AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1026290

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1026290 MtrunA17_Chr7g0242251 93.651 63 4 0 1 63 93 155 2.51e-18 74.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1026290 AT3G51880.2 55.224 67 27 1 5 71 99 162 2.06e-11 57.0
Msa1026290 AT1G20696.3 66.000 50 17 0 5 54 39 88 4.81e-11 54.3
Msa1026290 AT3G51880.5 61.538 52 17 1 5 56 99 147 5.64e-11 55.5
Msa1026290 AT3G51880.1 61.538 52 17 1 5 56 99 147 5.64e-11 55.5
Msa1026290 AT3G51880.3 61.538 52 17 1 5 56 99 147 5.64e-11 55.5

Find 32 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGCAGCCTTGGCTTCATA+TGG 0.316878 7_1:+57974599 None:intergenic
CTTGAACTTCCCTCAGTTGT+TGG 0.336610 7_1:-57973788 Msa1026290:three_prime_UTR
CAAACTACTCAAACTAAGTT+TGG 0.361366 7_1:+57973635 None:intergenic
GAATATTTATCTCTTATTGC+TGG 0.368858 7_1:-57973830 Msa1026290:three_prime_UTR
CTTGAAATATGACGTTTCAT+TGG 0.371105 7_1:-57973911 Msa1026290:three_prime_UTR
ATGAAGCCAAGGCTGCAAAA+AGG 0.405842 7_1:-57974595 Msa1026290:CDS
CATCCTCTTCCTCGTCATCT+TGG 0.407948 7_1:+57973990 None:intergenic
TACTTTAGCCAGCACATTTG+AGG 0.438345 7_1:+57973732 None:intergenic
TCGTCATCGTCCGCTGAACT+TGG 0.455762 7_1:+57974445 None:intergenic
GAAATATGACGTTTCATTGG+TGG 0.495166 7_1:-57973908 Msa1026290:three_prime_UTR
CCTCTTCCTCGTCATCTTGG+TGG 0.495432 7_1:+57973993 None:intergenic
CCACCAAGATGACGAGGAAG+AGG 0.514046 7_1:-57973993 Msa1026290:CDS
CTGAGGGAAGTTCAAGTGGC+TGG 0.523259 7_1:+57973795 None:intergenic
ATATGACGTTTCATTGGTGG+AGG 0.524750 7_1:-57973905 Msa1026290:three_prime_UTR
GCATTGTGCCTCAAATGTGC+TGG 0.552784 7_1:-57973740 Msa1026290:three_prime_UTR
AATAATGAAGATGAAGCAAG+TGG 0.555668 7_1:-57974391 Msa1026290:CDS
TGAAGATGAAGCAAGTGGAG+AGG 0.558529 7_1:-57974386 Msa1026290:intron
GACGTTTCATTGGTGGAGGG+AGG 0.575110 7_1:-57973901 Msa1026290:three_prime_UTR
AAAAGCTCCATATGAAGCCA+AGG 0.600500 7_1:-57974606 Msa1026290:CDS
TTCAGCGGACGATGACGAGG+AGG 0.606822 7_1:-57974440 Msa1026290:CDS
AAGTTCAGCGGACGATGACG+AGG 0.620749 7_1:-57974443 Msa1026290:CDS
ACAACTGAGGGAAGTTCAAG+TGG 0.622358 7_1:+57973791 None:intergenic
TTGGTGCATACATAGTGTGT+AGG 0.626919 7_1:+57973654 None:intergenic
ATGTTGACAGCCAAGTTCAG+CGG 0.635286 7_1:-57974455 Msa1026290:intron
GTACAATAACCAACAACTGA+GGG 0.647202 7_1:+57973779 None:intergenic
AGTACAATAACCAACAACTG+AGG 0.654621 7_1:+57973778 None:intergenic
TATGAATGCTTATAATAACA+AGG 0.656932 7_1:-57974552 Msa1026290:intron
TATGACGTTTCATTGGTGGA+GGG 0.664406 7_1:-57973904 Msa1026290:three_prime_UTR
TGACGAGGAAGAGGATGACG+AGG 0.681809 7_1:-57973984 Msa1026290:CDS
TGACGAGGAGGAATCAGACA+AGG 0.693157 7_1:-57974428 Msa1026290:CDS
GGATGACCACCAAGATGACG+AGG 0.697470 7_1:-57973999 Msa1026290:CDS
ATTTGAGGCACAATGCACAA+AGG 0.700540 7_1:+57973747 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CCTAATTTATTCTTAAAAAT+TGG + chr7_1:57974036-57974055 None:intergenic 15.0%
!!! CCAATTTTTAAGAATAAATT+AGG - chr7_1:57974033-57974052 Msa1026290:intron 15.0%
!! TTATTTCAAAGAAAAATATG+CGG + chr7_1:57974164-57974183 None:intergenic 15.0%
!! CCTAATTTATTCTTAAAAAT+TGG + chr7_1:57974036-57974055 None:intergenic 15.0%
!!! CCAATTTTTAAGAATAAATT+AGG - chr7_1:57974033-57974052 Msa1026290:intron 15.0%
!! TTATTTCAAAGAAAAATATG+CGG + chr7_1:57974164-57974183 None:intergenic 15.0%
!! TATGAATGCTTATAATAACA+AGG - chr7_1:57973700-57973719 Msa1026290:three_prime_UTR 20.0%
!! TATGAAAAAAACCTTCATTA+TGG - chr7_1:57974191-57974210 Msa1026290:intron 20.0%
!! TATGAATGCTTATAATAACA+AGG - chr7_1:57973700-57973719 Msa1026290:three_prime_UTR 20.0%
!! TATGAAAAAAACCTTCATTA+TGG - chr7_1:57974191-57974210 Msa1026290:intron 20.0%
! AAACAACAAAACTAGAAACA+CGG + chr7_1:57973736-57973755 None:intergenic 25.0%
!!! TTCTTAAAAATTGGCTTGTA+AGG + chr7_1:57974027-57974046 None:intergenic 25.0%
!! AACGTGTCATCTAAATTTTT+GGG + chr7_1:57974111-57974130 None:intergenic 25.0%
! GAATATTTATCTCTTATTGC+TGG - chr7_1:57974422-57974441 Msa1026290:CDS 25.0%
! AAACAACAAAACTAGAAACA+CGG + chr7_1:57973736-57973755 None:intergenic 25.0%
!!! TTCTTAAAAATTGGCTTGTA+AGG + chr7_1:57974027-57974046 None:intergenic 25.0%
!! AACGTGTCATCTAAATTTTT+GGG + chr7_1:57974111-57974130 None:intergenic 25.0%
! GAATATTTATCTCTTATTGC+TGG - chr7_1:57974422-57974441 Msa1026290:CDS 25.0%
AACAACAAAACTAGAAACAC+GGG + chr7_1:57973735-57973754 None:intergenic 30.0%
AATAATGAAGATGAAGCAAG+TGG - chr7_1:57973861-57973880 Msa1026290:three_prime_UTR 30.0%
! TTGTCCATCAAACTCTAAAA+GGG - chr7_1:57973992-57974011 Msa1026290:CDS 30.0%
! GAACGTGTCATCTAAATTTT+TGG + chr7_1:57974112-57974131 None:intergenic 30.0%
! TTTTATGCCCCTTTAAACTT+TGG + chr7_1:57974134-57974153 None:intergenic 30.0%
! CACATTTTATGCCATAATGA+AGG + chr7_1:57974205-57974224 None:intergenic 30.0%
CTTGAAATATGACGTTTCAT+TGG - chr7_1:57974341-57974360 Msa1026290:intron 30.0%
!! TTTCATTTTGATCGATGCTT+TGG - chr7_1:57974552-57974571 Msa1026290:intron 30.0%
CAAACTACTCAAACTAAGTT+TGG + chr7_1:57974620-57974639 None:intergenic 30.0%
AACAACAAAACTAGAAACAC+GGG + chr7_1:57973735-57973754 None:intergenic 30.0%
AATAATGAAGATGAAGCAAG+TGG - chr7_1:57973861-57973880 Msa1026290:three_prime_UTR 30.0%
! TTGTCCATCAAACTCTAAAA+GGG - chr7_1:57973992-57974011 Msa1026290:CDS 30.0%
! GAACGTGTCATCTAAATTTT+TGG + chr7_1:57974112-57974131 None:intergenic 30.0%
! TTTTATGCCCCTTTAAACTT+TGG + chr7_1:57974134-57974153 None:intergenic 30.0%
! CACATTTTATGCCATAATGA+AGG + chr7_1:57974205-57974224 None:intergenic 30.0%
CTTGAAATATGACGTTTCAT+TGG - chr7_1:57974341-57974360 Msa1026290:intron 30.0%
!! TTTCATTTTGATCGATGCTT+TGG - chr7_1:57974552-57974571 Msa1026290:intron 30.0%
CAAACTACTCAAACTAAGTT+TGG + chr7_1:57974620-57974639 None:intergenic 30.0%
GTTGTCCATCAAACTCTAAA+AGG - chr7_1:57973991-57974010 Msa1026290:CDS 35.0%
TATGAAGAATGAACCGTCTT+AGG + chr7_1:57974071-57974090 None:intergenic 35.0%
TGACACGTTCCAAAGTTTAA+AGG - chr7_1:57974122-57974141 Msa1026290:intron 35.0%
GACACGTTCCAAAGTTTAAA+GGG - chr7_1:57974123-57974142 Msa1026290:intron 35.0%
ACACGTTCCAAAGTTTAAAG+GGG - chr7_1:57974124-57974143 Msa1026290:intron 35.0%
GAAATATGACGTTTCATTGG+TGG - chr7_1:57974344-57974363 Msa1026290:intron 35.0%
!! TTTTCTAGTAGAGCAACTCA+TGG - chr7_1:57974384-57974403 Msa1026290:intron 35.0%
GTACAATAACCAACAACTGA+GGG + chr7_1:57974476-57974495 None:intergenic 35.0%
AGTACAATAACCAACAACTG+AGG + chr7_1:57974477-57974496 None:intergenic 35.0%
GTTGTCCATCAAACTCTAAA+AGG - chr7_1:57973991-57974010 Msa1026290:CDS 35.0%
TATGAAGAATGAACCGTCTT+AGG + chr7_1:57974071-57974090 None:intergenic 35.0%
TGACACGTTCCAAAGTTTAA+AGG - chr7_1:57974122-57974141 Msa1026290:intron 35.0%
GACACGTTCCAAAGTTTAAA+GGG - chr7_1:57974123-57974142 Msa1026290:intron 35.0%
ACACGTTCCAAAGTTTAAAG+GGG - chr7_1:57974124-57974143 Msa1026290:intron 35.0%
GAAATATGACGTTTCATTGG+TGG - chr7_1:57974344-57974363 Msa1026290:intron 35.0%
!! TTTTCTAGTAGAGCAACTCA+TGG - chr7_1:57974384-57974403 Msa1026290:intron 35.0%
GTACAATAACCAACAACTGA+GGG + chr7_1:57974476-57974495 None:intergenic 35.0%
AGTACAATAACCAACAACTG+AGG + chr7_1:57974477-57974496 None:intergenic 35.0%
AAAAGCTCCATATGAAGCCA+AGG - chr7_1:57973646-57973665 Msa1026290:three_prime_UTR 40.0%
! AACTTTCCTTTTTGCAGCCT+TGG + chr7_1:57973666-57973685 None:intergenic 40.0%
!!! GGTACCCTTTTAGAGTTTGA+TGG + chr7_1:57973999-57974018 None:intergenic 40.0%
!! AAATTGGCTTGTAAGGTGAG+CGG + chr7_1:57974020-57974039 None:intergenic 40.0%
GCTCAGTTCAAAACCTAAGA+CGG - chr7_1:57974055-57974074 Msa1026290:intron 40.0%
ATATGACGTTTCATTGGTGG+AGG - chr7_1:57974347-57974366 Msa1026290:intron 40.0%
TATGACGTTTCATTGGTGGA+GGG - chr7_1:57974348-57974367 Msa1026290:intron 40.0%
! ATTTGAGGCACAATGCACAA+AGG + chr7_1:57974508-57974527 None:intergenic 40.0%
TACTTTAGCCAGCACATTTG+AGG + chr7_1:57974523-57974542 None:intergenic 40.0%
TTGGTGCATACATAGTGTGT+AGG + chr7_1:57974601-57974620 None:intergenic 40.0%
AAAAGCTCCATATGAAGCCA+AGG - chr7_1:57973646-57973665 Msa1026290:three_prime_UTR 40.0%
! AACTTTCCTTTTTGCAGCCT+TGG + chr7_1:57973666-57973685 None:intergenic 40.0%
!!! GGTACCCTTTTAGAGTTTGA+TGG + chr7_1:57973999-57974018 None:intergenic 40.0%
!! AAATTGGCTTGTAAGGTGAG+CGG + chr7_1:57974020-57974039 None:intergenic 40.0%
GCTCAGTTCAAAACCTAAGA+CGG - chr7_1:57974055-57974074 Msa1026290:intron 40.0%
ATATGACGTTTCATTGGTGG+AGG - chr7_1:57974347-57974366 Msa1026290:intron 40.0%
TATGACGTTTCATTGGTGGA+GGG - chr7_1:57974348-57974367 Msa1026290:intron 40.0%
! ATTTGAGGCACAATGCACAA+AGG + chr7_1:57974508-57974527 None:intergenic 40.0%
TACTTTAGCCAGCACATTTG+AGG + chr7_1:57974523-57974542 None:intergenic 40.0%
TTGGTGCATACATAGTGTGT+AGG + chr7_1:57974601-57974620 None:intergenic 40.0%
TTTGCAGCCTTGGCTTCATA+TGG + chr7_1:57973656-57973675 None:intergenic 45.0%
ATGAAGCCAAGGCTGCAAAA+AGG - chr7_1:57973657-57973676 Msa1026290:three_prime_UTR 45.0%
ATGTTGACAGCCAAGTTCAG+CGG - chr7_1:57973797-57973816 Msa1026290:three_prime_UTR 45.0%
TGAAGATGAAGCAAGTGGAG+AGG - chr7_1:57973866-57973885 Msa1026290:three_prime_UTR 45.0%
TAACGATTGCTACCCCACAA+CGG - chr7_1:57973961-57973980 Msa1026290:CDS 45.0%
ACAACCATAACACCGTTGTG+GGG + chr7_1:57973976-57973995 None:intergenic 45.0%
GACAACCATAACACCGTTGT+GGG + chr7_1:57973977-57973996 None:intergenic 45.0%
! ACCATCTCTCCTTGTTGTAC+AGG - chr7_1:57974232-57974251 Msa1026290:intron 45.0%
TCCTGTACAACAAGGAGAGA+TGG + chr7_1:57974236-57974255 None:intergenic 45.0%
ACAACTGAGGGAAGTTCAAG+TGG + chr7_1:57974464-57974483 None:intergenic 45.0%
CTTGAACTTCCCTCAGTTGT+TGG - chr7_1:57974464-57974483 Msa1026290:intron 45.0%
TTTGCAGCCTTGGCTTCATA+TGG + chr7_1:57973656-57973675 None:intergenic 45.0%
ATGAAGCCAAGGCTGCAAAA+AGG - chr7_1:57973657-57973676 Msa1026290:three_prime_UTR 45.0%
ATGTTGACAGCCAAGTTCAG+CGG - chr7_1:57973797-57973816 Msa1026290:three_prime_UTR 45.0%
TGAAGATGAAGCAAGTGGAG+AGG - chr7_1:57973866-57973885 Msa1026290:three_prime_UTR 45.0%
TAACGATTGCTACCCCACAA+CGG - chr7_1:57973961-57973980 Msa1026290:CDS 45.0%
ACAACCATAACACCGTTGTG+GGG + chr7_1:57973976-57973995 None:intergenic 45.0%
GACAACCATAACACCGTTGT+GGG + chr7_1:57973977-57973996 None:intergenic 45.0%
! ACCATCTCTCCTTGTTGTAC+AGG - chr7_1:57974232-57974251 Msa1026290:intron 45.0%
TCCTGTACAACAAGGAGAGA+TGG + chr7_1:57974236-57974255 None:intergenic 45.0%
ACAACTGAGGGAAGTTCAAG+TGG + chr7_1:57974464-57974483 None:intergenic 45.0%
CTTGAACTTCCCTCAGTTGT+TGG - chr7_1:57974464-57974483 Msa1026290:intron 45.0%
TGACGAGGAGGAATCAGACA+AGG - chr7_1:57973824-57973843 Msa1026290:three_prime_UTR 50.0%
GGACAACCATAACACCGTTG+TGG + chr7_1:57973978-57973997 None:intergenic 50.0%
GGTGGTCATCCTGTACAACA+AGG + chr7_1:57974244-57974263 None:intergenic 50.0%
CATCCTCTTCCTCGTCATCT+TGG + chr7_1:57974265-57974284 None:intergenic 50.0%
GCATTGTGCCTCAAATGTGC+TGG - chr7_1:57974512-57974531 Msa1026290:intron 50.0%
TGACGAGGAGGAATCAGACA+AGG - chr7_1:57973824-57973843 Msa1026290:three_prime_UTR 50.0%
GGACAACCATAACACCGTTG+TGG + chr7_1:57973978-57973997 None:intergenic 50.0%
GGTGGTCATCCTGTACAACA+AGG + chr7_1:57974244-57974263 None:intergenic 50.0%
CATCCTCTTCCTCGTCATCT+TGG + chr7_1:57974265-57974284 None:intergenic 50.0%
GCATTGTGCCTCAAATGTGC+TGG - chr7_1:57974512-57974531 Msa1026290:intron 50.0%
TCGTCATCGTCCGCTGAACT+TGG + chr7_1:57973810-57973829 None:intergenic 55.0%
AAGTTCAGCGGACGATGACG+AGG - chr7_1:57973809-57973828 Msa1026290:three_prime_UTR 55.0%
! GCTACCCCACAACGGTGTTA+TGG - chr7_1:57973969-57973988 Msa1026290:CDS 55.0%
GGATGACCACCAAGATGACG+AGG - chr7_1:57974253-57974272 Msa1026290:intron 55.0%
CCTCTTCCTCGTCATCTTGG+TGG + chr7_1:57974262-57974281 None:intergenic 55.0%
CCACCAAGATGACGAGGAAG+AGG - chr7_1:57974259-57974278 Msa1026290:intron 55.0%
TGACGAGGAAGAGGATGACG+AGG - chr7_1:57974268-57974287 Msa1026290:intron 55.0%
GACGTTTCATTGGTGGAGGG+AGG - chr7_1:57974351-57974370 Msa1026290:intron 55.0%
CTGAGGGAAGTTCAAGTGGC+TGG + chr7_1:57974460-57974479 None:intergenic 55.0%
TCGTCATCGTCCGCTGAACT+TGG + chr7_1:57973810-57973829 None:intergenic 55.0%
AAGTTCAGCGGACGATGACG+AGG - chr7_1:57973809-57973828 Msa1026290:three_prime_UTR 55.0%
! GCTACCCCACAACGGTGTTA+TGG - chr7_1:57973969-57973988 Msa1026290:CDS 55.0%
GGATGACCACCAAGATGACG+AGG - chr7_1:57974253-57974272 Msa1026290:intron 55.0%
CCTCTTCCTCGTCATCTTGG+TGG + chr7_1:57974262-57974281 None:intergenic 55.0%
CCACCAAGATGACGAGGAAG+AGG - chr7_1:57974259-57974278 Msa1026290:intron 55.0%
TGACGAGGAAGAGGATGACG+AGG - chr7_1:57974268-57974287 Msa1026290:intron 55.0%
GACGTTTCATTGGTGGAGGG+AGG - chr7_1:57974351-57974370 Msa1026290:intron 55.0%
CTGAGGGAAGTTCAAGTGGC+TGG + chr7_1:57974460-57974479 None:intergenic 55.0%
TTCAGCGGACGATGACGAGG+AGG - chr7_1:57973812-57973831 Msa1026290:three_prime_UTR 60.0%
TTCAGCGGACGATGACGAGG+AGG - chr7_1:57973812-57973831 Msa1026290:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 57973632 57974642 57973632 ID=Msa1026290;Name=Msa1026290
chr7_1 mRNA 57973632 57974642 57973632 ID=Msa1026290-mRNA-1;Parent=Msa1026290;Name=Msa1026290-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|1|0.66|1|1|1|3|317|80
chr7_1 exon 57973632 57974020 57973632 ID=Msa1026290-mRNA-1:exon:11611;Parent=Msa1026290-mRNA-1
chr7_1 exon 57974387 57974467 57974387 ID=Msa1026290-mRNA-1:exon:11610;Parent=Msa1026290-mRNA-1
chr7_1 exon 57974553 57974642 57974553 ID=Msa1026290-mRNA-1:exon:11609;Parent=Msa1026290-mRNA-1
chr7_1 CDS 57974553 57974642 57974553 ID=Msa1026290-mRNA-1:cds;Parent=Msa1026290-mRNA-1
chr7_1 CDS 57974387 57974467 57974387 ID=Msa1026290-mRNA-1:cds;Parent=Msa1026290-mRNA-1
chr7_1 CDS 57973949 57974020 57973949 ID=Msa1026290-mRNA-1:cds;Parent=Msa1026290-mRNA-1
chr7_1 three_prime_UTR 57973632 57973948 57973632 ID=Msa1026290-mRNA-1:three_prime_utr;Parent=Msa1026290-mRNA-1
Gene Sequence

>Msa1026290

TTGAATGTAAAGGAAAAAGCTCCATATGAAGCCAAGGCTGCAAAAAGGAAAGTTGAGTATGAAAAGCTTATGAATGCTTATAATAACAAGCCAAGTTCAGCGGACGATGACGAGGAGGAATCAGACAAGGACAAATCTGAAGTTAATAATGAAGATGAAGCAAGTGGAGAGGATGACCACCAAGATGACGAGGAAGAGGATGACGAGGACGAAGATGACGACGACGATGAAGACGATGAGTGA
Protein sequence

>Msa1026290

LNVKEKAPYEAKAAKRKVEYEKLMNAYNNKPSSADDDEEESDKDKSEVNNEDEASGEDDHQDDEEEDDEDEDDDDDEDDE*