AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0669200


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0669200 MtrunA17_Chr4g0008421 98.515 202 3 0 1 202 88 289 5.94e-145 405
Msa0669200 MtrunA17_Chr4g0008411 73.659 205 45 3 1 201 1 200 1.02e-102 296
Msa0669200 MtrunA17_Chr7g0266341 36.098 205 106 9 10 202 101 292 9.85e-25 98.2
Msa0669200 MtrunA17_Chr2g0306771 33.673 196 99 7 10 202 210 377 2.46e-19 84.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0669200 AT2G37970.1 69.907 216 50 2 1 202 32 246 3.45e-103 298
Msa0669200 AT5G20140.1 32.653 196 102 6 10 202 205 373 3.02e-19 84.7
Msa0669200 AT3G10130.1 35.149 202 112 8 10 202 114 305 3.22e-19 84.0
Msa0669200 AT5G20140.2 31.892 185 98 5 10 191 205 364 6.26e-18 81.3

Find 42 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACAAAGATGGTGGCTTTA+TGG 0.188087 4_4:+10761315 Msa0669200:CDS
TCCATAATGGGTATGGTATT+TGG 0.221891 4_4:+10761172 None:intergenic
GAGGAAGGTGAGAGGAAATA+TGG 0.245932 4_4:+10761583 Msa0669200:CDS
GCAAACTATATTGGAGCATT+AGG 0.249418 4_4:+10761343 Msa0669200:CDS
GGAGAAGTTGAGGCTGAGTT+TGG 0.256967 4_4:+10761657 Msa0669200:CDS
GCAGAACCCTTTGTTATAAC+TGG 0.318494 4_4:-10761409 None:intergenic
CTTGGACACTTCCAATGTTT+AGG 0.339937 4_4:+10761734 Msa0669200:CDS
ACACATCATGTTCATTCAAT+AGG 0.342036 4_4:-10761775 None:intergenic
CACATCATGTTCATTCAATA+GGG 0.408624 4_4:-10761774 None:intergenic
TTGTTTCCTTTGAACTGTGA+TGG 0.417876 4_4:-10761298 None:intergenic
TCACTAGTCTTAGTCACAAC+TGG 0.426631 4_4:-10761454 None:intergenic
AGGGTTGTGATAAGAGAGGA+AGG 0.486753 4_4:+10761568 Msa0669200:CDS
AGGCTGAGTTTGGAGAGAGA+TGG 0.496209 4_4:+10761667 Msa0669200:CDS
TTCTCGATCCATAATGGGTA+TGG 0.500458 4_4:+10761165 None:intergenic
AGGAGAAGGTGGAGAAGTTG+AGG 0.502041 4_4:+10761647 Msa0669200:CDS
TGAGAGGGTTGTGATAAGAG+AGG 0.509523 4_4:+10761564 Msa0669200:CDS
TCCAATGTTTAGGACTAATG+AGG 0.518493 4_4:+10761744 Msa0669200:CDS
TGATAAGAGAGGAAGGTGAG+AGG 0.519680 4_4:+10761575 Msa0669200:CDS
ACCCTCTCATCAGTTGGCTT+AGG 0.522082 4_4:-10761550 None:intergenic
TGGGTAGGTACAATCCTCCT+TGG 0.525821 4_4:+10761716 Msa0669200:CDS
ATCACAACCCTCTCATCAGT+TGG 0.531851 4_4:-10761556 None:intergenic
TGAAGTGGTGAAGGAGAAGG+TGG 0.549018 4_4:+10761636 Msa0669200:CDS
CTAAACATTGGAAGTGTCCA+AGG 0.554694 4_4:-10761733 None:intergenic
TCTGATTTCATAGTCTTGTG+TGG 0.560504 4_4:-10761236 None:intergenic
ACTGCACCAGTTATAACAAA+GGG 0.563666 4_4:+10761403 Msa0669200:CDS
ACCTCATTAGTCCTAAACAT+TGG 0.572004 4_4:-10761745 None:intergenic
TGATGAAGTGGTGAAGGAGA+AGG 0.572950 4_4:+10761633 Msa0669200:CDS
ACCTAAGCCAACTGATGAGA+GGG 0.573313 4_4:+10761549 Msa0669200:CDS
GTGACTAAGACTAGTGAAGA+AGG 0.573970 4_4:+10761460 Msa0669200:CDS
GGCAAGTGATGAAGTGGTGA+AGG 0.580010 4_4:+10761627 Msa0669200:CDS
TATGATCCATCACAGTTCAA+AGG 0.581780 4_4:+10761292 Msa0669200:CDS
CAGTTCAAAGGAAACAAAGA+TGG 0.590535 4_4:+10761304 Msa0669200:CDS
GACTGCACCAGTTATAACAA+AGG 0.601218 4_4:+10761402 Msa0669200:CDS
CACCTAAGCCAACTGATGAG+AGG 0.602711 4_4:+10761548 Msa0669200:CDS
AGAAGGTGAGAGCAACAAGA+TGG 0.609784 4_4:+10761477 Msa0669200:CDS
TATGGAGTGGTGAAGTTCAG+TGG 0.611850 4_4:+10761601 Msa0669200:CDS
GTGACTTCAGCTGCTACAGA+AGG 0.612236 4_4:-10761268 None:intergenic
AGGTGAGAGGAAATATGGAG+TGG 0.613327 4_4:+10761588 Msa0669200:CDS
TTCAAAGGAAACAAAGATGG+TGG 0.644336 4_4:+10761307 Msa0669200:CDS
TGGTGTGGCAAGTGATGAAG+TGG 0.645405 4_4:+10761621 Msa0669200:CDS
AGTGGTGAAGTTCAGTGGTG+TGG 0.703765 4_4:+10761606 Msa0669200:CDS
AACATTGGAAGTGTCCAAGG+AGG 0.720771 4_4:-10761730 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTGTCACTTCATATTT+TGG - chr4_4:10761217-10761236 None:intergenic 25.0%
!!! ATGGTTTTAGCAAACTATAT+TGG + chr4_4:10761334-10761353 Msa0669200:CDS 25.0%
GGTATGGTATTTGGAAAAAT+TGG + chr4_4:10761181-10761200 Msa0669200:CDS 30.0%
!!! TCTGCTTTTTCATACATAGA+AGG - chr4_4:10761523-10761542 None:intergenic 30.0%
!!! AGAGATGGTTTTAAGGTTAT+TGG + chr4_4:10761682-10761701 Msa0669200:CDS 30.0%
!!! GAGATGGTTTTAAGGTTATT+GGG + chr4_4:10761683-10761702 Msa0669200:CDS 30.0%
!!! AGATGGTTTTAAGGTTATTG+GGG + chr4_4:10761684-10761703 Msa0669200:CDS 30.0%
!!! GTTATTGGGGATTTTTTGTT+GGG + chr4_4:10761697-10761716 Msa0669200:CDS 30.0%
!! TCTGATTTCATAGTCTTGTG+TGG - chr4_4:10761239-10761258 None:intergenic 35.0%
TATGATCCATCACAGTTCAA+AGG + chr4_4:10761292-10761311 Msa0669200:CDS 35.0%
TTGTTTCCTTTGAACTGTGA+TGG - chr4_4:10761301-10761320 None:intergenic 35.0%
CAGTTCAAAGGAAACAAAGA+TGG + chr4_4:10761304-10761323 Msa0669200:CDS 35.0%
TTCAAAGGAAACAAAGATGG+TGG + chr4_4:10761307-10761326 Msa0669200:CDS 35.0%
! AAACAAAGATGGTGGCTTTA+TGG + chr4_4:10761315-10761334 Msa0669200:CDS 35.0%
! GCAAACTATATTGGAGCATT+AGG + chr4_4:10761343-10761362 Msa0669200:CDS 35.0%
!!! TTTCAGGTTTTGTGTTCTGA+GGG - chr4_4:10761372-10761391 None:intergenic 35.0%
!!! TTTTCAGGTTTTGTGTTCTG+AGG - chr4_4:10761373-10761392 None:intergenic 35.0%
ACTGCACCAGTTATAACAAA+GGG + chr4_4:10761403-10761422 Msa0669200:CDS 35.0%
!! TTTGGAGAGAGATGGTTTTA+AGG + chr4_4:10761675-10761694 Msa0669200:CDS 35.0%
!!! GGTTATTGGGGATTTTTTGT+TGG + chr4_4:10761696-10761715 Msa0669200:CDS 35.0%
! TCCAATGTTTAGGACTAATG+AGG + chr4_4:10761744-10761763 Msa0669200:CDS 35.0%
ACCTCATTAGTCCTAAACAT+TGG - chr4_4:10761748-10761767 None:intergenic 35.0%
! GCAGTCATAGCAATCTTTTC+AGG - chr4_4:10761388-10761407 None:intergenic 40.0%
GACTGCACCAGTTATAACAA+AGG + chr4_4:10761402-10761421 Msa0669200:CDS 40.0%
! GCAGAACCCTTTGTTATAAC+TGG - chr4_4:10761412-10761431 None:intergenic 40.0%
!! TCACTAGTCTTAGTCACAAC+TGG - chr4_4:10761457-10761476 None:intergenic 40.0%
GTGACTAAGACTAGTGAAGA+AGG + chr4_4:10761460-10761479 Msa0669200:CDS 40.0%
!!! TTGGGGATTTTTTGTTGGGT+AGG + chr4_4:10761701-10761720 Msa0669200:CDS 40.0%
!! CTAAACATTGGAAGTGTCCA+AGG - chr4_4:10761736-10761755 None:intergenic 40.0%
CTTGGACACTTCCAATGTTT+AGG + chr4_4:10761734-10761753 Msa0669200:CDS 40.0%
AGAAGGTGAGAGCAACAAGA+TGG + chr4_4:10761477-10761496 Msa0669200:CDS 45.0%
ACCTAAGCCAACTGATGAGA+GGG + chr4_4:10761549-10761568 Msa0669200:CDS 45.0%
ATCACAACCCTCTCATCAGT+TGG - chr4_4:10761559-10761578 None:intergenic 45.0%
TGAGAGGGTTGTGATAAGAG+AGG + chr4_4:10761564-10761583 Msa0669200:CDS 45.0%
AGGGTTGTGATAAGAGAGGA+AGG + chr4_4:10761568-10761587 Msa0669200:CDS 45.0%
TGATAAGAGAGGAAGGTGAG+AGG + chr4_4:10761575-10761594 Msa0669200:CDS 45.0%
GAGGAAGGTGAGAGGAAATA+TGG + chr4_4:10761583-10761602 Msa0669200:CDS 45.0%
AGGTGAGAGGAAATATGGAG+TGG + chr4_4:10761588-10761607 Msa0669200:CDS 45.0%
TATGGAGTGGTGAAGTTCAG+TGG + chr4_4:10761601-10761620 Msa0669200:CDS 45.0%
TGATGAAGTGGTGAAGGAGA+AGG + chr4_4:10761633-10761652 Msa0669200:CDS 45.0%
!! AACATTGGAAGTGTCCAAGG+AGG - chr4_4:10761733-10761752 None:intergenic 45.0%
GTGACTTCAGCTGCTACAGA+AGG - chr4_4:10761271-10761290 None:intergenic 50.0%
CACCTAAGCCAACTGATGAG+AGG + chr4_4:10761548-10761567 Msa0669200:CDS 50.0%
! ACCCTCTCATCAGTTGGCTT+AGG - chr4_4:10761553-10761572 None:intergenic 50.0%
AGTGGTGAAGTTCAGTGGTG+TGG + chr4_4:10761606-10761625 Msa0669200:CDS 50.0%
TGGTGTGGCAAGTGATGAAG+TGG + chr4_4:10761621-10761640 Msa0669200:CDS 50.0%
GGCAAGTGATGAAGTGGTGA+AGG + chr4_4:10761627-10761646 Msa0669200:CDS 50.0%
TGAAGTGGTGAAGGAGAAGG+TGG + chr4_4:10761636-10761655 Msa0669200:CDS 50.0%
AGGAGAAGGTGGAGAAGTTG+AGG + chr4_4:10761647-10761666 Msa0669200:CDS 50.0%
GGAGAAGTTGAGGCTGAGTT+TGG + chr4_4:10761657-10761676 Msa0669200:CDS 50.0%
AGGCTGAGTTTGGAGAGAGA+TGG + chr4_4:10761667-10761686 Msa0669200:CDS 50.0%
TGGGTAGGTACAATCCTCCT+TGG + chr4_4:10761716-10761735 Msa0669200:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 10761178 10761786 10761178 ID=Msa0669200;Name=Msa0669200
chr4_4 mRNA 10761178 10761786 10761178 ID=Msa0669200-mRNA-1;Parent=Msa0669200;Name=Msa0669200-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|202
chr4_4 exon 10761178 10761786 10761178 ID=Msa0669200-mRNA-1:exon:3205;Parent=Msa0669200-mRNA-1
chr4_4 CDS 10761178 10761786 10761178 ID=Msa0669200-mRNA-1:cds;Parent=Msa0669200-mRNA-1
Gene Sequence

>Msa0669200

ATGGGTATGGTATTTGGAAAAATTGGTGTTGAGACACCAAAATATGAAGTGACAAAAACCACACAAGACTATGAAATCAGAATATATGCACCTTCTGTAGCAGCTGAAGTCACATATGATCCATCACAGTTCAAAGGAAACAAAGATGGTGGCTTTATGGTTTTAGCAAACTATATTGGAGCATTAGGAAACCCTCAGAACACAAAACCTGAAAAGATTGCTATGACTGCACCAGTTATAACAAAGGGTTCTGCAGAGAAGATTGCTATGACAGCACCAGTTGTGACTAAGACTAGTGAAGAAGGTGAGAGCAACAAGATGGTGACTATGCAGTTTATTTTGCCTTCTATGTATGAAAAAGCAGAAGAAGCACCTAAGCCAACTGATGAGAGGGTTGTGATAAGAGAGGAAGGTGAGAGGAAATATGGAGTGGTGAAGTTCAGTGGTGTGGCAAGTGATGAAGTGGTGAAGGAGAAGGTGGAGAAGTTGAGGCTGAGTTTGGAGAGAGATGGTTTTAAGGTTATTGGGGATTTTTTGTTGGGTAGGTACAATCCTCCTTGGACACTTCCAATGTTTAGGACTAATGAGGTTATGATCCCTATTGAATGA

Protein sequence

>Msa0669200

MGMVFGKIGVETPKYEVTKTTQDYEIRIYAPSVAAEVTYDPSQFKGNKDGGFMVLANYIGALGNPQNTKPEKIAMTAPVITKGSAEKIAMTAPVVTKTSEEGESNKMVTMQFILPSMYEKAEEAPKPTDERVVIREEGERKYGVVKFSGVASDEVVKEKVEKLRLSLERDGFKVIGDFLLGRYNPPWTLPMFRTNEVMIPIE*