AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1131420

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1131420 MtrunA17_Chr4g0073811 100.000 76 0 0 1 76 1 76 2.04e-50 152
Msa1131420 MtrunA17_Chr4g0073821 81.333 75 14 0 1 75 1 75 1.20e-40 127
Msa1131420 MtrunA17_Chr6g0462381 57.692 52 21 1 5 56 3 53 4.54e-14 60.1
Msa1131420 MtrunA17_Chr7g0271271 65.217 46 15 1 10 55 8 52 1.78e-13 58.5
Msa1131420 MtrunA17_Chr7g0271261 57.447 47 19 1 9 55 7 52 6.18e-12 54.7
Msa1131420 MtrunA17_Chr7g0271281 56.522 46 19 1 10 55 8 52 8.21e-12 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1131420 AT4G30660.1 76.712 73 17 0 1 73 1 73 2.09e-37 120
Msa1131420 AT4G30660.2 76.712 73 17 0 1 73 1 73 2.09e-37 120
Msa1131420 AT4G28088.1 70.833 72 21 0 1 72 1 72 5.93e-36 116
Msa1131420 AT2G24040.1 70.833 72 21 0 1 72 1 72 8.09e-34 110
Msa1131420 AT4G30650.1 75.410 61 15 0 1 61 1 61 1.03e-27 95.5
Msa1131420 AT2G38905.1 68.627 51 15 1 6 56 4 53 3.64e-16 65.9
Msa1131420 AT3G05880.1 71.739 46 12 1 10 55 8 52 6.63e-15 62.8
Msa1131420 AT3G05890.1 58.696 46 18 1 10 55 8 52 6.31e-13 57.8
Msa1131420 AT2G24040.2 76.667 30 7 0 1 30 1 30 4.98e-12 55.5

Find 28 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTGACGTTGGAGTCAATT+TGG 0.187395 7_3:-83966676 Msa1131420:three_prime_UTR
CTATCTGATTGTTGATTGTA+TGG 0.350406 7_3:-83966558 Msa1131420:three_prime_UTR
GTATGATATGAATATTTGAT+TGG 0.389091 7_3:-83966468 Msa1131420:three_prime_UTR
TTCAACTCTTTATTATGTAA+TGG 0.390988 7_3:-83966740 Msa1131420:three_prime_UTR
CGCTGTATTACTCCCTCCAT+TGG 0.403030 7_3:-83967243 Msa1131420:CDS
GTGGCTTATTAATAGACATT+TGG 0.459610 7_3:-83967370 Msa1131420:five_prime_UTR
TAAAGTGGTTAGTTATATTG+TGG 0.465212 7_3:-83966497 Msa1131420:three_prime_UTR
ACAATACTAGGATATATTCC+TGG 0.469022 7_3:-83966885 Msa1131420:CDS
GACATTTGGTGAAGATCAGT+TGG 0.475462 7_3:-83967356 Msa1131420:five_prime_UTR
ATTGGTTTATGATAGAGATA+AGG 0.489530 7_3:-83966450 Msa1131420:three_prime_UTR
TGCTTGCTGCTTACAATACT+AGG 0.494816 7_3:-83966897 Msa1131420:CDS
ATCAAATTATGAAAATAAAG+TGG 0.499775 7_3:-83966512 Msa1131420:three_prime_UTR
CAGATAATTTCACAAGTTGA+AGG 0.500488 7_3:+83967278 None:intergenic
GTTGTAATTCTCATTGACGT+TGG 0.504892 7_3:-83966687 Msa1131420:three_prime_UTR
GCTGTATTACTCCCTCCATT+GGG 0.519016 7_3:-83967242 Msa1131420:CDS
AGCCATCAACATCACTTCAT+AGG 0.526050 7_3:+83966413 None:intergenic
GTCCTATGAAGTGATGTTGA+TGG 0.544298 7_3:-83966415 None:intergenic
TTGGGTGTTTGTCTTCGCCA+TGG 0.568247 7_3:-83967224 Msa1131420:CDS
TTGTAAGCAGCAAGCAGATG+AGG 0.568939 7_3:+83966904 None:intergenic
TAGTATTTGTTTGCATACAA+AGG 0.574050 7_3:+83966795 None:intergenic
CATCAACAAGAATAAGCAGA+AGG 0.602168 7_3:-83967328 Msa1131420:five_prime_UTR
AGAGATAAGGTGCTATGAAG+TGG 0.607967 7_3:-83966437 Msa1131420:three_prime_UTR
TGGCGAAGACAAACACCCAA+TGG 0.619712 7_3:+83967227 None:intergenic
TACATACAGTGCAGCAACCA+TGG 0.624485 7_3:+83967207 None:intergenic
CGAAGACAAACACCCAATGG+AGG 0.631567 7_3:+83967230 None:intergenic
AGCAGTACTTTGATGAAGCT+AGG 0.636728 7_3:-83966821 Msa1131420:CDS
GAAGACAAACACCCAATGGA+GGG 0.640185 7_3:+83967231 None:intergenic
TAGATAGCATAAATAATACC+AGG 0.641061 7_3:+83966867 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTAAAAAATCATGAAAAAA+TGG + chr7_3:83966705-83966724 None:intergenic 15.0%
!!! TTTTCATGATTTTTTAGTTA+TGG - chr7_3:83966707-83966726 Msa1131420:three_prime_UTR 15.0%
!!! TTTCATGATTTTTTAGTTAT+GGG - chr7_3:83966708-83966727 Msa1131420:three_prime_UTR 15.0%
!! AGATAAAAATTAAATTCAAG+TGG + chr7_3:83967079-83967098 None:intergenic 15.0%
!! ATCAAATTATGAAAATAAAG+TGG - chr7_3:83967274-83967293 Msa1131420:CDS 15.0%
!! ACTAAAAAATCATGAAAAAA+TGG + chr7_3:83966705-83966724 None:intergenic 15.0%
!!! TTTTCATGATTTTTTAGTTA+TGG - chr7_3:83966707-83966726 Msa1131420:three_prime_UTR 15.0%
!!! TTTCATGATTTTTTAGTTAT+GGG - chr7_3:83966708-83966727 Msa1131420:three_prime_UTR 15.0%
!! AGATAAAAATTAAATTCAAG+TGG + chr7_3:83967079-83967098 None:intergenic 15.0%
!! ATCAAATTATGAAAATAAAG+TGG - chr7_3:83967274-83967293 Msa1131420:CDS 15.0%
!!! AATCATGAAAAAATGGATTT+TGG + chr7_3:83966698-83966717 None:intergenic 20.0%
!!! ATTGATAATTGTATTTATCC+CGG + chr7_3:83966739-83966758 None:intergenic 20.0%
!! TTCAACTCTTTATTATGTAA+TGG - chr7_3:83967046-83967065 Msa1131420:intron 20.0%
!! GTATGATATGAATATTTGAT+TGG - chr7_3:83967318-83967337 Msa1131420:five_prime_UTR 20.0%
!!! AATCATGAAAAAATGGATTT+TGG + chr7_3:83966698-83966717 None:intergenic 20.0%
!!! ATTGATAATTGTATTTATCC+CGG + chr7_3:83966739-83966758 None:intergenic 20.0%
!! TTCAACTCTTTATTATGTAA+TGG - chr7_3:83967046-83967065 Msa1131420:intron 20.0%
!! GTATGATATGAATATTTGAT+TGG - chr7_3:83967318-83967337 Msa1131420:five_prime_UTR 20.0%
! GAAAGAAAGTGAGATTAAAA+AGG + chr7_3:83966639-83966658 None:intergenic 25.0%
! AAAGGGAAAAAGAAGTAAAA+GGG + chr7_3:83966668-83966687 None:intergenic 25.0%
! AAAAGGGAAAAAGAAGTAAA+AGG + chr7_3:83966669-83966688 None:intergenic 25.0%
! TCAATCTCAAATTTATGATG+AGG - chr7_3:83966754-83966773 Msa1131420:three_prime_UTR 25.0%
! ATTGAAATCAAAGTCATTCA+TGG + chr7_3:83966841-83966860 None:intergenic 25.0%
! TAGATAGCATAAATAATACC+AGG + chr7_3:83966922-83966941 None:intergenic 25.0%
! TAGTATTTGTTTGCATACAA+AGG + chr7_3:83966994-83967013 None:intergenic 25.0%
!! TAAAGTGGTTAGTTATATTG+TGG - chr7_3:83967289-83967308 Msa1131420:exon 25.0%
!! ATTGGTTTATGATAGAGATA+AGG - chr7_3:83967336-83967355 Msa1131420:five_prime_UTR 25.0%
! GAAAGAAAGTGAGATTAAAA+AGG + chr7_3:83966639-83966658 None:intergenic 25.0%
! AAAGGGAAAAAGAAGTAAAA+GGG + chr7_3:83966668-83966687 None:intergenic 25.0%
! AAAAGGGAAAAAGAAGTAAA+AGG + chr7_3:83966669-83966688 None:intergenic 25.0%
! TCAATCTCAAATTTATGATG+AGG - chr7_3:83966754-83966773 Msa1131420:three_prime_UTR 25.0%
! ATTGAAATCAAAGTCATTCA+TGG + chr7_3:83966841-83966860 None:intergenic 25.0%
! TAGATAGCATAAATAATACC+AGG + chr7_3:83966922-83966941 None:intergenic 25.0%
! TAGTATTTGTTTGCATACAA+AGG + chr7_3:83966994-83967013 None:intergenic 25.0%
!! TAAAGTGGTTAGTTATATTG+TGG - chr7_3:83967289-83967308 Msa1131420:exon 25.0%
!! ATTGGTTTATGATAGAGATA+AGG - chr7_3:83967336-83967355 Msa1131420:five_prime_UTR 25.0%
GTGGCTTATTAATAGACATT+TGG - chr7_3:83966416-83966435 Msa1131420:three_prime_UTR 30.0%
! CAGATAATTTCACAAGTTGA+AGG + chr7_3:83966511-83966530 None:intergenic 30.0%
AAGGGAAAAAGAAGTAAAAG+GGG + chr7_3:83966667-83966686 None:intergenic 30.0%
! TGGATTTTGGATGTGAAAAA+GGG + chr7_3:83966685-83966704 None:intergenic 30.0%
! ATGGATTTTGGATGTGAAAA+AGG + chr7_3:83966686-83966705 None:intergenic 30.0%
!!! TTTTTAGTTATGGGTCAAAC+CGG - chr7_3:83966717-83966736 Msa1131420:three_prime_UTR 30.0%
ACAATACTAGGATATATTCC+TGG - chr7_3:83966901-83966920 Msa1131420:CDS 30.0%
!! TTAGACTTTTAGTTGAGAAC+AGG - chr7_3:83967160-83967179 Msa1131420:intron 30.0%
! CTATCTGATTGTTGATTGTA+TGG - chr7_3:83967228-83967247 Msa1131420:CDS 30.0%
GTGGCTTATTAATAGACATT+TGG - chr7_3:83966416-83966435 Msa1131420:three_prime_UTR 30.0%
! CAGATAATTTCACAAGTTGA+AGG + chr7_3:83966511-83966530 None:intergenic 30.0%
AAGGGAAAAAGAAGTAAAAG+GGG + chr7_3:83966667-83966686 None:intergenic 30.0%
! TGGATTTTGGATGTGAAAAA+GGG + chr7_3:83966685-83966704 None:intergenic 30.0%
! ATGGATTTTGGATGTGAAAA+AGG + chr7_3:83966686-83966705 None:intergenic 30.0%
!!! TTTTTAGTTATGGGTCAAAC+CGG - chr7_3:83966717-83966736 Msa1131420:three_prime_UTR 30.0%
ACAATACTAGGATATATTCC+TGG - chr7_3:83966901-83966920 Msa1131420:CDS 30.0%
!! TTAGACTTTTAGTTGAGAAC+AGG - chr7_3:83967160-83967179 Msa1131420:intron 30.0%
! CTATCTGATTGTTGATTGTA+TGG - chr7_3:83967228-83967247 Msa1131420:CDS 30.0%
CATCAACAAGAATAAGCAGA+AGG - chr7_3:83966458-83966477 Msa1131420:three_prime_UTR 35.0%
!! TTTTAGTTATGGGTCAAACC+GGG - chr7_3:83966718-83966737 Msa1131420:three_prime_UTR 35.0%
GTTGTAATTCTCATTGACGT+TGG - chr7_3:83967099-83967118 Msa1131420:intron 35.0%
CATCAACAAGAATAAGCAGA+AGG - chr7_3:83966458-83966477 Msa1131420:three_prime_UTR 35.0%
!! TTTTAGTTATGGGTCAAACC+GGG - chr7_3:83966718-83966737 Msa1131420:three_prime_UTR 35.0%
GTTGTAATTCTCATTGACGT+TGG - chr7_3:83967099-83967118 Msa1131420:intron 35.0%
! GACATTTGGTGAAGATCAGT+TGG - chr7_3:83966430-83966449 Msa1131420:three_prime_UTR 40.0%
! TGCTTGCTGCTTACAATACT+AGG - chr7_3:83966889-83966908 Msa1131420:CDS 40.0%
AGCAGTACTTTGATGAAGCT+AGG - chr7_3:83966965-83966984 Msa1131420:intron 40.0%
CATTGACGTTGGAGTCAATT+TGG - chr7_3:83967110-83967129 Msa1131420:intron 40.0%
! AGAGATAAGGTGCTATGAAG+TGG - chr7_3:83967349-83967368 Msa1131420:five_prime_UTR 40.0%
GTCCTATGAAGTGATGTTGA+TGG - chr7_3:83967371-83967390 Msa1131420:five_prime_UTR 40.0%
! GACATTTGGTGAAGATCAGT+TGG - chr7_3:83966430-83966449 Msa1131420:three_prime_UTR 40.0%
! TGCTTGCTGCTTACAATACT+AGG - chr7_3:83966889-83966908 Msa1131420:CDS 40.0%
AGCAGTACTTTGATGAAGCT+AGG - chr7_3:83966965-83966984 Msa1131420:intron 40.0%
CATTGACGTTGGAGTCAATT+TGG - chr7_3:83967110-83967129 Msa1131420:intron 40.0%
! AGAGATAAGGTGCTATGAAG+TGG - chr7_3:83967349-83967368 Msa1131420:five_prime_UTR 40.0%
GCTGTATTACTCCCTCCATT+GGG - chr7_3:83966544-83966563 Msa1131420:three_prime_UTR 45.0%
GAAGACAAACACCCAATGGA+GGG + chr7_3:83966558-83966577 None:intergenic 45.0%
TACATACAGTGCAGCAACCA+TGG + chr7_3:83966582-83966601 None:intergenic 45.0%
TTGTAAGCAGCAAGCAGATG+AGG + chr7_3:83966885-83966904 None:intergenic 45.0%
GCTGTATTACTCCCTCCATT+GGG - chr7_3:83966544-83966563 Msa1131420:three_prime_UTR 45.0%
GAAGACAAACACCCAATGGA+GGG + chr7_3:83966558-83966577 None:intergenic 45.0%
TACATACAGTGCAGCAACCA+TGG + chr7_3:83966582-83966601 None:intergenic 45.0%
TTGTAAGCAGCAAGCAGATG+AGG + chr7_3:83966885-83966904 None:intergenic 45.0%
CGCTGTATTACTCCCTCCAT+TGG - chr7_3:83966543-83966562 Msa1131420:three_prime_UTR 50.0%
CGAAGACAAACACCCAATGG+AGG + chr7_3:83966559-83966578 None:intergenic 50.0%
TGGCGAAGACAAACACCCAA+TGG + chr7_3:83966562-83966581 None:intergenic 50.0%
TTGGGTGTTTGTCTTCGCCA+TGG - chr7_3:83966562-83966581 Msa1131420:three_prime_UTR 50.0%
CGCTGTATTACTCCCTCCAT+TGG - chr7_3:83966543-83966562 Msa1131420:three_prime_UTR 50.0%
CGAAGACAAACACCCAATGG+AGG + chr7_3:83966559-83966578 None:intergenic 50.0%
TGGCGAAGACAAACACCCAA+TGG + chr7_3:83966562-83966581 None:intergenic 50.0%
TTGGGTGTTTGTCTTCGCCA+TGG - chr7_3:83966562-83966581 Msa1131420:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 83966416 83967392 83966416 ID=Msa1131420;Name=Msa1131420
chr7_3 mRNA 83966416 83967392 83966416 ID=Msa1131420-mRNA-1;Parent=Msa1131420;Name=Msa1131420-mRNA-1;_AED=0.28;_eAED=0.28;_QI=89|1|1|1|1|1|2|378|76
chr7_3 exon 83966416 83966934 83966416 ID=Msa1131420-mRNA-1:exon:24971;Parent=Msa1131420-mRNA-1
chr7_3 exon 83967214 83967392 83967214 ID=Msa1131420-mRNA-1:exon:24970;Parent=Msa1131420-mRNA-1
chr7_3 five_prime_UTR 83967304 83967392 83967304 ID=Msa1131420-mRNA-1:five_prime_utr;Parent=Msa1131420-mRNA-1
chr7_3 CDS 83967214 83967303 83967214 ID=Msa1131420-mRNA-1:cds;Parent=Msa1131420-mRNA-1
chr7_3 CDS 83966794 83966934 83966794 ID=Msa1131420-mRNA-1:cds;Parent=Msa1131420-mRNA-1
chr7_3 three_prime_UTR 83966416 83966793 83966416 ID=Msa1131420-mRNA-1:three_prime_utr;Parent=Msa1131420-mRNA-1
Gene Sequence

>Msa1131420

ATGCCTTCAACTTGTGAAATTATCTGTGAGATTTTGATCGCTGTATTACTCCCTCCATTGGGTGTTTGTCTTCGCCATGGTTGCTGCACTAATCAATTCCTCATCTGCTTGCTGCTTACAATACTAGGATATATTCCTGGTATTATTTATGCTATCTATGTCATTATCTTTGTTGATCGTGAGCAGTACTTTGATGAAGCTAGGCGTCCTTTGTATGCAAACAAATACTAG
Protein sequence

>Msa1131420

MPSTCEIICEILIAVLLPPLGVCLRHGCCTNQFLICLLLTILGYIPGIIYAIYVIIFVDREQYFDEARRPLYANKY*