AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0068060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0068060 MtrunA17_Chr1g0171721 97.895 95 2 0 1 95 509 603 9.86e-63 199
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0068060 AT3G47930.1 80.851 94 18 0 1 94 516 609 2.10e-50 167
Msa0068060 AT3G47930.2 84.091 44 7 0 1 44 516 559 1.13e-21 88.2

Find 41 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGAAGAATTCTTTCATTAT+AGG 0.147623 1_2:-33555133 Msa0068060:CDS
TCAGAAACCATATGAAATTA+TGG 0.172416 1_2:-33554526 Msa0068060:exon
GTTGTTCGAAAGAATCTTAT+TGG 0.249470 1_2:+33554573 None:intergenic
ACAAGTTCATCCTTGTTCTT+TGG 0.255312 1_2:+33554667 None:intergenic
GTACTGGATTTAATACAAAT+TGG 0.268900 1_2:+33555339 None:intergenic
ATCTGACTCAGGCAAAATTA+TGG 0.271596 1_2:-33555109 Msa0068060:CDS
TTGGACTGCAGTCACATCTT+TGG 0.288615 1_2:-33554466 Msa0068060:three_prime_UTR
CGTTATAATGTTAAAATTTG+TGG 0.324013 1_2:+33555259 None:intergenic
TTTAACATTATAACGTTGTT+TGG 0.325143 1_2:-33555251 Msa0068060:five_prime_UTR
TTGTTCGAAAGAATCTTATT+GGG 0.335515 1_2:+33554574 None:intergenic
CAATAAGGCAAGAAATGAAT+TGG 0.368870 1_2:-33554599 Msa0068060:CDS
TTGGAAGTGTAAACACAATC+AGG 0.373541 1_2:-33554386 Msa0068060:three_prime_UTR
TCCGGTGGATGCATACAATA+AGG 0.381817 1_2:-33554614 Msa0068060:CDS
TTCATATGGTTTCTGATTGT+GGG 0.396366 1_2:+33554533 None:intergenic
TTTCATATGGTTTCTGATTG+TGG 0.398119 1_2:+33554532 None:intergenic
CAGAAACCATATGAAATTAT+GGG 0.404629 1_2:-33554525 Msa0068060:exon
AAGGCTGAGAAAGCGGTTTC+CGG 0.405807 1_2:-33554632 Msa0068060:CDS
AACCGACCCATAATTTCATA+TGG 0.407857 1_2:+33554519 None:intergenic
ACCGCTTTCTCAGCCTTGCT+TGG 0.420653 1_2:+33554638 None:intergenic
AGTCACATCTTTGGAACTTC+AGG 0.421836 1_2:-33554457 Msa0068060:three_prime_UTR
ATTTATGATTTGTAACGAAT+GGG 0.434395 1_2:+33554341 None:intergenic
TCTGACTCAGGCAAAATTAT+GGG 0.438770 1_2:-33555108 Msa0068060:CDS
CATTTATGATTTGTAACGAA+TGG 0.457507 1_2:+33554340 None:intergenic
TCATTATAGGCATCTGACTC+AGG 0.474529 1_2:-33555120 Msa0068060:CDS
TTAGTCAAACAAACACAATC+AGG 0.483027 1_2:-33554424 Msa0068060:three_prime_UTR
GCCTTATTGTATGCATCCAC+CGG 0.501214 1_2:+33554613 None:intergenic
ACATTATAACGTTGTTTGGA+AGG 0.510680 1_2:-33555247 Msa0068060:five_prime_UTR
GATTCTTTCGAACAACAAGT+TGG 0.517004 1_2:-33554566 Msa0068060:CDS
CTCTGGCGAGCATCCATGGT+AGG 0.519853 1_2:+33555167 None:intergenic
ATTACTCTGCTTATGAACAC+TGG 0.529551 1_2:-33555082 Msa0068060:CDS
GATTATTATACATAAATATG+AGG 0.533079 1_2:-33554364 Msa0068060:three_prime_UTR
TGAACACTGGGCAAAGATTG+AGG 0.547142 1_2:-33555069 Msa0068060:intron
TTACTCTGCTTATGAACACT+GGG 0.568910 1_2:-33555081 Msa0068060:CDS
TCTGGCGAGCATCCATGGTA+GGG 0.571749 1_2:+33555168 None:intergenic
TCCAAGCAAGGCTGAGAAAG+CGG 0.589344 1_2:-33554639 Msa0068060:CDS
AACTTGTAGCTCTCCAAGCA+AGG 0.596854 1_2:-33554651 Msa0068060:CDS
AATAATGTACCTCCCTACCA+TGG 0.623870 1_2:-33555180 Msa0068060:exon
GCTGAGAAAGCGGTTTCCGG+TGG 0.625300 1_2:-33554629 Msa0068060:CDS
AACCATATGAAATTATGGGT+CGG 0.627064 1_2:-33554521 Msa0068060:exon
GGCGAGCATCCATGGTAGGG+AGG 0.637490 1_2:+33555171 None:intergenic
TCTGTAGGTTCCAAAGAACA+AGG 0.671681 1_2:-33554677 Msa0068060:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTAAAGTATGACAATAAT+TGG + chr1_2:33554711-33554730 None:intergenic 15.0%
!!! ATTTTTTCAATTGAAATCTT+TGG + chr1_2:33554950-33554969 None:intergenic 15.0%
!!! CAGGATATTTTTATTTTTTT+TGG - chr1_2:33555290-33555309 Msa0068060:five_prime_UTR 15.0%
!! GATTATTATACATAAATATG+AGG - chr1_2:33555331-33555350 Msa0068060:five_prime_UTR 15.0%
!!! ATTTAAAGTATGACAATAAT+TGG + chr1_2:33554711-33554730 None:intergenic 15.0%
!!! ATTTTTTCAATTGAAATCTT+TGG + chr1_2:33554950-33554969 None:intergenic 15.0%
!!! CAGGATATTTTTATTTTTTT+TGG - chr1_2:33555290-33555309 Msa0068060:five_prime_UTR 15.0%
!! GATTATTATACATAAATATG+AGG - chr1_2:33555331-33555350 Msa0068060:five_prime_UTR 15.0%
!! CGTTATAATGTTAAAATTTG+TGG + chr1_2:33554439-33554458 None:intergenic 20.0%
!! TTTAACATTATAACGTTGTT+TGG - chr1_2:33554444-33554463 Msa0068060:three_prime_UTR 20.0%
!!! TATGTCTCTTATTTTGTTTT+AGG - chr1_2:33554485-33554504 Msa0068060:three_prime_UTR 20.0%
!! TTATGCAGAGAAAATAAAAT+TGG + chr1_2:33554770-33554789 None:intergenic 20.0%
!! CGTTATAATGTTAAAATTTG+TGG + chr1_2:33554439-33554458 None:intergenic 20.0%
!! TTTAACATTATAACGTTGTT+TGG - chr1_2:33554444-33554463 Msa0068060:three_prime_UTR 20.0%
!!! TATGTCTCTTATTTTGTTTT+AGG - chr1_2:33554485-33554504 Msa0068060:three_prime_UTR 20.0%
!! TTATGCAGAGAAAATAAAAT+TGG + chr1_2:33554770-33554789 None:intergenic 20.0%
! GTACTGGATTTAATACAAAT+TGG + chr1_2:33554359-33554378 None:intergenic 25.0%
!!! TCTCTTATTTTGTTTTAGGT+TGG - chr1_2:33554489-33554508 Msa0068060:three_prime_UTR 25.0%
! CTGAAGAATTCTTTCATTAT+AGG - chr1_2:33554562-33554581 Msa0068060:CDS 25.0%
!!! CTATGTTCGATCATTTTTTA+GGG + chr1_2:33554673-33554692 None:intergenic 25.0%
! AGAAATTTGAGAAACATCAA+TGG + chr1_2:33554734-33554753 None:intergenic 25.0%
! CTGAAGATATAAATAAACTC+AGG - chr1_2:33554897-33554916 Msa0068060:intron 25.0%
! TAAATAAACTCAGGAGTTAA+AGG - chr1_2:33554906-33554925 Msa0068060:intron 25.0%
! TTGTTCGAAAGAATCTTATT+GGG + chr1_2:33555124-33555143 None:intergenic 25.0%
! TCAGAAACCATATGAAATTA+TGG - chr1_2:33555169-33555188 Msa0068060:CDS 25.0%
! CAGAAACCATATGAAATTAT+GGG - chr1_2:33555170-33555189 Msa0068060:CDS 25.0%
!!! TTTTCCTTTTTTGTACATCT+TGG - chr1_2:33555210-33555229 Msa0068060:five_prime_UTR 25.0%
! GTACTGGATTTAATACAAAT+TGG + chr1_2:33554359-33554378 None:intergenic 25.0%
!!! TCTCTTATTTTGTTTTAGGT+TGG - chr1_2:33554489-33554508 Msa0068060:three_prime_UTR 25.0%
! CTGAAGAATTCTTTCATTAT+AGG - chr1_2:33554562-33554581 Msa0068060:CDS 25.0%
!!! CTATGTTCGATCATTTTTTA+GGG + chr1_2:33554673-33554692 None:intergenic 25.0%
! AGAAATTTGAGAAACATCAA+TGG + chr1_2:33554734-33554753 None:intergenic 25.0%
! CTGAAGATATAAATAAACTC+AGG - chr1_2:33554897-33554916 Msa0068060:intron 25.0%
! TAAATAAACTCAGGAGTTAA+AGG - chr1_2:33554906-33554925 Msa0068060:intron 25.0%
! TTGTTCGAAAGAATCTTATT+GGG + chr1_2:33555124-33555143 None:intergenic 25.0%
! TCAGAAACCATATGAAATTA+TGG - chr1_2:33555169-33555188 Msa0068060:CDS 25.0%
! CAGAAACCATATGAAATTAT+GGG - chr1_2:33555170-33555189 Msa0068060:CDS 25.0%
!!! TTTTCCTTTTTTGTACATCT+TGG - chr1_2:33555210-33555229 Msa0068060:five_prime_UTR 25.0%
GCAAAAATAAAGACAAGTAC+TGG + chr1_2:33554375-33554394 None:intergenic 30.0%
ACATTATAACGTTGTTTGGA+AGG - chr1_2:33554448-33554467 Msa0068060:three_prime_UTR 30.0%
! CTTCAGTTATATCTTTTCTC+TGG + chr1_2:33554548-33554567 None:intergenic 30.0%
!!! GCTATGTTCGATCATTTTTT+AGG + chr1_2:33554674-33554693 None:intergenic 30.0%
!! GAACTTTACATTCTAGTTCT+AGG + chr1_2:33554810-33554829 None:intergenic 30.0%
CAATAAGGCAAGAAATGAAT+TGG - chr1_2:33555096-33555115 Msa0068060:CDS 30.0%
GTTGTTCGAAAGAATCTTAT+TGG + chr1_2:33555125-33555144 None:intergenic 30.0%
TTCATATGGTTTCTGATTGT+GGG + chr1_2:33555165-33555184 None:intergenic 30.0%
TTTCATATGGTTTCTGATTG+TGG + chr1_2:33555166-33555185 None:intergenic 30.0%
AACCATATGAAATTATGGGT+CGG - chr1_2:33555174-33555193 Msa0068060:CDS 30.0%
TTAGTCAAACAAACACAATC+AGG - chr1_2:33555271-33555290 Msa0068060:five_prime_UTR 30.0%
GCAAAAATAAAGACAAGTAC+TGG + chr1_2:33554375-33554394 None:intergenic 30.0%
ACATTATAACGTTGTTTGGA+AGG - chr1_2:33554448-33554467 Msa0068060:three_prime_UTR 30.0%
! CTTCAGTTATATCTTTTCTC+TGG + chr1_2:33554548-33554567 None:intergenic 30.0%
!!! GCTATGTTCGATCATTTTTT+AGG + chr1_2:33554674-33554693 None:intergenic 30.0%
!! GAACTTTACATTCTAGTTCT+AGG + chr1_2:33554810-33554829 None:intergenic 30.0%
CAATAAGGCAAGAAATGAAT+TGG - chr1_2:33555096-33555115 Msa0068060:CDS 30.0%
GTTGTTCGAAAGAATCTTAT+TGG + chr1_2:33555125-33555144 None:intergenic 30.0%
TTCATATGGTTTCTGATTGT+GGG + chr1_2:33555165-33555184 None:intergenic 30.0%
TTTCATATGGTTTCTGATTG+TGG + chr1_2:33555166-33555185 None:intergenic 30.0%
AACCATATGAAATTATGGGT+CGG - chr1_2:33555174-33555193 Msa0068060:CDS 30.0%
TTAGTCAAACAAACACAATC+AGG - chr1_2:33555271-33555290 Msa0068060:five_prime_UTR 30.0%
ATCTGACTCAGGCAAAATTA+TGG - chr1_2:33554586-33554605 Msa0068060:CDS 35.0%
TCTGACTCAGGCAAAATTAT+GGG - chr1_2:33554587-33554606 Msa0068060:CDS 35.0%
ATTACTCTGCTTATGAACAC+TGG - chr1_2:33554613-33554632 Msa0068060:CDS 35.0%
TTACTCTGCTTATGAACACT+GGG - chr1_2:33554614-33554633 Msa0068060:CDS 35.0%
ACAAGTTCATCCTTGTTCTT+TGG + chr1_2:33555031-33555050 None:intergenic 35.0%
GATTCTTTCGAACAACAAGT+TGG - chr1_2:33555129-33555148 Msa0068060:CDS 35.0%
AACCGACCCATAATTTCATA+TGG + chr1_2:33555179-33555198 None:intergenic 35.0%
CAGTCCAAGATGTACAAAAA+AGG + chr1_2:33555217-33555236 None:intergenic 35.0%
! TTGGAAGTGTAAACACAATC+AGG - chr1_2:33555309-33555328 Msa0068060:five_prime_UTR 35.0%
ATCTGACTCAGGCAAAATTA+TGG - chr1_2:33554586-33554605 Msa0068060:CDS 35.0%
TCTGACTCAGGCAAAATTAT+GGG - chr1_2:33554587-33554606 Msa0068060:CDS 35.0%
ATTACTCTGCTTATGAACAC+TGG - chr1_2:33554613-33554632 Msa0068060:CDS 35.0%
TTACTCTGCTTATGAACACT+GGG - chr1_2:33554614-33554633 Msa0068060:CDS 35.0%
ACAAGTTCATCCTTGTTCTT+TGG + chr1_2:33555031-33555050 None:intergenic 35.0%
GATTCTTTCGAACAACAAGT+TGG - chr1_2:33555129-33555148 Msa0068060:CDS 35.0%
AACCGACCCATAATTTCATA+TGG + chr1_2:33555179-33555198 None:intergenic 35.0%
CAGTCCAAGATGTACAAAAA+AGG + chr1_2:33555217-33555236 None:intergenic 35.0%
! TTGGAAGTGTAAACACAATC+AGG - chr1_2:33555309-33555328 Msa0068060:five_prime_UTR 35.0%
AATAATGTACCTCCCTACCA+TGG - chr1_2:33554515-33554534 Msa0068060:exon 40.0%
TCATTATAGGCATCTGACTC+AGG - chr1_2:33554575-33554594 Msa0068060:CDS 40.0%
!! CATTCTAGTTCTAGGAACGA+TGG + chr1_2:33554802-33554821 None:intergenic 40.0%
CAGTATGCACTCATTGTATG+TGG + chr1_2:33554843-33554862 None:intergenic 40.0%
TCTGTAGGTTCCAAAGAACA+AGG - chr1_2:33555018-33555037 Msa0068060:intron 40.0%
!! AGTCACATCTTTGGAACTTC+AGG - chr1_2:33555238-33555257 Msa0068060:five_prime_UTR 40.0%
AATAATGTACCTCCCTACCA+TGG - chr1_2:33554515-33554534 Msa0068060:exon 40.0%
TCATTATAGGCATCTGACTC+AGG - chr1_2:33554575-33554594 Msa0068060:CDS 40.0%
!! CATTCTAGTTCTAGGAACGA+TGG + chr1_2:33554802-33554821 None:intergenic 40.0%
CAGTATGCACTCATTGTATG+TGG + chr1_2:33554843-33554862 None:intergenic 40.0%
TCTGTAGGTTCCAAAGAACA+AGG - chr1_2:33555018-33555037 Msa0068060:intron 40.0%
!! AGTCACATCTTTGGAACTTC+AGG - chr1_2:33555238-33555257 Msa0068060:five_prime_UTR 40.0%
TGAACACTGGGCAAAGATTG+AGG - chr1_2:33554626-33554645 Msa0068060:CDS 45.0%
CAATGAGTGCATACTGCACA+TGG - chr1_2:33554847-33554866 Msa0068060:intron 45.0%
CATACTGCACATGGTCATGT+TGG - chr1_2:33554856-33554875 Msa0068060:intron 45.0%
GTGCATATTACCTGCTCTGT+AGG - chr1_2:33555003-33555022 Msa0068060:intron 45.0%
!! TTCTTTGGAACCTACAGAGC+AGG + chr1_2:33555016-33555035 None:intergenic 45.0%
AACTTGTAGCTCTCCAAGCA+AGG - chr1_2:33555044-33555063 Msa0068060:intron 45.0%
TCCGGTGGATGCATACAATA+AGG - chr1_2:33555081-33555100 Msa0068060:CDS 45.0%
! GCCTTATTGTATGCATCCAC+CGG + chr1_2:33555085-33555104 None:intergenic 45.0%
TTGGACTGCAGTCACATCTT+TGG - chr1_2:33555229-33555248 Msa0068060:five_prime_UTR 45.0%
TGAACACTGGGCAAAGATTG+AGG - chr1_2:33554626-33554645 Msa0068060:CDS 45.0%
CAATGAGTGCATACTGCACA+TGG - chr1_2:33554847-33554866 Msa0068060:intron 45.0%
CATACTGCACATGGTCATGT+TGG - chr1_2:33554856-33554875 Msa0068060:intron 45.0%
GTGCATATTACCTGCTCTGT+AGG - chr1_2:33555003-33555022 Msa0068060:intron 45.0%
!! TTCTTTGGAACCTACAGAGC+AGG + chr1_2:33555016-33555035 None:intergenic 45.0%
AACTTGTAGCTCTCCAAGCA+AGG - chr1_2:33555044-33555063 Msa0068060:intron 45.0%
TCCGGTGGATGCATACAATA+AGG - chr1_2:33555081-33555100 Msa0068060:CDS 45.0%
! GCCTTATTGTATGCATCCAC+CGG + chr1_2:33555085-33555104 None:intergenic 45.0%
TTGGACTGCAGTCACATCTT+TGG - chr1_2:33555229-33555248 Msa0068060:five_prime_UTR 45.0%
! TTTTCTCTGGCGAGCATCCA+TGG + chr1_2:33554535-33554554 None:intergenic 50.0%
TCCAAGCAAGGCTGAGAAAG+CGG - chr1_2:33555056-33555075 Msa0068060:intron 50.0%
AAGGCTGAGAAAGCGGTTTC+CGG - chr1_2:33555063-33555082 Msa0068060:intron 50.0%
! TTTTCTCTGGCGAGCATCCA+TGG + chr1_2:33554535-33554554 None:intergenic 50.0%
TCCAAGCAAGGCTGAGAAAG+CGG - chr1_2:33555056-33555075 Msa0068060:intron 50.0%
AAGGCTGAGAAAGCGGTTTC+CGG - chr1_2:33555063-33555082 Msa0068060:intron 50.0%
TCTGGCGAGCATCCATGGTA+GGG + chr1_2:33554530-33554549 None:intergenic 55.0%
ACCGCTTTCTCAGCCTTGCT+TGG + chr1_2:33555060-33555079 None:intergenic 55.0%
TCTGGCGAGCATCCATGGTA+GGG + chr1_2:33554530-33554549 None:intergenic 55.0%
ACCGCTTTCTCAGCCTTGCT+TGG + chr1_2:33555060-33555079 None:intergenic 55.0%
CTCTGGCGAGCATCCATGGT+AGG + chr1_2:33554531-33554550 None:intergenic 60.0%
GCTGAGAAAGCGGTTTCCGG+TGG - chr1_2:33555066-33555085 Msa0068060:intron 60.0%
CTCTGGCGAGCATCCATGGT+AGG + chr1_2:33554531-33554550 None:intergenic 60.0%
GCTGAGAAAGCGGTTTCCGG+TGG - chr1_2:33555066-33555085 Msa0068060:intron 60.0%
GGCGAGCATCCATGGTAGGG+AGG + chr1_2:33554527-33554546 None:intergenic 65.0%
GGCGAGCATCCATGGTAGGG+AGG + chr1_2:33554527-33554546 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 33554350 33555367 33554350 ID=Msa0068060;Name=Msa0068060
chr1_2 mRNA 33554350 33555367 33554350 ID=Msa0068060-mRNA-1;Parent=Msa0068060;Name=Msa0068060-mRNA-1;_AED=0.00;_eAED=0.00;_QI=169|1|1|1|1|1|2|184|95
chr1_2 exon 33554350 33554692 33554350 ID=Msa0068060-mRNA-1:exon:11018;Parent=Msa0068060-mRNA-1
chr1_2 exon 33555070 33555367 33555070 ID=Msa0068060-mRNA-1:exon:11017;Parent=Msa0068060-mRNA-1
chr1_2 five_prime_UTR 33555199 33555367 33555199 ID=Msa0068060-mRNA-1:five_prime_utr;Parent=Msa0068060-mRNA-1
chr1_2 CDS 33555070 33555198 33555070 ID=Msa0068060-mRNA-1:cds;Parent=Msa0068060-mRNA-1
chr1_2 CDS 33554534 33554692 33554534 ID=Msa0068060-mRNA-1:cds;Parent=Msa0068060-mRNA-1
chr1_2 three_prime_UTR 33554350 33554533 33554350 ID=Msa0068060-mRNA-1:three_prime_utr;Parent=Msa0068060-mRNA-1
Gene Sequence

>Msa0068060

ATGTACCTCCCTACCATGGATGCTCGCCAGAGAAAAGATATAACTGAAGAATTCTTTCATTATAGGCATCTGACTCAGGCAAAATTATGGGATAATTACTCTGCTTATGAACACTGGGCAAAGATTGAGGTTCCAAAGAACAAGGATGAACTTGTAGCTCTCCAAGCAAGGCTGAGAAAGCGGTTTCCGGTGGATGCATACAATAAGGCAAGAAATGAATTGGATCCCAATAAGATTCTTTCGAACAACAAGTTGGAAAAGCTCTTCCCACAATCAGAAACCATATGA
Protein sequence

>Msa0068060

MYLPTMDARQRKDITEEFFHYRHLTQAKLWDNYSAYEHWAKIEVPKNKDELVALQARLRKRFPVDAYNKARNELDPNKILSNNKLEKLFPQSETI*