AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0534420


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0534420 MtrunA17_Chr4g0008421 98.515 202 3 0 1 202 88 289 1.90e-145 406
Msa0534420 MtrunA17_Chr4g0008411 74.146 205 44 3 1 201 1 200 1.83e-103 298
Msa0534420 MtrunA17_Chr7g0266341 36.098 205 106 9 10 202 101 292 6.17e-25 98.6
Msa0534420 MtrunA17_Chr2g0306771 33.673 196 99 7 10 202 210 377 2.34e-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
Msa0534420 AT2G37970.1 69.907 216 50 2 1 202 32 246 1.37e-103 298
Msa0534420 AT3G10130.1 35.149 202 112 8 10 202 114 305 1.98e-19 84.7
Msa0534420 AT5G20140.1 32.143 196 103 6 10 202 205 373 4.27e-19 84.3
Msa0534420 AT5G20140.2 31.351 185 99 5 10 191 205 364 9.09e-18 80.9

Find 42 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACAAAGATGGTGGCTTTA+TGG 0.188087 4_1:+9880531 Msa0534420:CDS
TCCATAATGGGTATGGTATT+TGG 0.231563 4_1:+9880388 None:intergenic
GAGGAAGGTGAGAGGAAATA+TGG 0.245932 4_1:+9880799 Msa0534420:CDS
GCAAACTATATTGGAGCATT+AGG 0.249418 4_1:+9880559 Msa0534420:CDS
GGAGAAGTTGAGGCTGAGTT+TGG 0.256967 4_1:+9880873 Msa0534420:CDS
ACACATCATGTTCATTCAAT+AGG 0.342036 4_1:-9880991 None:intergenic
CTTGGACACTTCCAATGTTT+AGG 0.347372 4_1:+9880950 Msa0534420:CDS
GCAGAACCCTTTGTGATAAC+TGG 0.387111 4_1:-9880625 None:intergenic
CACATCATGTTCATTCAATA+GGG 0.408624 4_1:-9880990 None:intergenic
TTGTTTCCTTTGAACTGTGA+TGG 0.417876 4_1:-9880514 None:intergenic
TCACTAGCCTTAGTCACAAC+TGG 0.437262 4_1:-9880670 None:intergenic
GACAGCACCAGTTGTGACTA+AGG 0.455361 4_1:+9880663 Msa0534420:CDS
TATGGAGTGGTGAAGTTTAG+TGG 0.463832 4_1:+9880817 Msa0534420:CDS
AGGGTTGTGATAAGAGAGGA+AGG 0.486753 4_1:+9880784 Msa0534420:CDS
AGGCTGAGTTTGGAGAGAGA+TGG 0.496209 4_1:+9880883 Msa0534420:CDS
AGGAGAAGGTGGAGAAGTTG+AGG 0.502041 4_1:+9880863 Msa0534420:CDS
TTCTCGGTCCATAATGGGTA+TGG 0.507942 4_1:+9880381 None:intergenic
TGAGAGGGTTGTGATAAGAG+AGG 0.509523 4_1:+9880780 Msa0534420:CDS
GTGACTAAGGCTAGTGAAGA+AGG 0.510099 4_1:+9880676 Msa0534420:CDS
TCCAATGTTTAGGACTAATG+AGG 0.518493 4_1:+9880960 Msa0534420:CDS
TGATAAGAGAGGAAGGTGAG+AGG 0.519680 4_1:+9880791 Msa0534420:CDS
ACCCTCTCATCAGTAGGCTT+AGG 0.529518 4_1:-9880766 None:intergenic
AGCTAGTGATGAAGTGGTGA+AGG 0.543102 4_1:+9880843 Msa0534420:CDS
TGAAGTGGTGAAGGAGAAGG+TGG 0.549018 4_1:+9880852 Msa0534420:CDS
CTAAACATTGGAAGTGTCCA+AGG 0.551702 4_1:-9880949 None:intergenic
TGATGAAGTGGTGAAGGAGA+AGG 0.557865 4_1:+9880849 Msa0534420:CDS
TCTGATTTCATAGTCTTGTG+TGG 0.560504 4_1:-9880452 None:intergenic
ACCTAAGCCTACTGATGAGA+GGG 0.571140 4_1:+9880765 Msa0534420:CDS
ACCTCATTAGTCCTAAACAT+TGG 0.572004 4_1:-9880961 None:intergenic
AGAAGGTGAGAAGAATAAGA+TGG 0.575015 4_1:+9880693 Msa0534420:CDS
ACTGCACCAGTTATCACAAA+GGG 0.579442 4_1:+9880619 Msa0534420:CDS
TATGATCCATCACAGTTCAA+AGG 0.581780 4_1:+9880508 Msa0534420:CDS
CAGTTCAAAGGAAACAAAGA+TGG 0.590535 4_1:+9880520 Msa0534420:CDS
CACCTAAGCCTACTGATGAG+AGG 0.606748 4_1:+9880764 Msa0534420:CDS
GTGACTTCAGCTGCTACAGA+AGG 0.612236 4_1:-9880484 None:intergenic
AGGTGAGAGGAAATATGGAG+TGG 0.613327 4_1:+9880804 Msa0534420:CDS
TGGGTAGGTACAATCCACCT+TGG 0.629812 4_1:+9880932 Msa0534420:CDS
TTCAAAGGAAACAAAGATGG+TGG 0.644336 4_1:+9880523 Msa0534420:CDS
GACTGCACCAGTTATCACAA+AGG 0.644397 4_1:+9880618 Msa0534420:CDS
TGGTGTAGCTAGTGATGAAG+TGG 0.645460 4_1:+9880837 Msa0534420:CDS
ATCACAACCCTCTCATCAGT+AGG 0.648561 4_1:-9880772 None:intergenic
AACATTGGAAGTGTCCAAGG+TGG 0.685808 4_1:-9880946 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTGTCACTTCATATTT+TGG - chr4_1:9880433-9880452 None:intergenic 25.0%
!!! ATGGTTTTAGCAAACTATAT+TGG + chr4_1:9880550-9880569 Msa0534420:CDS 25.0%
GGTATGGTATTTGGAAAAAT+TGG + chr4_1:9880397-9880416 Msa0534420:CDS 30.0%
!!! TTCTTCTGCTTTTTCATACA+TGG - chr4_1:9880743-9880762 None:intergenic 30.0%
!!! AGAGATGGTTTTAAGGTTAT+TGG + chr4_1:9880898-9880917 Msa0534420:CDS 30.0%
!!! GAGATGGTTTTAAGGTTATT+GGG + chr4_1:9880899-9880918 Msa0534420:CDS 30.0%
!!! AGATGGTTTTAAGGTTATTG+GGG + chr4_1:9880900-9880919 Msa0534420:CDS 30.0%
!!! GTTATTGGGGATTTTTTGTT+GGG + chr4_1:9880913-9880932 Msa0534420:CDS 30.0%
!! TCTGATTTCATAGTCTTGTG+TGG - chr4_1:9880455-9880474 None:intergenic 35.0%
TATGATCCATCACAGTTCAA+AGG + chr4_1:9880508-9880527 Msa0534420:CDS 35.0%
TTGTTTCCTTTGAACTGTGA+TGG - chr4_1:9880517-9880536 None:intergenic 35.0%
CAGTTCAAAGGAAACAAAGA+TGG + chr4_1:9880520-9880539 Msa0534420:CDS 35.0%
TTCAAAGGAAACAAAGATGG+TGG + chr4_1:9880523-9880542 Msa0534420:CDS 35.0%
! AAACAAAGATGGTGGCTTTA+TGG + chr4_1:9880531-9880550 Msa0534420:CDS 35.0%
! GCAAACTATATTGGAGCATT+AGG + chr4_1:9880559-9880578 Msa0534420:CDS 35.0%
!!! TTTCAGGTTTTGTGTTCTGA+GGG - chr4_1:9880588-9880607 None:intergenic 35.0%
!!! TTTTCAGGTTTTGTGTTCTG+AGG - chr4_1:9880589-9880608 None:intergenic 35.0%
AGAAGGTGAGAAGAATAAGA+TGG + chr4_1:9880693-9880712 Msa0534420:CDS 35.0%
!!! TCTGCTTTTTCATACATGGA+GGG - chr4_1:9880739-9880758 None:intergenic 35.0%
!!! TTCTGCTTTTTCATACATGG+AGG - chr4_1:9880740-9880759 None:intergenic 35.0%
!! TTTGGAGAGAGATGGTTTTA+AGG + chr4_1:9880891-9880910 Msa0534420:CDS 35.0%
!!! GGTTATTGGGGATTTTTTGT+TGG + chr4_1:9880912-9880931 Msa0534420:CDS 35.0%
! TCCAATGTTTAGGACTAATG+AGG + chr4_1:9880960-9880979 Msa0534420:CDS 35.0%
ACCTCATTAGTCCTAAACAT+TGG - chr4_1:9880964-9880983 None:intergenic 35.0%
! GCAGTCATAGCAATCTTTTC+AGG - chr4_1:9880604-9880623 None:intergenic 40.0%
ACTGCACCAGTTATCACAAA+GGG + chr4_1:9880619-9880638 Msa0534420:CDS 40.0%
TATGGAGTGGTGAAGTTTAG+TGG + chr4_1:9880817-9880836 Msa0534420:CDS 40.0%
!!! TTGGGGATTTTTTGTTGGGT+AGG + chr4_1:9880917-9880936 Msa0534420:CDS 40.0%
!! CTAAACATTGGAAGTGTCCA+AGG - chr4_1:9880952-9880971 None:intergenic 40.0%
CTTGGACACTTCCAATGTTT+AGG + chr4_1:9880950-9880969 Msa0534420:CDS 40.0%
GACTGCACCAGTTATCACAA+AGG + chr4_1:9880618-9880637 Msa0534420:CDS 45.0%
GCAGAACCCTTTGTGATAAC+TGG - chr4_1:9880628-9880647 None:intergenic 45.0%
!! TCACTAGCCTTAGTCACAAC+TGG - chr4_1:9880673-9880692 None:intergenic 45.0%
GTGACTAAGGCTAGTGAAGA+AGG + chr4_1:9880676-9880695 Msa0534420:CDS 45.0%
ACCTAAGCCTACTGATGAGA+GGG + chr4_1:9880765-9880784 Msa0534420:CDS 45.0%
ATCACAACCCTCTCATCAGT+AGG - chr4_1:9880775-9880794 None:intergenic 45.0%
TGAGAGGGTTGTGATAAGAG+AGG + chr4_1:9880780-9880799 Msa0534420:CDS 45.0%
AGGGTTGTGATAAGAGAGGA+AGG + chr4_1:9880784-9880803 Msa0534420:CDS 45.0%
TGATAAGAGAGGAAGGTGAG+AGG + chr4_1:9880791-9880810 Msa0534420:CDS 45.0%
GAGGAAGGTGAGAGGAAATA+TGG + chr4_1:9880799-9880818 Msa0534420:CDS 45.0%
AGGTGAGAGGAAATATGGAG+TGG + chr4_1:9880804-9880823 Msa0534420:CDS 45.0%
TGGTGTAGCTAGTGATGAAG+TGG + chr4_1:9880837-9880856 Msa0534420:CDS 45.0%
AGCTAGTGATGAAGTGGTGA+AGG + chr4_1:9880843-9880862 Msa0534420:CDS 45.0%
TGATGAAGTGGTGAAGGAGA+AGG + chr4_1:9880849-9880868 Msa0534420:CDS 45.0%
!! AACATTGGAAGTGTCCAAGG+TGG - chr4_1:9880949-9880968 None:intergenic 45.0%
GTGACTTCAGCTGCTACAGA+AGG - chr4_1:9880487-9880506 None:intergenic 50.0%
GACAGCACCAGTTGTGACTA+AGG + chr4_1:9880663-9880682 Msa0534420:CDS 50.0%
CACCTAAGCCTACTGATGAG+AGG + chr4_1:9880764-9880783 Msa0534420:CDS 50.0%
ACCCTCTCATCAGTAGGCTT+AGG - chr4_1:9880769-9880788 None:intergenic 50.0%
TGAAGTGGTGAAGGAGAAGG+TGG + chr4_1:9880852-9880871 Msa0534420:CDS 50.0%
AGGAGAAGGTGGAGAAGTTG+AGG + chr4_1:9880863-9880882 Msa0534420:CDS 50.0%
GGAGAAGTTGAGGCTGAGTT+TGG + chr4_1:9880873-9880892 Msa0534420:CDS 50.0%
AGGCTGAGTTTGGAGAGAGA+TGG + chr4_1:9880883-9880902 Msa0534420:CDS 50.0%
TGGGTAGGTACAATCCACCT+TGG + chr4_1:9880932-9880951 Msa0534420:CDS 50.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 9880394 9881002 9880394 ID=Msa0534420;Name=Msa0534420
chr4_1 mRNA 9880394 9881002 9880394 ID=Msa0534420-mRNA-1;Parent=Msa0534420;Name=Msa0534420-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|202
chr4_1 exon 9880394 9881002 9880394 ID=Msa0534420-mRNA-1:exon:3181;Parent=Msa0534420-mRNA-1
chr4_1 CDS 9880394 9881002 9880394 ID=Msa0534420-mRNA-1:cds;Parent=Msa0534420-mRNA-1
Gene Sequence

>Msa0534420

ATGGGTATGGTATTTGGAAAAATTGGTGTTGAGACACCAAAATATGAAGTGACAAAAACCACACAAGACTATGAAATCAGAATATATGCACCTTCTGTAGCAGCTGAAGTCACATATGATCCATCACAGTTCAAAGGAAACAAAGATGGTGGCTTTATGGTTTTAGCAAACTATATTGGAGCATTAGGAAACCCTCAGAACACAAAACCTGAAAAGATTGCTATGACTGCACCAGTTATCACAAAGGGTTCTGCAGAGAAGATTGCTATGACAGCACCAGTTGTGACTAAGGCTAGTGAAGAAGGTGAGAAGAATAAGATGGTGACTATGCAGTTTATTTTGCCCTCCATGTATGAAAAAGCAGAAGAAGCACCTAAGCCTACTGATGAGAGGGTTGTGATAAGAGAGGAAGGTGAGAGGAAATATGGAGTGGTGAAGTTTAGTGGTGTAGCTAGTGATGAAGTGGTGAAGGAGAAGGTGGAGAAGTTGAGGCTGAGTTTGGAGAGAGATGGTTTTAAGGTTATTGGGGATTTTTTGTTGGGTAGGTACAATCCACCTTGGACACTTCCAATGTTTAGGACTAATGAGGTTATGATCCCTATTGAATGA

Protein sequence

>Msa0534420

MGMVFGKIGVETPKYEVTKTTQDYEIRIYAPSVAAEVTYDPSQFKGNKDGGFMVLANYIGALGNPQNTKPEKIAMTAPVITKGSAEKIAMTAPVVTKASEEGEKNKMVTMQFILPSMYEKAEEAPKPTDERVVIREEGERKYGVVKFSGVASDEVVKEKVEKLRLSLERDGFKVIGDFLLGRYNPPWTLPMFRTNEVMIPIE*