AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0276030


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0276030 MtrunA17_Chr2g0288451 98.930 374 4 0 1 374 1 374 0.0 751
Msa0276030 MtrunA17_Chr3g0099081 68.155 336 101 2 44 373 12 347 1.33e-168 474
Msa0276030 MtrunA17_Chr8g0376321 79.402 301 11 1 74 374 1 250 9.31e-165 461
Msa0276030 MtrunA17_Chr4g0073341 29.380 371 194 12 9 373 17 325 6.97e-27 108
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0276030 AT4G04640.1 81.383 376 65 3 1 374 1 373 0.0 603
Msa0276030 AT1G15700.1 70.725 345 100 1 30 373 39 383 2.55e-177 498
Msa0276030 AT2G33040.1 31.661 319 171 10 57 373 48 321 4.90e-28 112

Find 62 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTTAGACCACACTGAATT+TGG 0.110416 2_3:-8218599 None:intergenic
TATTATCAGTGTTGGTAAAA+AGG 0.215367 2_3:+8218953 Msa0276030:CDS
GGTGAAATCTGTGATATTAA+TGG 0.242769 2_3:+8219194 Msa0276030:CDS
GCTCAAGAAGCTGTTGTTAA+TGG 0.249925 2_3:+8218708 Msa0276030:CDS
TCAAATCTTGAGGGCTTTGC+AGG 0.276662 2_3:+8219391 Msa0276030:CDS
GTGACAGTGGAAGCAAAGTA+TGG 0.339355 2_3:-8219166 None:intergenic
GGAAGCAAAGTATGGATTAT+AGG 0.339933 2_3:-8219158 None:intergenic
ATATCACAGATTTCACCTTT+TGG 0.359402 2_3:-8219188 None:intergenic
AACCTATCAACAGGTATATA+AGG 0.362640 2_3:-8218999 None:intergenic
TCCTGCTCAAACTGCAAAAT+CGG 0.366440 2_3:-8219323 None:intergenic
TCTTAGACCACACTGAATTT+GGG 0.374759 2_3:-8218598 None:intergenic
ACTGGTCTAAGCTTAGTTAG+AGG 0.375333 2_3:-8218807 None:intergenic
CAGCACCAGCAACAATTTCC+AGG 0.387882 2_3:-8219544 None:intergenic
TGAATTTGGGTTGGTCTTGA+AGG 0.393465 2_3:-8218585 None:intergenic
ATTGCTGAGTTGAAAGGTCT+TGG 0.399341 2_3:+8218918 Msa0276030:CDS
GACCTTATATACCTGTTGAT+AGG 0.399954 2_3:+8218997 Msa0276030:CDS
CTGTTGAAAGAGATGCTGTT+AGG 0.407775 2_3:+8219279 Msa0276030:CDS
TGCATCAGGTAATGAAGGTT+TGG 0.412967 2_3:-8218490 None:intergenic
CCTGTTGATAGGTTTCTTGA+AGG 0.420186 2_3:+8219008 Msa0276030:CDS
TTCAGGTTAACAACGAAAGA+AGG 0.449455 2_3:+8219248 Msa0276030:CDS
TTTGAACAGTCAAATCTTGA+GGG 0.462626 2_3:+8219382 Msa0276030:CDS
GTTGCTCTTGTTGTTTGCAC+TGG 0.463249 2_3:+8218837 Msa0276030:CDS
TGTTGCTGGTGCTGATGCCT+TGG 0.464852 2_3:+8219553 Msa0276030:CDS
CCTTCAAGAAACCTATCAAC+AGG 0.466272 2_3:-8219008 None:intergenic
TCAACTAGTGTCTGTGAGAA+AGG 0.467803 2_3:-8218735 None:intergenic
ATTTGACTGTTCAAATAAAG+TGG 0.475054 2_3:-8219374 None:intergenic
TAAGATCACTGGTGAAATCC+TGG 0.483893 2_3:+8219526 Msa0276030:CDS
AGTGCATCAAGAATCTGAAC+AGG 0.485687 2_3:-8219347 None:intergenic
GAAATCCTGGAAATTGTTGC+TGG 0.495138 2_3:+8219539 Msa0276030:CDS
AAGGAGAGGTTAGATGCATC+AGG 0.495737 2_3:-8218504 None:intergenic
GTTGTTTGCACTGGTGATAG+AGG 0.498449 2_3:+8218846 Msa0276030:CDS
GTGCTTCTTTAGCAGTAGGA+AGG 0.507770 2_3:-8219037 None:intergenic
TTGCTTCCACTGTCACCAAA+AGG 0.509640 2_3:+8219173 Msa0276030:CDS
TTAGATGCATCAGGTAATGA+AGG 0.514624 2_3:-8218495 None:intergenic
GTTGATAGGTTTCTTGAAGG+TGG 0.518256 2_3:+8219011 Msa0276030:CDS
TTTCACCAGTGATCTTAGCT+TGG 0.530031 2_3:-8219520 None:intergenic
AATAGGATTGCTGAGTTGAA+AGG 0.535194 2_3:+8218912 Msa0276030:CDS
GTTTGTGCTTCTTTAGCAGT+AGG 0.537662 2_3:-8219041 None:intergenic
ATTTGAACAGTCAAATCTTG+AGG 0.540431 2_3:+8219381 Msa0276030:CDS
CAACTTCTTCACTAACAAAG+AGG 0.544704 2_3:-8219085 None:intergenic
GATTACACTATTATCAGTGT+TGG 0.547808 2_3:+8218945 Msa0276030:CDS
ATCAGGTAATGAAGGTTTGG+AGG 0.549600 2_3:-8218487 None:intergenic
GCTGTTCGTTGATGCTGTAA+AGG 0.551485 2_3:-8218761 None:intergenic
TTTGTGAAGGAAGCTGAAAA+GGG 0.553199 2_3:-8218542 None:intergenic
AGACCACACTGAATTTGGGT+TGG 0.556222 2_3:-8218594 None:intergenic
GTTGAAGAAGAATTTGTCAA+GGG 0.556839 2_3:+8219481 Msa0276030:CDS
AGGGCTGAGAGCTGAACGGA+AGG 0.577278 2_3:-8218523 None:intergenic
AGTTGAAGAAGAATTTGTCA+AGG 0.578085 2_3:+8219480 Msa0276030:CDS
CAACGCCAAGCTAAGATCAC+TGG 0.583862 2_3:+8219515 Msa0276030:CDS
TAGAGGAGCTTCGATATCGT+CGG 0.592502 2_3:-8218790 None:intergenic
AACTTCTTCACTAACAAAGA+GGG 0.594771 2_3:-8219084 None:intergenic
GGTGATAGAGGTCTCTGTGG+TGG 0.597310 2_3:+8218858 Msa0276030:CDS
CACTGAAGCAATGAAGCTTG+TGG 0.611051 2_3:+8218665 Msa0276030:CDS
TTGCTCAAATATCACCATGT+TGG 0.614531 2_3:+8218461 Msa0276030:CDS
TGAGAGCTGAACGGAAGGAG+AGG 0.630596 2_3:-8218518 None:intergenic
AAACTGTGTTGATGCTGCTG+AGG 0.639433 2_3:+8219217 Msa0276030:CDS
GAAAAGGGCTGAGAGCTGAA+CGG 0.641643 2_3:-8218527 None:intergenic
TATAAATACACTCTATACCA+AGG 0.641733 2_3:-8219570 None:intergenic
CAGGTATATAAGGTCTACGA+AGG 0.649710 2_3:-8218989 None:intergenic
AGGTTTGGAGGAGACCAACA+TGG 0.658294 2_3:-8218475 None:intergenic
ACTGGTGATAGAGGTCTCTG+TGG 0.722605 2_3:+8218855 Msa0276030:CDS
AGACCAACCCAAATTCAGTG+TGG 0.755194 2_3:+8218591 Msa0276030:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTGAAAAAAGCTGAAAAT+AGG + chr2_3:8218895-8218914 Msa0276030:CDS 20.0%
!!! TATTATCAGTGTTGGTAAAA+AGG + chr2_3:8218953-8218972 Msa0276030:CDS 25.0%
!!! ATTATCAGTGTTGGTAAAAA+GGG + chr2_3:8218954-8218973 Msa0276030:CDS 25.0%
! ATTTGACTGTTCAAATAAAG+TGG - chr2_3:8219377-8219396 None:intergenic 25.0%
!! TGTTTTTGACAGAGTCAATA+CGG - chr2_3:8218635-8218654 None:intergenic 30.0%
GATTACACTATTATCAGTGT+TGG + chr2_3:8218945-8218964 Msa0276030:CDS 30.0%
AACCTATCAACAGGTATATA+AGG - chr2_3:8219002-8219021 None:intergenic 30.0%
AACTTCTTCACTAACAAAGA+GGG - chr2_3:8219087-8219106 None:intergenic 30.0%
! ATATCACAGATTTCACCTTT+TGG - chr2_3:8219191-8219210 None:intergenic 30.0%
GGTGAAATCTGTGATATTAA+TGG + chr2_3:8219194-8219213 Msa0276030:CDS 30.0%
ATTTGAACAGTCAAATCTTG+AGG + chr2_3:8219381-8219400 Msa0276030:CDS 30.0%
TTTGAACAGTCAAATCTTGA+GGG + chr2_3:8219382-8219401 Msa0276030:CDS 30.0%
AGTTGAAGAAGAATTTGTCA+AGG + chr2_3:8219480-8219499 Msa0276030:CDS 30.0%
GTTGAAGAAGAATTTGTCAA+GGG + chr2_3:8219481-8219500 Msa0276030:CDS 30.0%
TTGCTCAAATATCACCATGT+TGG + chr2_3:8218461-8218480 Msa0276030:CDS 35.0%
TTAGATGCATCAGGTAATGA+AGG - chr2_3:8218498-8218517 None:intergenic 35.0%
TTTGTGAAGGAAGCTGAAAA+GGG - chr2_3:8218545-8218564 None:intergenic 35.0%
! TTTTGTGAAGGAAGCTGAAA+AGG - chr2_3:8218546-8218565 None:intergenic 35.0%
!! GAAGATGATGAGTTTTGTGA+AGG - chr2_3:8218558-8218577 None:intergenic 35.0%
TCTTAGACCACACTGAATTT+GGG - chr2_3:8218601-8218620 None:intergenic 35.0%
!!! ACAAGAGCAACTTTTTTCAC+TGG - chr2_3:8218828-8218847 None:intergenic 35.0%
! AATAGGATTGCTGAGTTGAA+AGG + chr2_3:8218912-8218931 Msa0276030:CDS 35.0%
GACCTTATATACCTGTTGAT+AGG + chr2_3:8218997-8219016 Msa0276030:CDS 35.0%
CAACTTCTTCACTAACAAAG+AGG - chr2_3:8219088-8219107 None:intergenic 35.0%
! GGAAGCAAAGTATGGATTAT+AGG - chr2_3:8219161-8219180 None:intergenic 35.0%
! TTCAGGTTAACAACGAAAGA+AGG + chr2_3:8219248-8219267 Msa0276030:CDS 35.0%
ATCAGGTAATGAAGGTTTGG+AGG - chr2_3:8218490-8218509 None:intergenic 40.0%
TGCATCAGGTAATGAAGGTT+TGG - chr2_3:8218493-8218512 None:intergenic 40.0%
!! TGAATTTGGGTTGGTCTTGA+AGG - chr2_3:8218588-8218607 None:intergenic 40.0%
CTCTTAGACCACACTGAATT+TGG - chr2_3:8218602-8218621 None:intergenic 40.0%
GCTCAAGAAGCTGTTGTTAA+TGG + chr2_3:8218708-8218727 Msa0276030:CDS 40.0%
TCAACTAGTGTCTGTGAGAA+AGG - chr2_3:8218738-8218757 None:intergenic 40.0%
! ACTGGTCTAAGCTTAGTTAG+AGG - chr2_3:8218810-8218829 None:intergenic 40.0%
! ATTGCTGAGTTGAAAGGTCT+TGG + chr2_3:8218918-8218937 Msa0276030:CDS 40.0%
CAGGTATATAAGGTCTACGA+AGG - chr2_3:8218992-8219011 None:intergenic 40.0%
CCTTCAAGAAACCTATCAAC+AGG - chr2_3:8219011-8219030 None:intergenic 40.0%
! CCTGTTGATAGGTTTCTTGA+AGG + chr2_3:8219008-8219027 Msa0276030:CDS 40.0%
! GTTGATAGGTTTCTTGAAGG+TGG + chr2_3:8219011-8219030 Msa0276030:CDS 40.0%
GTTTGTGCTTCTTTAGCAGT+AGG - chr2_3:8219044-8219063 None:intergenic 40.0%
!! ATTTCACCTTTTGGTGACAG+TGG - chr2_3:8219182-8219201 None:intergenic 40.0%
CTGTTGAAAGAGATGCTGTT+AGG + chr2_3:8219279-8219298 Msa0276030:CDS 40.0%
TCCTGCTCAAACTGCAAAAT+CGG - chr2_3:8219326-8219345 None:intergenic 40.0%
AGTGCATCAAGAATCTGAAC+AGG - chr2_3:8219350-8219369 None:intergenic 40.0%
TTTCACCAGTGATCTTAGCT+TGG - chr2_3:8219523-8219542 None:intergenic 40.0%
TAAGATCACTGGTGAAATCC+TGG + chr2_3:8219526-8219545 Msa0276030:CDS 40.0%
GAAATCCTGGAAATTGTTGC+TGG + chr2_3:8219539-8219558 Msa0276030:CDS 40.0%
AAGGAGAGGTTAGATGCATC+AGG - chr2_3:8218507-8218526 None:intergenic 45.0%
AGACCAACCCAAATTCAGTG+TGG + chr2_3:8218591-8218610 Msa0276030:CDS 45.0%
AGACCACACTGAATTTGGGT+TGG - chr2_3:8218597-8218616 None:intergenic 45.0%
CACTGAAGCAATGAAGCTTG+TGG + chr2_3:8218665-8218684 Msa0276030:CDS 45.0%
GCTGTTCGTTGATGCTGTAA+AGG - chr2_3:8218764-8218783 None:intergenic 45.0%
TAGAGGAGCTTCGATATCGT+CGG - chr2_3:8218793-8218812 None:intergenic 45.0%
!! GTTGCTCTTGTTGTTTGCAC+TGG + chr2_3:8218837-8218856 Msa0276030:CDS 45.0%
! GTTGTTTGCACTGGTGATAG+AGG + chr2_3:8218846-8218865 Msa0276030:CDS 45.0%
GTGCTTCTTTAGCAGTAGGA+AGG - chr2_3:8219040-8219059 None:intergenic 45.0%
GTGACAGTGGAAGCAAAGTA+TGG - chr2_3:8219169-8219188 None:intergenic 45.0%
TTGCTTCCACTGTCACCAAA+AGG + chr2_3:8219173-8219192 Msa0276030:CDS 45.0%
! AAACTGTGTTGATGCTGCTG+AGG + chr2_3:8219217-8219236 Msa0276030:CDS 45.0%
TCAAATCTTGAGGGCTTTGC+AGG + chr2_3:8219391-8219410 Msa0276030:CDS 45.0%
AGGTTTGGAGGAGACCAACA+TGG - chr2_3:8218478-8218497 None:intergenic 50.0%
GAAAAGGGCTGAGAGCTGAA+CGG - chr2_3:8218530-8218549 None:intergenic 50.0%
ACTGGTGATAGAGGTCTCTG+TGG + chr2_3:8218855-8218874 Msa0276030:CDS 50.0%
! CTGCTGAGGATGAGCTTTTC+AGG + chr2_3:8219231-8219250 Msa0276030:CDS 50.0%
!! GCCGATTTTGCAGTTTGAGC+AGG + chr2_3:8219322-8219341 Msa0276030:CDS 50.0%
CAACGCCAAGCTAAGATCAC+TGG + chr2_3:8219515-8219534 Msa0276030:CDS 50.0%
CAGCACCAGCAACAATTTCC+AGG - chr2_3:8219547-8219566 None:intergenic 50.0%
TGAGAGCTGAACGGAAGGAG+AGG - chr2_3:8218521-8218540 None:intergenic 55.0%
GGTGATAGAGGTCTCTGTGG+TGG + chr2_3:8218858-8218877 Msa0276030:CDS 55.0%
!! TGTTGCTGGTGCTGATGCCT+TGG + chr2_3:8219553-8219572 Msa0276030:CDS 55.0%
AGGGCTGAGAGCTGAACGGA+AGG - chr2_3:8218526-8218545 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 8218456 8219580 8218456 ID=Msa0276030;Name=Msa0276030
chr2_3 mRNA 8218456 8219580 8218456 ID=Msa0276030-mRNA-1;Parent=Msa0276030;Name=Msa0276030-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|374
chr2_3 exon 8218456 8219580 8218456 ID=Msa0276030-mRNA-1:exon:3748;Parent=Msa0276030-mRNA-1
chr2_3 CDS 8218456 8219580 8218456 ID=Msa0276030-mRNA-1:cds;Parent=Msa0276030-mRNA-1
Gene Sequence

>Msa0276030

ATGTCTTGCTCAAATATCACCATGTTGGTCTCCTCCAAACCTTCATTACCTGATGCATCTAACCTCTCCTTCCGTTCAGCTCTCAGCCCTTTTCAGCTTCCTTCACAAAACTCATCATCTTCTTGCACTCCTTCAAGACCAACCCAAATTCAGTGTGGTCTAAGAGAACTTAGAAACCGTATTGACTCTGTCAAAAACACTCAGAAAATCACTGAAGCAATGAAGCTTGTGGCTGCTGCAAAAGTCAGAAGAGCTCAAGAAGCTGTTGTTAATGGCAGACCTTTCTCACAGACACTAGTTGAAGTCCTTTACAGCATCAACGAACAGCTTCAAACCGACGATATCGAAGCTCCTCTAACTAAGCTTAGACCAGTGAAAAAAGTTGCTCTTGTTGTTTGCACTGGTGATAGAGGTCTCTGTGGTGGATTCAACAATGCAATATTGAAAAAAGCTGAAAATAGGATTGCTGAGTTGAAAGGTCTTGGACTTGATTACACTATTATCAGTGTTGGTAAAAAGGGTAACTCTTATTTCCTTCGTAGACCTTATATACCTGTTGATAGGTTTCTTGAAGGTGGAAACCTTCCTACTGCTAAAGAAGCACAAACTATTGCTGATGATGTTTTCTCCCTCTTTGTTAGTGAAGAAGTTGATAAAGTTGAACTATTGTACACTAAATTTGTGTCATTAGTGAAATCAGAGCCTATAATCCATACTTTGCTTCCACTGTCACCAAAAGGTGAAATCTGTGATATTAATGGAAACTGTGTTGATGCTGCTGAGGATGAGCTTTTCAGGTTAACAACGAAAGAAGGAAAGTTAACTGTTGAAAGAGATGCTGTTAGGTCTAAGACGATTGATTTTTCGCCGATTTTGCAGTTTGAGCAGGATCCTGTTCAGATTCTTGATGCACTTTTGCCACTTTATTTGAACAGTCAAATCTTGAGGGCTTTGCAGGAATCACTTGCTAGTGAATTAGCTGCTAGAATGAGTGCTATGAGTAGTGCTTGTGATAATGCTATTGAGTTGAAGAAGAATTTGTCAAGGGTTTATAATAGACAACGCCAAGCTAAGATCACTGGTGAAATCCTGGAAATTGTTGCTGGTGCTGATGCCTTGGTATAG

Protein sequence

>Msa0276030

MSCSNITMLVSSKPSLPDASNLSFRSALSPFQLPSQNSSSSCTPSRPTQIQCGLRELRNRIDSVKNTQKITEAMKLVAAAKVRRAQEAVVNGRPFSQTLVEVLYSINEQLQTDDIEAPLTKLRPVKKVALVVCTGDRGLCGGFNNAILKKAENRIAELKGLGLDYTIISVGKKGNSYFLRRPYIPVDRFLEGGNLPTAKEAQTIADDVFSLFVSEEVDKVELLYTKFVSLVKSEPIIHTLLPLSPKGEICDINGNCVDAAEDELFRLTTKEGKLTVERDAVRSKTIDFSPILQFEQDPVQILDALLPLYLNSQILRALQESLASELAARMSAMSSACDNAIELKKNLSRVYNRQRQAKITGEILEIVAGADALV*