ACTCGTATGCACAATAGAAG+GGG - chr4_2:4956277-4956296 None:intergenic 40.0%
GACTCGTATGCACAATAGAA+GGG - chr4_2:4956278-4956297 None:intergenic 40.0%
TGACTCGTATGCACAATAGA+AGG - chr4_2:4956279-4956298 None:intergenic 40.0%
AAGTGAAGATGGAGCAGAAA+AGG + chr4_2:4956391-4956410 Msa0584850:CDS 40.0%
GCTTTCTGATAAGTGCTTCT+TGG - chr4_2:4956428-4956447 None:intergenic 40.0%
GAGAATGCAACAACAACACT+TGG + chr4_2:4956464-4956483 Msa0584850:CDS 40.0%
AACAACACTTGGAAACTACC+AGG + chr4_2:4956475-4956494 Msa0584850:CDS 40.0%
GAAACAACATGAGGAGACAA+TGG + chr4_2:4956548-4956567 Msa0584850:CDS 40.0%
! GAGCAATCTAAGACAAATGC+TGG + chr4_2:4956573-4956592 Msa0584850:CDS 40.0%
GTTGCTTCTTCATCATCTCA+AGG - chr4_2:4956611-4956630 None:intergenic 40.0%
ACTGCTAAAACATGGGGAGA+TGG - chr4_2:4956054-4956073 None:intergenic 45.0%
! GGATGGTTATTTGGTGGTAG+AGG - chr4_2:4956129-4956148 None:intergenic 45.0%
GGTTGAGGATGGTTATTTGG+TGG - chr4_2:4956135-4956154 None:intergenic 45.0%
GGTGGTTGAGGATGGTTATT+TGG - chr4_2:4956138-4956157 None:intergenic 45.0%
! GGTTATTTGGTGGTTGAGGA+TGG - chr4_2:4956146-4956165 None:intergenic 45.0%
! TGTGGTTGAGGCTGGTTATT+TGG - chr4_2:4956159-4956178 None:intergenic 45.0%
! TTGCATTTTGTGGTTGAGGC+TGG - chr4_2:4956167-4956186 None:intergenic 45.0%
! GGTCGATGTGTTGCATTTTG+TGG - chr4_2:4956177-4956196 None:intergenic 45.0%
TTAATTGGCTGCACATGTGG+AGG - chr4_2:4956213-4956232 None:intergenic 45.0%
GCACAATAGAAGGGGGATTA+AGG - chr4_2:4956269-4956288 None:intergenic 45.0%
CTCGTATGCACAATAGAAGG+GGG - chr4_2:4956276-4956295 None:intergenic 45.0%
TACCAGGAAGCAAGAGGAAA+TGG + chr4_2:4956491-4956510 Msa0584850:CDS 45.0%
! GGCTGGTTATTTGGTGGTTG+AGG - chr4_2:4956150-4956169 None:intergenic 50.0%
! GGTTGAGGCTGGTTATTTGG+TGG - chr4_2:4956156-4956175 None:intergenic 50.0%
TGTGGAGGTGATGCATTGTG+TGG - chr4_2:4956198-4956217 None:intergenic 50.0%
! GGAGGCTGGCTCAAGTTAAT+TGG - chr4_2:4956228-4956247 None:intergenic 50.0%
AAGCTCGAACATTAGGAGGC+TGG - chr4_2:4956242-4956261 None:intergenic 50.0%
GCATACGAGTCAAGATCCTG+AGG + chr4_2:4956287-4956306 Msa0584850:CDS 50.0%
GGAAACTACCAGGAAGCAAG+AGG + chr4_2:4956485-4956504 Msa0584850:CDS 50.0%
! TGCCATTTCCTCTTGCTTCC+TGG - chr4_2:4956496-4956515 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 4956006 4956641 4956006 ID=Msa0584850;Name=Msa0584850
chr4_2 mRNA 4956006 4956641 4956006 ID=Msa0584850-mRNA-1;Parent=Msa0584850;Name=Msa0584850-mRNA-1;_AED=0.31;_eAED=0.31;_QI=0|-1|0|1|-1|1|1|0|211
chr4_2 exon 4956006 4956641 4956006 ID=Msa0584850-mRNA-1:exon:1236;Parent=Msa0584850-mRNA-1
chr4_2 CDS 4956006 4956641 4956006 ID=Msa0584850-mRNA-1:cds;Parent=Msa0584850-mRNA-1
Gene Sequence

>Msa0584850

ATGACCAAGCTAGAATTCTTATGCAGTGATTGTGACGCAAAGTTTCCATCTCCCCATGTTTTAGCAGTGCATGTTATCGAACAACATCATCCAAATTTAATATTAGATTCGAGTGCAAATCCTCTACCACCAAATAACCATCCTCAACCACCAAATAACCAGCCTCAACCACAAAATGCAACACATCGACCACACAATGCATCACCTCCACATGTGCAGCCAATTAACTTGAGCCAGCCTCCTAATGTTCGAGCTTTGAACCTTAATCCCCCTTCTATTGTGCATACGAGTCAAGATCCTGAGGTTATTATCGTTCAAAATAATTTACAAGATGATATGGGAAATCAGAAGCTGACAACAGAAGTTGTGCAAGCTCAACTGTTAGAAGTGAAGATGGAGCAGAAAAGGCAGAATGATATCCAAGAAGCACTTATCAGAAAGCAAGAAGCTTTGGAAAAGAGAATGCAACAACAACACTTGGAAACTACCAGGAAGCAAGAGGAAATGGCAAAGAAGCAAGAAGAACTTGAAAGAAACATGCAGAAACAACATGAGGAGACAATGGCTGAGCAATCTAAGACAAATGCTGGCATTGCTGCTATCCTTGAGATGATGAAGAAGCAACAACAACCTTAA
Protein sequence

>Msa0584850

MTKLEFLCSDCDAKFPSPHVLAVHVIEQHHPNLILDSSANPLPPNNHPQPPNNQPQPQNATHRPHNASPPHVQPINLSQPPNVRALNLNPPSIVHTSQDPEVIIVQNNLQDDMGNQKLTTEVVQAQLLEVKMEQKRQNDIQEALIRKQEALEKRMQQQHLETTRKQEEMAKKQEELERNMQKQHEETMAEQSKTNAGIAAILEMMKKQQQP*