AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1377710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377710 MtrunA17_Chr5g0400761 93.893 131 7 1 1 130 1 131 7.04e-90 256
Msa1377710 MtrunA17_Chr4g0054461 65.625 96 33 0 35 130 7 102 2.13e-44 140
Msa1377710 MtrunA17_Chr3g0140691 59.155 71 26 2 61 130 30 98 3.09e-23 86.7
Msa1377710 MtrunA17_Chr3g0123851 39.474 76 42 2 59 130 46 121 3.74e-13 61.6
Msa1377710 MtrunA17_Chr8g0381891 39.474 76 42 2 59 130 48 123 1.03e-11 57.8
Msa1377710 MtrunA17_Chr4g0063871 32.000 125 68 4 6 130 7 114 1.89e-11 57.0
Msa1377710 MtrunA17_Chr2g0330071 30.216 139 65 5 11 130 3 128 3.98e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377710 AT4G37810.1 47.706 109 49 3 30 130 20 128 9.72e-26 94.4
Msa1377710 AT5G10310.2 40.244 82 35 3 59 130 51 128 2.97e-11 57.0
Msa1377710 AT5G10310.1 40.244 82 35 3 59 130 45 122 3.80e-11 56.6

Find 39 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCACCTTGTATCACATTT+TGG 0.211299 tig0019970:-69860 None:intergenic
GAATATCATCATGTCATTTA+TGG 0.231378 tig0019970:+69354 Msa1377710:CDS
CATCTAAATGAGCTACATTA+TGG 0.294334 tig0019970:-70066 None:intergenic
GTCATTGCTCGAGGATTTGC+TGG 0.332737 tig0019970:-69914 None:intergenic
CATTTGCATTTCCAACTCAT+AGG 0.395492 tig0019970:-70007 None:intergenic
TAGAGAAAGGTGTTCAAGAA+AGG 0.412468 tig0019970:-69306 None:intergenic
CCAACTCATAGGTTTATAGT+TGG 0.415908 tig0019970:-69996 None:intergenic
AGGGAGAATTCTTTAGAGAA+AGG 0.416869 tig0019970:-69319 None:intergenic
TATGAGAAAGAGAAGAGAAA+TGG 0.420044 tig0019970:-69397 None:intergenic
TGTTGATTTGTGCAGACAAT+AGG 0.427844 tig0019970:+69794 Msa1377710:intron
AGTTTCAAGCTTGACACAAA+AGG 0.454396 tig0019970:+69419 Msa1377710:CDS
AGAGAAAGGTGTTCAAGAAA+GGG 0.460515 tig0019970:-69305 None:intergenic
TGATATTCATTCCTCATTTG+AGG 0.464024 tig0019970:-69339 None:intergenic
TTATGGAACAAATCAAATCA+AGG 0.478334 tig0019970:-70049 None:intergenic
GATATTCATTCCTCATTTGA+GGG 0.488619 tig0019970:-69338 None:intergenic
GTTTCAAGCTTGACACAAAA+GGG 0.500719 tig0019970:+69420 Msa1377710:CDS
ATCTTTCCTGTCATTGCTCG+AGG 0.500929 tig0019970:-69923 None:intergenic
GCAACTGCAGACAGAGTTGA+AGG 0.512648 tig0019970:-69950 None:intergenic
GTAGCTCATTTAGATGATCA+AGG 0.537745 tig0019970:+70073 Msa1377710:three_prime_UTR
GCAAATCCTCGAGCAATGAC+AGG 0.547611 tig0019970:+69917 Msa1377710:CDS
GTGATGGTGAGGAAGCAGAT+AGG 0.550422 tig0019970:+69827 Msa1377710:CDS
AAAGAATTCTCCCTCAAATG+AGG 0.557496 tig0019970:+69328 Msa1377710:exon
CCAACTATAAACCTATGAGT+TGG 0.573239 tig0019970:+69996 Msa1377710:CDS
GGCCACCAAAATGTGATACA+AGG 0.578748 tig0019970:+69855 Msa1377710:CDS
TGTCTGCAGTTGCTTATGCT+AGG 0.585427 tig0019970:+69960 Msa1377710:CDS
TTACCTGGTGAAAACCATGT+TGG 0.587700 tig0019970:-69565 None:intergenic
GTGATAACAAGGTGATGGTG+AGG 0.587937 tig0019970:+69816 Msa1377710:CDS
TATGGAACAAATCAAATCAA+GGG 0.596622 tig0019970:-70048 None:intergenic
CTGCAGTTGCTTATGCTAGG+AGG 0.607524 tig0019970:+69963 Msa1377710:CDS
ATGAGTTGGAAATGCAAATG+TGG 0.611058 tig0019970:+70010 Msa1377710:CDS
AGAAAGACTTTGAACCAACA+TGG 0.614586 tig0019970:+69551 Msa1377710:CDS
CAAAAGGGACTTGTAACTGA+AGG 0.617750 tig0019970:+69435 Msa1377710:CDS
AATAGGTGATAACAAGGTGA+TGG 0.620627 tig0019970:+69811 Msa1377710:CDS
TGAGGAAGCAGATAGGATCA+AGG 0.622434 tig0019970:+69834 Msa1377710:CDS
GATACAAGGTGCAGATTCTG+TGG 0.657438 tig0019970:+69869 Msa1377710:CDS
GCAGACAATAGGTGATAACA+AGG 0.666495 tig0019970:+69805 Msa1377710:intron
CAGATTCTGTGGTCACTGCG+AGG 0.669680 tig0019970:+69880 Msa1377710:CDS
TGAGTTGGAAATGCAAATGT+GGG 0.678868 tig0019970:+70011 Msa1377710:CDS
CAACTGCAGACAGAGTTGAA+GGG 0.720563 tig0019970:-69949 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATTATTTTTCTCATTTG+AGG + tig0019970:69651-69670 Msa1377710:intron 15.0%
!!! TTAATTATTTTTCTCATTTG+AGG + tig0019970:69651-69670 Msa1377710:intron 15.0%
!! AAATGTAAACAAAATTTACC+TGG - tig0019970:69583-69602 None:intergenic 20.0%
!! AAGTTATAAGAATTTAGAAG+AGG - tig0019970:69622-69641 None:intergenic 20.0%
!! AAATGTAAACAAAATTTACC+TGG - tig0019970:69583-69602 None:intergenic 20.0%
!! AAGTTATAAGAATTTAGAAG+AGG - tig0019970:69622-69641 None:intergenic 20.0%
!! GAATATCATCATGTCATTTA+TGG + tig0019970:69354-69373 Msa1377710:CDS 25.0%
! TTGAAGTAAGAGTTATAAGT+TGG - tig0019970:69485-69504 None:intergenic 25.0%
! TATGGAACAAATCAAATCAA+GGG - tig0019970:70051-70070 None:intergenic 25.0%
! TTATGGAACAAATCAAATCA+AGG - tig0019970:70052-70071 None:intergenic 25.0%
!! GAATATCATCATGTCATTTA+TGG + tig0019970:69354-69373 Msa1377710:CDS 25.0%
! TTGAAGTAAGAGTTATAAGT+TGG - tig0019970:69485-69504 None:intergenic 25.0%
! TATGGAACAAATCAAATCAA+GGG - tig0019970:70051-70070 None:intergenic 25.0%
! TTATGGAACAAATCAAATCA+AGG - tig0019970:70052-70071 None:intergenic 25.0%
GATATTCATTCCTCATTTGA+GGG - tig0019970:69341-69360 None:intergenic 30.0%
TGATATTCATTCCTCATTTG+AGG - tig0019970:69342-69361 None:intergenic 30.0%
TATGAGAAAGAGAAGAGAAA+TGG - tig0019970:69400-69419 None:intergenic 30.0%
ATAAGAATTTAGAAGAGGCA+GGG - tig0019970:69617-69636 None:intergenic 30.0%
TATAAGAATTTAGAAGAGGC+AGG - tig0019970:69618-69637 None:intergenic 30.0%
CTAATTAAGATGAGTGATGT+AGG + tig0019970:69757-69776 Msa1377710:intron 30.0%
CATCTAAATGAGCTACATTA+TGG - tig0019970:70069-70088 None:intergenic 30.0%
GATATTCATTCCTCATTTGA+GGG - tig0019970:69341-69360 None:intergenic 30.0%
TGATATTCATTCCTCATTTG+AGG - tig0019970:69342-69361 None:intergenic 30.0%
TATGAGAAAGAGAAGAGAAA+TGG - tig0019970:69400-69419 None:intergenic 30.0%
ATAAGAATTTAGAAGAGGCA+GGG - tig0019970:69617-69636 None:intergenic 30.0%
TATAAGAATTTAGAAGAGGC+AGG - tig0019970:69618-69637 None:intergenic 30.0%
CTAATTAAGATGAGTGATGT+AGG + tig0019970:69757-69776 Msa1377710:intron 30.0%
CATCTAAATGAGCTACATTA+TGG - tig0019970:70069-70088 None:intergenic 30.0%
!! AGAGAAAGGTGTTCAAGAAA+GGG - tig0019970:69308-69327 None:intergenic 35.0%
!! TAGAGAAAGGTGTTCAAGAA+AGG - tig0019970:69309-69328 None:intergenic 35.0%
! AGGGAGAATTCTTTAGAGAA+AGG - tig0019970:69322-69341 None:intergenic 35.0%
AAAGAATTCTCCCTCAAATG+AGG + tig0019970:69328-69347 Msa1377710:exon 35.0%
AGTTTCAAGCTTGACACAAA+AGG + tig0019970:69419-69438 Msa1377710:CDS 35.0%
GTTTCAAGCTTGACACAAAA+GGG + tig0019970:69420-69439 Msa1377710:CDS 35.0%
AGAAAGACTTTGAACCAACA+TGG + tig0019970:69551-69570 Msa1377710:CDS 35.0%
!! TGTTGATTTGTGCAGACAAT+AGG + tig0019970:69794-69813 Msa1377710:intron 35.0%
AATAGGTGATAACAAGGTGA+TGG + tig0019970:69811-69830 Msa1377710:CDS 35.0%
CCAACTCATAGGTTTATAGT+TGG - tig0019970:69999-70018 None:intergenic 35.0%
CCAACTATAAACCTATGAGT+TGG + tig0019970:69996-70015 Msa1377710:CDS 35.0%
CATTTGCATTTCCAACTCAT+AGG - tig0019970:70010-70029 None:intergenic 35.0%
! ATGAGTTGGAAATGCAAATG+TGG + tig0019970:70010-70029 Msa1377710:CDS 35.0%
! TGAGTTGGAAATGCAAATGT+GGG + tig0019970:70011-70030 Msa1377710:CDS 35.0%
GTAGCTCATTTAGATGATCA+AGG + tig0019970:70073-70092 Msa1377710:three_prime_UTR 35.0%
!! AGAGAAAGGTGTTCAAGAAA+GGG - tig0019970:69308-69327 None:intergenic 35.0%
!! TAGAGAAAGGTGTTCAAGAA+AGG - tig0019970:69309-69328 None:intergenic 35.0%
! AGGGAGAATTCTTTAGAGAA+AGG - tig0019970:69322-69341 None:intergenic 35.0%
AAAGAATTCTCCCTCAAATG+AGG + tig0019970:69328-69347 Msa1377710:exon 35.0%
AGTTTCAAGCTTGACACAAA+AGG + tig0019970:69419-69438 Msa1377710:CDS 35.0%
GTTTCAAGCTTGACACAAAA+GGG + tig0019970:69420-69439 Msa1377710:CDS 35.0%
AGAAAGACTTTGAACCAACA+TGG + tig0019970:69551-69570 Msa1377710:CDS 35.0%
!! TGTTGATTTGTGCAGACAAT+AGG + tig0019970:69794-69813 Msa1377710:intron 35.0%
AATAGGTGATAACAAGGTGA+TGG + tig0019970:69811-69830 Msa1377710:CDS 35.0%
CCAACTCATAGGTTTATAGT+TGG - tig0019970:69999-70018 None:intergenic 35.0%
CCAACTATAAACCTATGAGT+TGG + tig0019970:69996-70015 Msa1377710:CDS 35.0%
CATTTGCATTTCCAACTCAT+AGG - tig0019970:70010-70029 None:intergenic 35.0%
! ATGAGTTGGAAATGCAAATG+TGG + tig0019970:70010-70029 Msa1377710:CDS 35.0%
! TGAGTTGGAAATGCAAATGT+GGG + tig0019970:70011-70030 Msa1377710:CDS 35.0%
GTAGCTCATTTAGATGATCA+AGG + tig0019970:70073-70092 Msa1377710:three_prime_UTR 35.0%
CAAAAGGGACTTGTAACTGA+AGG + tig0019970:69435-69454 Msa1377710:CDS 40.0%
TCTTCTTCTTCTGCTCTTAC+AGG + tig0019970:69527-69546 Msa1377710:intron 40.0%
TTACCTGGTGAAAACCATGT+TGG - tig0019970:69568-69587 None:intergenic 40.0%
AGACTGAGTAAACGAGTTGT+CGG - tig0019970:69734-69753 None:intergenic 40.0%
GCAGACAATAGGTGATAACA+AGG + tig0019970:69805-69824 Msa1377710:intron 40.0%
! CACCTTGTATCACATTTTGG+TGG - tig0019970:69860-69879 None:intergenic 40.0%
! CTGCACCTTGTATCACATTT+TGG - tig0019970:69863-69882 None:intergenic 40.0%
CAAAAGGGACTTGTAACTGA+AGG + tig0019970:69435-69454 Msa1377710:CDS 40.0%
TCTTCTTCTTCTGCTCTTAC+AGG + tig0019970:69527-69546 Msa1377710:intron 40.0%
TTACCTGGTGAAAACCATGT+TGG - tig0019970:69568-69587 None:intergenic 40.0%
AGACTGAGTAAACGAGTTGT+CGG - tig0019970:69734-69753 None:intergenic 40.0%
GCAGACAATAGGTGATAACA+AGG + tig0019970:69805-69824 Msa1377710:intron 40.0%
! CACCTTGTATCACATTTTGG+TGG - tig0019970:69860-69879 None:intergenic 40.0%
! CTGCACCTTGTATCACATTT+TGG - tig0019970:69863-69882 None:intergenic 40.0%
! GAACCAACATGGTTTTCACC+AGG + tig0019970:69562-69581 Msa1377710:CDS 45.0%
! GTGATAACAAGGTGATGGTG+AGG + tig0019970:69816-69835 Msa1377710:CDS 45.0%
TGAGGAAGCAGATAGGATCA+AGG + tig0019970:69834-69853 Msa1377710:CDS 45.0%
GGCCACCAAAATGTGATACA+AGG + tig0019970:69855-69874 Msa1377710:CDS 45.0%
GATACAAGGTGCAGATTCTG+TGG + tig0019970:69869-69888 Msa1377710:CDS 45.0%
ATCTTTCCTGTCATTGCTCG+AGG - tig0019970:69926-69945 None:intergenic 45.0%
CAACTGCAGACAGAGTTGAA+GGG - tig0019970:69952-69971 None:intergenic 45.0%
TGTCTGCAGTTGCTTATGCT+AGG + tig0019970:69960-69979 Msa1377710:CDS 45.0%
! GAACCAACATGGTTTTCACC+AGG + tig0019970:69562-69581 Msa1377710:CDS 45.0%
! GTGATAACAAGGTGATGGTG+AGG + tig0019970:69816-69835 Msa1377710:CDS 45.0%
TGAGGAAGCAGATAGGATCA+AGG + tig0019970:69834-69853 Msa1377710:CDS 45.0%
GGCCACCAAAATGTGATACA+AGG + tig0019970:69855-69874 Msa1377710:CDS 45.0%
GATACAAGGTGCAGATTCTG+TGG + tig0019970:69869-69888 Msa1377710:CDS 45.0%
ATCTTTCCTGTCATTGCTCG+AGG - tig0019970:69926-69945 None:intergenic 45.0%
CAACTGCAGACAGAGTTGAA+GGG - tig0019970:69952-69971 None:intergenic 45.0%
TGTCTGCAGTTGCTTATGCT+AGG + tig0019970:69960-69979 Msa1377710:CDS 45.0%
!! TAAACGAGTTGTCGGCTCAG+TGG - tig0019970:69726-69745 None:intergenic 50.0%
! GTGATGGTGAGGAAGCAGAT+AGG + tig0019970:69827-69846 Msa1377710:CDS 50.0%
GTCATTGCTCGAGGATTTGC+TGG - tig0019970:69917-69936 None:intergenic 50.0%
GCAAATCCTCGAGCAATGAC+AGG + tig0019970:69917-69936 Msa1377710:CDS 50.0%
GCAACTGCAGACAGAGTTGA+AGG - tig0019970:69953-69972 None:intergenic 50.0%
CTGCAGTTGCTTATGCTAGG+AGG + tig0019970:69963-69982 Msa1377710:CDS 50.0%
!! TAAACGAGTTGTCGGCTCAG+TGG - tig0019970:69726-69745 None:intergenic 50.0%
! GTGATGGTGAGGAAGCAGAT+AGG + tig0019970:69827-69846 Msa1377710:CDS 50.0%
GTCATTGCTCGAGGATTTGC+TGG - tig0019970:69917-69936 None:intergenic 50.0%
GCAAATCCTCGAGCAATGAC+AGG + tig0019970:69917-69936 Msa1377710:CDS 50.0%
GCAACTGCAGACAGAGTTGA+AGG - tig0019970:69953-69972 None:intergenic 50.0%
CTGCAGTTGCTTATGCTAGG+AGG + tig0019970:69963-69982 Msa1377710:CDS 50.0%
CAGATTCTGTGGTCACTGCG+AGG + tig0019970:69880-69899 Msa1377710:CDS 55.0%
CAGATTCTGTGGTCACTGCG+AGG + tig0019970:69880-69899 Msa1377710:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0019970 gene 69297 70165 69297 ID=Msa1377710;Name=Msa1377710
tig0019970 mRNA 69297 70165 69297 ID=Msa1377710-mRNA-1;Parent=Msa1377710;Name=Msa1377710-mRNA-1;_AED=0.03;_eAED=0.03;_QI=48|1|1|1|1|1|3|111|130
tig0019970 exon 69297 69456 69297 ID=Msa1377710-mRNA-1:exon:5752;Parent=Msa1377710-mRNA-1
tig0019970 exon 69549 69583 69549 ID=Msa1377710-mRNA-1:exon:5753;Parent=Msa1377710-mRNA-1
tig0019970 exon 69809 70165 69809 ID=Msa1377710-mRNA-1:exon:5754;Parent=Msa1377710-mRNA-1
tig0019970 five_prime_UTR 69297 69344 69297 ID=Msa1377710-mRNA-1:five_prime_utr;Parent=Msa1377710-mRNA-1
tig0019970 CDS 69345 69456 69345 ID=Msa1377710-mRNA-1:cds;Parent=Msa1377710-mRNA-1
tig0019970 CDS 69549 69583 69549 ID=Msa1377710-mRNA-1:cds;Parent=Msa1377710-mRNA-1
tig0019970 CDS 69809 70054 69809 ID=Msa1377710-mRNA-1:cds;Parent=Msa1377710-mRNA-1
tig0019970 three_prime_UTR 70055 70165 70055 ID=Msa1377710-mRNA-1:three_prime_utr;Parent=Msa1377710-mRNA-1
Gene Sequence

>Msa1377710

ATGAGGAATGAATATCATCATGTCATTTATGGTCAAAGATTCATTTTCATTACCATTTCTCTTCTCTTTCTCATAGTTTCAAGCTTGACACAAAAGGGACTTGTAACTGAAGGTAGAAAGACTTTGAACCAACATGGTTTTCACCAGACAATAGGTGATAACAAGGTGATGGTGAGGAAGCAGATAGGATCAAGGCCACCAAAATGTGATACAAGGTGCAGATTCTGTGGTCACTGCGAGGCTATTCAAGTTCCAGCAAATCCTCGAGCAATGACAGGAAAGATCAACCCTTCAACTCTGTCTGCAGTTGCTTATGCTAGGAGGCAAGATAATTCCAACTATAAACCTATGAGTTGGAAATGCAAATGTGGGAACATTATTTTCAACCCTTGA

Protein sequence

>Msa1377710

MRNEYHHVIYGQRFIFITISLLFLIVSSLTQKGLVTEGRKTLNQHGFHQTIGDNKVMVRKQIGSRPPKCDTRCRFCGHCEAIQVPANPRAMTGKINPSTLSAVAYARRQDNSNYKPMSWKCKCGNIIFNP*