AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0266350


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0266350 MtrunA17_Chr2g0326131 88.073 109 10 1 23 128 126 234 5.73e-63 192
Msa0266350 MtrunA17_Chr2g0331681 88.073 109 10 1 23 128 412 520 5.05e-61 195
Msa0266350 MtrunA17_Chr4g0029181 34.409 93 60 1 34 125 462 554 5.88e-15 70.1
Msa0266350 MtrunA17_Chr2g0326581 33.333 87 57 1 34 119 440 526 1.12e-14 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0266350 AT3G16110.1 66.316 95 32 0 34 128 440 534 1.52e-39 139
Msa0266350 AT1G52260.1 57.407 108 42 3 23 128 432 537 3.70e-32 119
Msa0266350 AT5G60640.1 35.632 87 55 1 34 119 465 551 2.29e-15 71.6
Msa0266350 AT5G60640.3 35.632 87 55 1 34 119 401 487 2.57e-15 71.2
Msa0266350 AT3G54960.1 31.034 87 59 1 34 119 461 547 2.57e-14 68.6
Msa0266350 AT5G60640.2 41.270 63 37 0 34 96 465 527 6.95e-14 67.4

Find 33 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATAATGCTTGTATCTTATA+GGG 0.209909 2_2:-66846493 None:intergenic
ATAACACTTACTTGCAGTTT+TGG 0.236921 2_2:-66845860 None:intergenic
TCATAATGCTTGTATCTTAT+AGG 0.240632 2_2:-66846494 None:intergenic
TATAGAACAAATCAATGTTT+TGG 0.253555 2_2:+66846241 Msa0266350:exon
CCTTTAGAAAGGAAACATTA+TGG 0.306129 2_2:+66846279 Msa0266350:three_prime_UTR
GAAATCTAGTTTGAAAGAAT+TGG 0.324131 2_2:+66846164 Msa0266350:CDS
TTTGTTCTATAGCTCATCTT+TGG 0.362837 2_2:-66846229 None:intergenic
GACTTTAACGTGTTTGTTGA+TGG 0.366916 2_2:-66846193 None:intergenic
CCATAATGTTTCCTTTCTAA+AGG 0.403180 2_2:-66846279 None:intergenic
CGTGAATCATTACGTAAAAC+AGG 0.406684 2_2:+66845715 Msa0266350:CDS
ATAACAATCTAAATTACATC+TGG 0.414686 2_2:-66846375 None:intergenic
AGAGTTAGCTCACTGCAAAA+TGG 0.434735 2_2:+66846399 Msa0266350:three_prime_UTR
TTGCTTATCTGCTTATGCCT+TGG 0.443431 2_2:+66845673 Msa0266350:CDS
AAGCTTGAGCAGTGATGAAC+CGG 0.450565 2_2:+66846426 Msa0266350:three_prime_UTR
AAAGTAGTTAACCTTTAGAA+AGG 0.452039 2_2:+66846268 Msa0266350:three_prime_UTR
AAGCAAGCAAGTAGAGAAGT+TGG 0.475868 2_2:+66845772 Msa0266350:CDS
AAGCAGATAAGCAATATGAC+AGG 0.521829 2_2:-66845664 None:intergenic
TGCTTTGTAAAGTAAAAGTG+TGG 0.524790 2_2:-66846019 None:intergenic
AGCAAATGATAAGACAAATC+CGG 0.525248 2_2:+66846038 Msa0266350:CDS
ATAAGATACAAGCATTATGA+TGG 0.540559 2_2:+66846497 Msa0266350:three_prime_UTR
TCATTTAGTTGTTGAGACAA+GGG 0.543971 2_2:-66846556 None:intergenic
TTCATTTAGTTGTTGAGACA+AGG 0.546096 2_2:-66846557 None:intergenic
ATGCTTGTATCTTATAGGGG+TGG 0.575992 2_2:-66846489 None:intergenic
CAACAAACACGTTAAAGTCA+AGG 0.593096 2_2:+66846197 Msa0266350:CDS
GCTTTGTAAAGTAAAAGTGT+GGG 0.593935 2_2:-66846018 None:intergenic
ATAATGCTTGTATCTTATAG+GGG 0.612816 2_2:-66846492 None:intergenic
TAAAACAGGTATTCACACCT+TGG 0.615751 2_2:+66845729 Msa0266350:CDS
GCAGTGATGAACCGGTGCAC+TGG 0.621327 2_2:+66846434 Msa0266350:three_prime_UTR
ACCTTGGTGTTTCAACTGTG+AGG 0.643924 2_2:+66845745 Msa0266350:CDS
AGTTTGAAAATGCTCAAGCA+AGG 0.644474 2_2:-66846321 None:intergenic
AGCAGATAAGCAATATGACA+GGG 0.675041 2_2:-66845663 None:intergenic
TCCTCACAGTTGAAACACCA+AGG 0.681229 2_2:-66845746 None:intergenic
CCGCGAGTTAAAATCAACCA+AGG 0.684503 2_2:-66845690 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATGGAAAAATATATATT+AGG + chr2_2:66846295-66846314 Msa0266350:three_prime_UTR 10.0%
!! ATTATGGAAAAATATATATT+AGG + chr2_2:66846295-66846314 Msa0266350:three_prime_UTR 10.0%
!!! TCTCGTCTTTTTTTATTTAA+TGG + chr2_2:66845896-66845915 Msa0266350:intron 20.0%
!! AAATTATATCACCAAAATCA+GGG - chr2_2:66846080-66846099 None:intergenic 20.0%
!! AAAATTATATCACCAAAATC+AGG - chr2_2:66846081-66846100 None:intergenic 20.0%
!!! TATAGAACAAATCAATGTTT+TGG + chr2_2:66846241-66846260 Msa0266350:exon 20.0%
!!! ATAGAACAAATCAATGTTTT+GGG + chr2_2:66846242-66846261 Msa0266350:exon 20.0%
!! ATAACAATCTAAATTACATC+TGG - chr2_2:66846378-66846397 None:intergenic 20.0%
!!! TCTCGTCTTTTTTTATTTAA+TGG + chr2_2:66845896-66845915 Msa0266350:intron 20.0%
!! AAATTATATCACCAAAATCA+GGG - chr2_2:66846080-66846099 None:intergenic 20.0%
!! AAAATTATATCACCAAAATC+AGG - chr2_2:66846081-66846100 None:intergenic 20.0%
!!! TATAGAACAAATCAATGTTT+TGG + chr2_2:66846241-66846260 Msa0266350:exon 20.0%
!!! ATAGAACAAATCAATGTTTT+GGG + chr2_2:66846242-66846261 Msa0266350:exon 20.0%
!! ATAACAATCTAAATTACATC+TGG - chr2_2:66846378-66846397 None:intergenic 20.0%
! TCAAAATTTATGTCTACTGA+AGG + chr2_2:66845956-66845975 Msa0266350:intron 25.0%
!! TTTACCTTTCCTAATTTTTC+AGG + chr2_2:66845984-66846003 Msa0266350:intron 25.0%
!! GAAATCTAGTTTGAAAGAAT+TGG + chr2_2:66846164-66846183 Msa0266350:CDS 25.0%
!! AAAGTAGTTAACCTTTAGAA+AGG + chr2_2:66846268-66846287 Msa0266350:three_prime_UTR 25.0%
! ATAATGCTTGTATCTTATAG+GGG - chr2_2:66846495-66846514 None:intergenic 25.0%
! CATAATGCTTGTATCTTATA+GGG - chr2_2:66846496-66846515 None:intergenic 25.0%
! TCATAATGCTTGTATCTTAT+AGG - chr2_2:66846497-66846516 None:intergenic 25.0%
! ATAAGATACAAGCATTATGA+TGG + chr2_2:66846497-66846516 Msa0266350:three_prime_UTR 25.0%
! TCAAAATTTATGTCTACTGA+AGG + chr2_2:66845956-66845975 Msa0266350:intron 25.0%
!! TTTACCTTTCCTAATTTTTC+AGG + chr2_2:66845984-66846003 Msa0266350:intron 25.0%
!! GAAATCTAGTTTGAAAGAAT+TGG + chr2_2:66846164-66846183 Msa0266350:CDS 25.0%
!! AAAGTAGTTAACCTTTAGAA+AGG + chr2_2:66846268-66846287 Msa0266350:three_prime_UTR 25.0%
! ATAATGCTTGTATCTTATAG+GGG - chr2_2:66846495-66846514 None:intergenic 25.0%
! CATAATGCTTGTATCTTATA+GGG - chr2_2:66846496-66846515 None:intergenic 25.0%
! TCATAATGCTTGTATCTTAT+AGG - chr2_2:66846497-66846516 None:intergenic 25.0%
! ATAAGATACAAGCATTATGA+TGG + chr2_2:66846497-66846516 Msa0266350:three_prime_UTR 25.0%
! ATAACACTTACTTGCAGTTT+TGG - chr2_2:66845863-66845882 None:intergenic 30.0%
TTCACCTGAAAAATTAGGAA+AGG - chr2_2:66845991-66846010 None:intergenic 30.0%
AGTCATTCACCTGAAAAATT+AGG - chr2_2:66845996-66846015 None:intergenic 30.0%
! GCTTTGTAAAGTAAAAGTGT+GGG - chr2_2:66846021-66846040 None:intergenic 30.0%
TGCTTTGTAAAGTAAAAGTG+TGG - chr2_2:66846022-66846041 None:intergenic 30.0%
AGCAAATGATAAGACAAATC+CGG + chr2_2:66846038-66846057 Msa0266350:CDS 30.0%
TTTGTTCTATAGCTCATCTT+TGG - chr2_2:66846232-66846251 None:intergenic 30.0%
CCATAATGTTTCCTTTCTAA+AGG - chr2_2:66846282-66846301 None:intergenic 30.0%
! CCTTTAGAAAGGAAACATTA+TGG + chr2_2:66846279-66846298 Msa0266350:three_prime_UTR 30.0%
TCATTTAGTTGTTGAGACAA+GGG - chr2_2:66846559-66846578 None:intergenic 30.0%
TTCATTTAGTTGTTGAGACA+AGG - chr2_2:66846560-66846579 None:intergenic 30.0%
! ATAACACTTACTTGCAGTTT+TGG - chr2_2:66845863-66845882 None:intergenic 30.0%
TTCACCTGAAAAATTAGGAA+AGG - chr2_2:66845991-66846010 None:intergenic 30.0%
AGTCATTCACCTGAAAAATT+AGG - chr2_2:66845996-66846015 None:intergenic 30.0%
! GCTTTGTAAAGTAAAAGTGT+GGG - chr2_2:66846021-66846040 None:intergenic 30.0%
TGCTTTGTAAAGTAAAAGTG+TGG - chr2_2:66846022-66846041 None:intergenic 30.0%
AGCAAATGATAAGACAAATC+CGG + chr2_2:66846038-66846057 Msa0266350:CDS 30.0%
TTTGTTCTATAGCTCATCTT+TGG - chr2_2:66846232-66846251 None:intergenic 30.0%
CCATAATGTTTCCTTTCTAA+AGG - chr2_2:66846282-66846301 None:intergenic 30.0%
! CCTTTAGAAAGGAAACATTA+TGG + chr2_2:66846279-66846298 Msa0266350:three_prime_UTR 30.0%
TCATTTAGTTGTTGAGACAA+GGG - chr2_2:66846559-66846578 None:intergenic 30.0%
TTCATTTAGTTGTTGAGACA+AGG - chr2_2:66846560-66846579 None:intergenic 30.0%
AGCAGATAAGCAATATGACA+GGG - chr2_2:66845666-66845685 None:intergenic 35.0%
AAGCAGATAAGCAATATGAC+AGG - chr2_2:66845667-66845686 None:intergenic 35.0%
CGTGAATCATTACGTAAAAC+AGG + chr2_2:66845715-66845734 Msa0266350:CDS 35.0%
TAAAACAGGTATTCACACCT+TGG + chr2_2:66845729-66845748 Msa0266350:CDS 35.0%
CAAATCCGGTAATTACTCAA+TGG + chr2_2:66846052-66846071 Msa0266350:intron 35.0%
! GACTTTAACGTGTTTGTTGA+TGG - chr2_2:66846196-66846215 None:intergenic 35.0%
CAACAAACACGTTAAAGTCA+AGG + chr2_2:66846197-66846216 Msa0266350:CDS 35.0%
AGTTTGAAAATGCTCAAGCA+AGG - chr2_2:66846324-66846343 None:intergenic 35.0%
AAAAATGTTAACCAGTGCAC+CGG - chr2_2:66846448-66846467 None:intergenic 35.0%
AGCAGATAAGCAATATGACA+GGG - chr2_2:66845666-66845685 None:intergenic 35.0%
AAGCAGATAAGCAATATGAC+AGG - chr2_2:66845667-66845686 None:intergenic 35.0%
CGTGAATCATTACGTAAAAC+AGG + chr2_2:66845715-66845734 Msa0266350:CDS 35.0%
TAAAACAGGTATTCACACCT+TGG + chr2_2:66845729-66845748 Msa0266350:CDS 35.0%
CAAATCCGGTAATTACTCAA+TGG + chr2_2:66846052-66846071 Msa0266350:intron 35.0%
! GACTTTAACGTGTTTGTTGA+TGG - chr2_2:66846196-66846215 None:intergenic 35.0%
CAACAAACACGTTAAAGTCA+AGG + chr2_2:66846197-66846216 Msa0266350:CDS 35.0%
AGTTTGAAAATGCTCAAGCA+AGG - chr2_2:66846324-66846343 None:intergenic 35.0%
AAAAATGTTAACCAGTGCAC+CGG - chr2_2:66846448-66846467 None:intergenic 35.0%
TTGCTTATCTGCTTATGCCT+TGG + chr2_2:66845673-66845692 Msa0266350:CDS 40.0%
!!! CCTTGGTTGATTTTAACTCG+CGG + chr2_2:66845690-66845709 Msa0266350:CDS 40.0%
AAGCAAGCAAGTAGAGAAGT+TGG + chr2_2:66845772-66845791 Msa0266350:CDS 40.0%
!!! TTCAGTTTCCCCCTCTTTTT+TGG + chr2_2:66846347-66846366 Msa0266350:three_prime_UTR 40.0%
!!! TCAGTTTCCCCCTCTTTTTT+GGG + chr2_2:66846348-66846367 Msa0266350:three_prime_UTR 40.0%
TCTGGATCACCCAAAAAAGA+GGG - chr2_2:66846360-66846379 None:intergenic 40.0%
ATCTGGATCACCCAAAAAAG+AGG - chr2_2:66846361-66846380 None:intergenic 40.0%
AGAGTTAGCTCACTGCAAAA+TGG + chr2_2:66846399-66846418 Msa0266350:three_prime_UTR 40.0%
ATGCTTGTATCTTATAGGGG+TGG - chr2_2:66846492-66846511 None:intergenic 40.0%
TTGCTTATCTGCTTATGCCT+TGG + chr2_2:66845673-66845692 Msa0266350:CDS 40.0%
!!! CCTTGGTTGATTTTAACTCG+CGG + chr2_2:66845690-66845709 Msa0266350:CDS 40.0%
AAGCAAGCAAGTAGAGAAGT+TGG + chr2_2:66845772-66845791 Msa0266350:CDS 40.0%
!!! TTCAGTTTCCCCCTCTTTTT+TGG + chr2_2:66846347-66846366 Msa0266350:three_prime_UTR 40.0%
!!! TCAGTTTCCCCCTCTTTTTT+GGG + chr2_2:66846348-66846367 Msa0266350:three_prime_UTR 40.0%
TCTGGATCACCCAAAAAAGA+GGG - chr2_2:66846360-66846379 None:intergenic 40.0%
ATCTGGATCACCCAAAAAAG+AGG - chr2_2:66846361-66846380 None:intergenic 40.0%
AGAGTTAGCTCACTGCAAAA+TGG + chr2_2:66846399-66846418 Msa0266350:three_prime_UTR 40.0%
ATGCTTGTATCTTATAGGGG+TGG - chr2_2:66846492-66846511 None:intergenic 40.0%
CCGCGAGTTAAAATCAACCA+AGG - chr2_2:66845693-66845712 None:intergenic 45.0%
!! ACCTTGGTGTTTCAACTGTG+AGG + chr2_2:66845745-66845764 Msa0266350:CDS 45.0%
TCCTCACAGTTGAAACACCA+AGG - chr2_2:66845749-66845768 None:intergenic 45.0%
!! GGGTGCCATTGAGTAATTAC+CGG - chr2_2:66846060-66846079 None:intergenic 45.0%
! ACTCAATGGCACCCTGATTT+TGG + chr2_2:66846066-66846085 Msa0266350:intron 45.0%
AGCGTTTCGTTATAGAAGCG+AGG - chr2_2:66846118-66846137 None:intergenic 45.0%
TGGATCACCCAAAAAAGAGG+GGG - chr2_2:66846358-66846377 None:intergenic 45.0%
CTGGATCACCCAAAAAAGAG+GGG - chr2_2:66846359-66846378 None:intergenic 45.0%
AAGCTTGAGCAGTGATGAAC+CGG + chr2_2:66846426-66846445 Msa0266350:three_prime_UTR 45.0%
CCGCGAGTTAAAATCAACCA+AGG - chr2_2:66845693-66845712 None:intergenic 45.0%
!! ACCTTGGTGTTTCAACTGTG+AGG + chr2_2:66845745-66845764 Msa0266350:CDS 45.0%
TCCTCACAGTTGAAACACCA+AGG - chr2_2:66845749-66845768 None:intergenic 45.0%
!! GGGTGCCATTGAGTAATTAC+CGG - chr2_2:66846060-66846079 None:intergenic 45.0%
! ACTCAATGGCACCCTGATTT+TGG + chr2_2:66846066-66846085 Msa0266350:intron 45.0%
AGCGTTTCGTTATAGAAGCG+AGG - chr2_2:66846118-66846137 None:intergenic 45.0%
TGGATCACCCAAAAAAGAGG+GGG - chr2_2:66846358-66846377 None:intergenic 45.0%
CTGGATCACCCAAAAAAGAG+GGG - chr2_2:66846359-66846378 None:intergenic 45.0%
AAGCTTGAGCAGTGATGAAC+CGG + chr2_2:66846426-66846445 Msa0266350:three_prime_UTR 45.0%
GCAGTGATGAACCGGTGCAC+TGG + chr2_2:66846434-66846453 Msa0266350:three_prime_UTR 60.0%
GCAGTGATGAACCGGTGCAC+TGG + chr2_2:66846434-66846453 Msa0266350:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 66845635 66846601 66845635 ID=Msa0266350;Name=Msa0266350
chr2_2 mRNA 66845635 66846601 66845635 ID=Msa0266350-mRNA-1;Parent=Msa0266350;Name=Msa0266350-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|1|0.66|1|0.5|0.66|3|356|128
chr2_2 exon 66845635 66845871 66845635 ID=Msa0266350-mRNA-1:exon:21249;Parent=Msa0266350-mRNA-1
chr2_2 exon 66846006 66846059 66846006 ID=Msa0266350-mRNA-1:exon:21250;Parent=Msa0266350-mRNA-1
chr2_2 exon 66846150 66846601 66846150 ID=Msa0266350-mRNA-1:exon:21251;Parent=Msa0266350-mRNA-1
chr2_2 CDS 66845635 66845871 66845635 ID=Msa0266350-mRNA-1:cds;Parent=Msa0266350-mRNA-1
chr2_2 CDS 66846006 66846059 66846006 ID=Msa0266350-mRNA-1:cds;Parent=Msa0266350-mRNA-1
chr2_2 CDS 66846150 66846245 66846150 ID=Msa0266350-mRNA-1:cds;Parent=Msa0266350-mRNA-1
chr2_2 three_prime_UTR 66846246 66846601 66846246 ID=Msa0266350-mRNA-1:three_prime_utr;Parent=Msa0266350-mRNA-1
Gene Sequence

>Msa0266350

TTCAATAAGAGCTACTACGCGATAGAGACCCTGTCATATTGCTTATCTGCTTATGCCTTGGTTGATTTTAACTCGCGGCTCGTGAATCATTACGTAAAACAGGTATTCACACCTTGGTGTTTCAACTGTGAGGACACAAGCAAGCAAGTAGAGAAGTTGGCAAAACACTACAAAAGTTCGAGTAATTTAATATTTGCAAAGATAGATGCTTCAGCAAATGAACATCCAAAACTGCAAGTGAATGACTTTCCCACACTTTTACTTTACAAAGCAAATGATAAGACAAATCCGATCAAGCTTTCTACGAAATCTAGTTTGAAAGAATTGGCTGCATCCATCAACAAACACGTTAAAGTCAAGGATCAAGTCGCCAAAGATGAGCTATAG

Protein sequence

>Msa0266350

FNKSYYAIETLSYCLSAYALVDFNSRLVNHYVKQVFTPWCFNCEDTSKQVEKLAKHYKSSSNLIFAKIDASANEHPKLQVNDFPTLLLYKANDKTNPIKLSTKSSLKELAASINKHVKVKDQVAKDEL*