AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1123990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1123990 MtrunA17_Chr7g0263871 88.462 78 4 1 7 84 1 73 1.03e-41 130
Msa1123990 MtrunA17_Chr7g0263831 94.048 84 5 0 1 84 1 84 8.78e-31 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1123990 AT2G37120.1 76.190 63 15 0 22 84 14 76 2.41e-15 64.7
Msa1123990 AT3G53370.1 80.000 60 12 0 25 84 17 76 6.03e-13 58.5

Find 35 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATAGTTCTCCTGGTTAT+TGG 0.281375 7_3:-75021256 Msa1123990:CDS
TTATGTAAGTATAATCAATT+AGG 0.364072 7_3:+75020909 None:intergenic
CAATGGACTCAAATGTTCTA+TGG 0.367098 7_3:-75021082 Msa1123990:three_prime_UTR
ACAAACCGTGGTGCAAACTT+TGG 0.386650 7_3:-75021724 Msa1123990:five_prime_UTR
TGGGGAAATGTTTAGAAAGC+TGG 0.417081 7_3:-75021301 Msa1123990:intron
GTCTCTGCACCTGGAGAGTA+GGG 0.431630 7_3:-75021106 Msa1123990:exon
TACTTTAGCAATATATTTCG+TGG 0.434438 7_3:-75020952 Msa1123990:three_prime_UTR
GTCCATTGCCCCTACTCTCC+AGG 0.446840 7_3:+75021097 None:intergenic
ATGGCCGATGACTTTGAATT+CGG 0.448197 7_3:-75021654 Msa1123990:CDS
ACCAGGAGAACTATTAAGCC+TGG 0.450176 7_3:+75021262 None:intergenic
TTGCTGTTGACATTCCTCAT+AGG 0.463310 7_3:-75021229 Msa1123990:CDS
CCCAGGCTTAATAGTTCTCC+TGG 0.470539 7_3:-75021263 Msa1123990:CDS
ATAGTTCTCCTGGTTATTGG+TGG 0.478741 7_3:-75021253 Msa1123990:CDS
GTTTAGAAAGCTGGATCTCA+AGG 0.480415 7_3:-75021292 Msa1123990:intron
TCCTCCTTCCTTTGATCGCA+TGG 0.481901 7_3:-75021622 Msa1123990:intron
TAGTTCTCCTGGTTATTGGT+GGG 0.495632 7_3:-75021252 Msa1123990:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.523372 7_3:-75021115 Msa1123990:CDS
AGTCTCTGCACCTGGAGAGT+AGG 0.526480 7_3:-75021107 Msa1123990:exon
GAAGAGTACCATGCGATCAA+AGG 0.548062 7_3:+75021614 None:intergenic
GAATTCAAAGTCATCGGCCA+TGG 0.568004 7_3:+75021656 None:intergenic
CACCTGGAGAGTAGGGGCAA+TGG 0.575695 7_3:-75021099 Msa1123990:exon
ATCACTCACATCTTCAACCA+TGG 0.576797 7_3:-75021673 Msa1123990:exon
AGAGTGCATAATTTCCTATG+AGG 0.578802 7_3:+75021215 None:intergenic
ATCACCGAATTCAAAGTCAT+CGG 0.579370 7_3:+75021650 None:intergenic
CCAGGAGAACTATTAAGCCT+GGG 0.597197 7_3:+75021263 None:intergenic
CTCAAATGTTCTATGGAATG+TGG 0.598269 7_3:-75021075 Msa1123990:three_prime_UTR
ACAGCAACCCACCAATAACC+AGG 0.598951 7_3:+75021245 None:intergenic
TTTAGAAAGCTGGATCTCAA+GGG 0.612528 7_3:-75021291 Msa1123990:intron
AGTACCATGCGATCAAAGGA+AGG 0.619049 7_3:+75021618 None:intergenic
GGATCTCAAGGGTTCAACCC+AGG 0.620507 7_3:-75021280 Msa1123990:CDS
CGAATCCAAAGTTTGCACCA+CGG 0.626371 7_3:+75021719 None:intergenic
AATCTATTTAAAACAAACCG+TGG 0.654277 7_3:-75021736 Msa1123990:five_prime_UTR
ACCATGCGATCAAAGGAAGG+AGG 0.683503 7_3:+75021621 None:intergenic
TCTCTGCACCTGGAGAGTAG+GGG 0.689358 7_3:-75021105 Msa1123990:exon
ACTTTCTGTCAATAACACAC+AGG 0.703987 7_3:+75020992 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGATAAAAAACTTGATTA+AGG + chr7_3:75021288-75021307 None:intergenic 15.0%
!! TTATGTAAGTATAATCAATT+AGG + chr7_3:75021715-75021734 None:intergenic 15.0%
!! AAAGATAAAAAACTTGATTA+AGG + chr7_3:75021288-75021307 None:intergenic 15.0%
!! TTATGTAAGTATAATCAATT+AGG + chr7_3:75021715-75021734 None:intergenic 15.0%
!! TTAAGTTTAACTATATGTGT+TGG + chr7_3:75021152-75021171 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG + chr7_3:75021576-75021595 None:intergenic 20.0%
!! TTAAGTTTAACTATATGTGT+TGG + chr7_3:75021152-75021171 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG + chr7_3:75021576-75021595 None:intergenic 20.0%
!! AATCTATTTAAAACAAACCG+TGG - chr7_3:75020885-75020904 Msa1123990:three_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG + chr7_3:75021032-75021051 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG - chr7_3:75021184-75021203 Msa1123990:CDS 25.0%
! ATAACACAGAGCAATTAAAT+CGG + chr7_3:75021256-75021275 None:intergenic 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG - chr7_3:75021475-75021494 Msa1123990:intron 25.0%
! TACTTTAGCAATATATTTCG+TGG - chr7_3:75021669-75021688 Msa1123990:exon 25.0%
!! AATCTATTTAAAACAAACCG+TGG - chr7_3:75020885-75020904 Msa1123990:three_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG + chr7_3:75021032-75021051 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG - chr7_3:75021184-75021203 Msa1123990:CDS 25.0%
! ATAACACAGAGCAATTAAAT+CGG + chr7_3:75021256-75021275 None:intergenic 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG - chr7_3:75021475-75021494 Msa1123990:intron 25.0%
! TACTTTAGCAATATATTTCG+TGG - chr7_3:75021669-75021688 Msa1123990:exon 25.0%
TCTTTAGATTAGACATGTCT+TGG - chr7_3:75021100-75021119 Msa1123990:exon 30.0%
! TTAACTATATGTGTTGGTGT+TGG + chr7_3:75021146-75021165 None:intergenic 30.0%
!!! TTATCTTTTGTTGTTGCTCT+TGG - chr7_3:75021300-75021319 Msa1123990:intron 30.0%
!!! TATCTTTTGTTGTTGCTCTT+GGG - chr7_3:75021301-75021320 Msa1123990:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG - chr7_3:75021365-75021384 Msa1123990:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG + chr7_3:75021473-75021492 None:intergenic 30.0%
TCTTTAGATTAGACATGTCT+TGG - chr7_3:75021100-75021119 Msa1123990:exon 30.0%
! TTAACTATATGTGTTGGTGT+TGG + chr7_3:75021146-75021165 None:intergenic 30.0%
!!! TTATCTTTTGTTGTTGCTCT+TGG - chr7_3:75021300-75021319 Msa1123990:intron 30.0%
!!! TATCTTTTGTTGTTGCTCTT+GGG - chr7_3:75021301-75021320 Msa1123990:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG - chr7_3:75021365-75021384 Msa1123990:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG + chr7_3:75021473-75021492 None:intergenic 30.0%
ATCACCGAATTCAAAGTCAT+CGG + chr7_3:75020974-75020993 None:intergenic 35.0%
!!! ATCTTTTGTTGTTGCTCTTG+GGG - chr7_3:75021302-75021321 Msa1123990:intron 35.0%
TTTAGAAAGCTGGATCTCAA+GGG - chr7_3:75021330-75021349 Msa1123990:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG + chr7_3:75021409-75021428 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG - chr7_3:75021539-75021558 Msa1123990:intron 35.0%
CTCAAATGTTCTATGGAATG+TGG - chr7_3:75021546-75021565 Msa1123990:intron 35.0%
ACTTTCTGTCAATAACACAC+AGG + chr7_3:75021632-75021651 None:intergenic 35.0%
ATCACCGAATTCAAAGTCAT+CGG + chr7_3:75020974-75020993 None:intergenic 35.0%
!!! ATCTTTTGTTGTTGCTCTTG+GGG - chr7_3:75021302-75021321 Msa1123990:intron 35.0%
TTTAGAAAGCTGGATCTCAA+GGG - chr7_3:75021330-75021349 Msa1123990:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG + chr7_3:75021409-75021428 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG - chr7_3:75021539-75021558 Msa1123990:intron 35.0%
CTCAAATGTTCTATGGAATG+TGG - chr7_3:75021546-75021565 Msa1123990:intron 35.0%
ACTTTCTGTCAATAACACAC+AGG + chr7_3:75021632-75021651 None:intergenic 35.0%
ATCACTCACATCTTCAACCA+TGG - chr7_3:75020948-75020967 Msa1123990:three_prime_UTR 40.0%
ATGGCCGATGACTTTGAATT+CGG - chr7_3:75020967-75020986 Msa1123990:three_prime_UTR 40.0%
! GATTAGACATGTCTTGGTGT+AGG - chr7_3:75021106-75021125 Msa1123990:exon 40.0%
!! CTATATGTGTTGGTGTTGGA+CGG + chr7_3:75021142-75021161 None:intergenic 40.0%
! ATTATTATGCTAGCTCGGTG+TGG - chr7_3:75021189-75021208 Msa1123990:CDS 40.0%
TGGGGAAATGTTTAGAAAGC+TGG - chr7_3:75021320-75021339 Msa1123990:intron 40.0%
GTTTAGAAAGCTGGATCTCA+AGG - chr7_3:75021329-75021348 Msa1123990:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG - chr7_3:75021368-75021387 Msa1123990:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG - chr7_3:75021369-75021388 Msa1123990:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG - chr7_3:75021392-75021411 Msa1123990:intron 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG + chr7_3:75021450-75021469 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG + chr7_3:75021454-75021473 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG + chr7_3:75021455-75021474 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG + chr7_3:75021458-75021477 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG - chr7_3:75021491-75021510 Msa1123990:intron 40.0%
ATCACTCACATCTTCAACCA+TGG - chr7_3:75020948-75020967 Msa1123990:three_prime_UTR 40.0%
ATGGCCGATGACTTTGAATT+CGG - chr7_3:75020967-75020986 Msa1123990:three_prime_UTR 40.0%
! GATTAGACATGTCTTGGTGT+AGG - chr7_3:75021106-75021125 Msa1123990:exon 40.0%
!! CTATATGTGTTGGTGTTGGA+CGG + chr7_3:75021142-75021161 None:intergenic 40.0%
! ATTATTATGCTAGCTCGGTG+TGG - chr7_3:75021189-75021208 Msa1123990:CDS 40.0%
TGGGGAAATGTTTAGAAAGC+TGG - chr7_3:75021320-75021339 Msa1123990:intron 40.0%
GTTTAGAAAGCTGGATCTCA+AGG - chr7_3:75021329-75021348 Msa1123990:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG - chr7_3:75021368-75021387 Msa1123990:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG - chr7_3:75021369-75021388 Msa1123990:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG - chr7_3:75021392-75021411 Msa1123990:intron 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG + chr7_3:75021450-75021469 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG + chr7_3:75021454-75021473 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG + chr7_3:75021455-75021474 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG + chr7_3:75021458-75021477 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG - chr7_3:75021491-75021510 Msa1123990:intron 40.0%
ACAAACCGTGGTGCAAACTT+TGG - chr7_3:75020897-75020916 Msa1123990:three_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG + chr7_3:75020905-75020924 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG + chr7_3:75020968-75020987 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG + chr7_3:75021006-75021025 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG + chr7_3:75021010-75021029 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG + chr7_3:75021361-75021380 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG + chr7_3:75021362-75021381 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG + chr7_3:75021451-75021470 None:intergenic 45.0%
ACAAACCGTGGTGCAAACTT+TGG - chr7_3:75020897-75020916 Msa1123990:three_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG + chr7_3:75020905-75020924 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG + chr7_3:75020968-75020987 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG + chr7_3:75021006-75021025 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG + chr7_3:75021010-75021029 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG + chr7_3:75021361-75021380 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG + chr7_3:75021362-75021381 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG + chr7_3:75021451-75021470 None:intergenic 45.0%
TCCTCCTTCCTTTGATCGCA+TGG - chr7_3:75020999-75021018 Msa1123990:three_prime_UTR 50.0%
ACCATGCGATCAAAGGAAGG+AGG + chr7_3:75021003-75021022 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG + chr7_3:75021084-75021103 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG - chr7_3:75021358-75021377 Msa1123990:intron 50.0%
ACAGCAACCCACCAATAACC+AGG + chr7_3:75021379-75021398 None:intergenic 50.0%
TCCTCCTTCCTTTGATCGCA+TGG - chr7_3:75020999-75021018 Msa1123990:three_prime_UTR 50.0%
ACCATGCGATCAAAGGAAGG+AGG + chr7_3:75021003-75021022 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG + chr7_3:75021084-75021103 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG - chr7_3:75021358-75021377 Msa1123990:intron 50.0%
ACAGCAACCCACCAATAACC+AGG + chr7_3:75021379-75021398 None:intergenic 50.0%
GGATCTCAAGGGTTCAACCC+AGG - chr7_3:75021341-75021360 Msa1123990:intron 55.0%
AAGCAAGGAGTCTCTGCACC+TGG - chr7_3:75021506-75021525 Msa1123990:intron 55.0%
AGTCTCTGCACCTGGAGAGT+AGG - chr7_3:75021514-75021533 Msa1123990:intron 55.0%
GTCTCTGCACCTGGAGAGTA+GGG - chr7_3:75021515-75021534 Msa1123990:intron 55.0%
TCTCTGCACCTGGAGAGTAG+GGG - chr7_3:75021516-75021535 Msa1123990:intron 55.0%
GGATCTCAAGGGTTCAACCC+AGG - chr7_3:75021341-75021360 Msa1123990:intron 55.0%
AAGCAAGGAGTCTCTGCACC+TGG - chr7_3:75021506-75021525 Msa1123990:intron 55.0%
AGTCTCTGCACCTGGAGAGT+AGG - chr7_3:75021514-75021533 Msa1123990:intron 55.0%
GTCTCTGCACCTGGAGAGTA+GGG - chr7_3:75021515-75021534 Msa1123990:intron 55.0%
TCTCTGCACCTGGAGAGTAG+GGG - chr7_3:75021516-75021535 Msa1123990:intron 55.0%
CACCTGGAGAGTAGGGGCAA+TGG - chr7_3:75021522-75021541 Msa1123990:intron 60.0%
GTCCATTGCCCCTACTCTCC+AGG + chr7_3:75021527-75021546 None:intergenic 60.0%
CACCTGGAGAGTAGGGGCAA+TGG - chr7_3:75021522-75021541 Msa1123990:intron 60.0%
GTCCATTGCCCCTACTCTCC+AGG + chr7_3:75021527-75021546 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 75020876 75021767 75020876 ID=Msa1123990;Name=Msa1123990
chr7_3 mRNA 75020876 75021767 75020876 ID=Msa1123990-mRNA-1;Parent=Msa1123990;Name=Msa1123990-mRNA-1;_AED=0.00;_eAED=0.00;_QI=91|1|1|1|1|1|2|232|84
chr7_3 exon 75020876 75021308 75020876 ID=Msa1123990-mRNA-1:exon:20139;Parent=Msa1123990-mRNA-1
chr7_3 exon 75021623 75021767 75021623 ID=Msa1123990-mRNA-1:exon:20138;Parent=Msa1123990-mRNA-1
chr7_3 five_prime_UTR 75021677 75021767 75021677 ID=Msa1123990-mRNA-1:five_prime_utr;Parent=Msa1123990-mRNA-1
chr7_3 CDS 75021623 75021676 75021623 ID=Msa1123990-mRNA-1:cds;Parent=Msa1123990-mRNA-1
chr7_3 CDS 75021108 75021308 75021108 ID=Msa1123990-mRNA-1:cds;Parent=Msa1123990-mRNA-1
chr7_3 three_prime_UTR 75020876 75021107 75020876 ID=Msa1123990-mRNA-1:three_prime_utr;Parent=Msa1123990-mRNA-1
Gene Sequence

>Msa1123990

ATGGCCGATGACTTTGAATTCGGTGATAAAGTTCCTCCTTCCTTTGATCGCATGAAAGCTGGATCTCAAGGGTTCAACCCAGGCTTAATAGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTCCTCATAGGAAATTATGCACTCTACGTTTATGCACAGAAGACCCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGACTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>Msa1123990

MADDFEFGDKVPPSFDRMKAGSQGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKTLPPRKKKPVSKKKMKKERLKQGVSAPGE*