AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1181290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1181290 MtrunA17_Chr8g0337271 81.122 196 37 0 1 196 1 196 3.49e-117 331
Msa1181290 MtrunA17_Chr8g0358731 32.836 201 98 4 1 199 1 166 4.54e-24 93.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1181290 AT3G50510.1 25.974 154 99 4 1 153 3 142 2.91e-11 60.5
Msa1181290 AT3G50510.2 25.974 154 99 4 1 153 3 142 2.91e-11 60.5
Msa1181290 AT2G19820.1 30.864 81 55 1 5 84 7 87 4.49e-11 58.5

Find 52 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCCAAGGATGTGCTTATT+TGG 0.063042 8_1:-15625772 None:intergenic
TCAGTGTGTCATTCAAATTT+TGG 0.153883 8_1:+15625607 Msa1181290:CDS
CTGACTTAAACTTGAGTATA+TGG 0.197296 8_1:+15625888 Msa1181290:CDS
CAAATTCCCCATCTTACTTT+GGG 0.270367 8_1:-15626408 None:intergenic
ATCCAAGGATGTGCTTATTT+GGG 0.326625 8_1:-15625771 None:intergenic
TCAAATTCCCCATCTTACTT+TGG 0.356414 8_1:-15626409 None:intergenic
CATGACACTGACTGTGAATT+TGG 0.372038 8_1:+15625551 Msa1181290:CDS
AAAGTCTTCATCCTCATTAC+TGG 0.397078 8_1:-15626383 None:intergenic
TCTTGAACACCAATTGGTGC+TGG 0.399679 8_1:+15625745 Msa1181290:CDS
GGGAATGGTGGCTGATGAAA+AGG 0.430935 8_1:+15626330 Msa1181290:CDS
TGACTTAAACTTGAGTATAT+GGG 0.443514 8_1:+15625889 Msa1181290:CDS
CATGCCTTCTTCTCATATGT+TGG 0.454074 8_1:-15625532 None:intergenic
TTCATCAGCCACCATTCCCT+TGG 0.455807 8_1:-15626326 None:intergenic
TTTGGGCACCCAGCACCAAT+TGG 0.466511 8_1:-15625754 None:intergenic
TTGGCGAAGTAACTCAGATC+GGG 0.471484 8_1:+15625718 Msa1181290:CDS
TGCCCAAATAAGCACATCCT+TGG 0.475102 8_1:+15625769 Msa1181290:CDS
AGCAATTTCAATTTCATCCA+AGG 0.478006 8_1:-15625786 None:intergenic
CATATACTCAAGTTTAAGTC+AGG 0.479889 8_1:-15625887 None:intergenic
CTTGAACACCAATTGGTGCT+GGG 0.482127 8_1:+15625746 Msa1181290:CDS
CTGAAAATCAGCATGCCTAC+TGG 0.485199 8_1:-15625588 None:intergenic
TGTGCCAACATATGAGAAGA+AGG 0.488999 8_1:+15625528 Msa1181290:CDS
TTAATCGCATAATTCTCATC+AGG 0.493767 8_1:-15625640 None:intergenic
TCTCCTCTTTCACAAGTACA+TGG 0.497829 8_1:-15626138 None:intergenic
TCAGGAATTTGAGTGCTAGA+AGG 0.498016 8_1:-15625869 None:intergenic
TCCTTCTGTGAGAAGCGAAT+CGG 0.511515 8_1:-15625690 None:intergenic
TACTGAACACATGGGTGACA+TGG 0.514848 8_1:+15626086 Msa1181290:CDS
GCCGATTCGCTTCTCACAGA+AGG 0.517177 8_1:+15625689 Msa1181290:CDS
ATTCCATGTACTTGTGAAAG+AGG 0.523001 8_1:+15626135 Msa1181290:CDS
GTGGCTGATGAAAAGGGAAA+AGG 0.537842 8_1:+15626337 Msa1181290:CDS
CTTGGCGAAGTAACTCAGAT+CGG 0.541406 8_1:+15625717 Msa1181290:CDS
GTCTTCATCCTCATTACTGG+TGG 0.547436 8_1:-15626380 None:intergenic
TGTACACAGTAATCTATCCA+AGG 0.549486 8_1:+15626309 Msa1181290:intron
TTCTCACAGAAGGAGAAGCT+TGG 0.549947 8_1:+15625699 Msa1181290:CDS
GTGCTAGAAGGCATGGAAGA+AGG 0.561567 8_1:-15625857 None:intergenic
CAGTAATCTATCCAAGGGAA+TGG 0.569736 8_1:+15626315 Msa1181290:intron
AATTTGAGTGCTAGAAGGCA+TGG 0.572126 8_1:-15625864 None:intergenic
AAATTCCCCATCTTACTTTG+GGG 0.573119 8_1:-15626407 None:intergenic
GCAACAACTTGTCTTTGATG+TGG 0.579471 8_1:-15625668 None:intergenic
TAATCTATCCAAGGGAATGG+TGG 0.591476 8_1:+15626318 Msa1181290:CDS
AAATGCATCAGAGAAATACA+AGG 0.593981 8_1:+15625489 None:intergenic
ACAAGGACCCACCAGTAATG+AGG 0.613595 8_1:+15626372 Msa1181290:CDS
CTTGTGAAAGAGGAGAATCA+AGG 0.617523 8_1:+15626145 Msa1181290:CDS
GGAATGGTGGCTGATGAAAA+GGG 0.618900 8_1:+15626331 Msa1181290:CDS
CATGGGTGACATGGACATCA+CGG 0.621521 8_1:+15626095 Msa1181290:CDS
TTAATAGAGTACTGAACACA+TGG 0.626411 8_1:+15626077 Msa1181290:intron
GTACACAGTAATCTATCCAA+GGG 0.631300 8_1:+15626310 Msa1181290:intron
TCTTCATCCTCATTACTGGT+GGG 0.637097 8_1:-15626379 None:intergenic
AAAGGAATTCTTAATGAACA+AGG 0.657272 8_1:+15626355 Msa1181290:CDS
TGGCGAAGTAACTCAGATCG+GGG 0.662365 8_1:+15625719 Msa1181290:CDS
ATCACGGAACATGACATGCA+AGG 0.668838 8_1:+15626111 Msa1181290:CDS
AATGCATCAGAGAAATACAA+GGG 0.687321 8_1:+15625490 None:intergenic
TAATAGAGTACTGAACACAT+GGG 0.740993 8_1:+15626078 Msa1181290:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAATATAAAATGTGTATT+AGG - chr8_1:15626285-15626304 None:intergenic 10.0%
!! TTTAATATAAAATGTGTATT+AGG - chr8_1:15626285-15626304 None:intergenic 10.0%
! TGACTTAAACTTGAGTATAT+GGG + chr8_1:15625889-15625908 Msa1181290:CDS 25.0%
! TTGAAAAGAATGATAGATCT+TGG - chr8_1:15626033-15626052 None:intergenic 25.0%
! AAAGGAATTCTTAATGAACA+AGG + chr8_1:15626355-15626374 Msa1181290:CDS 25.0%
! TGACTTAAACTTGAGTATAT+GGG + chr8_1:15625889-15625908 Msa1181290:CDS 25.0%
! TTGAAAAGAATGATAGATCT+TGG - chr8_1:15626033-15626052 None:intergenic 25.0%
! AAAGGAATTCTTAATGAACA+AGG + chr8_1:15626355-15626374 Msa1181290:CDS 25.0%
!! TCAGTGTGTCATTCAAATTT+TGG + chr8_1:15625607-15625626 Msa1181290:CDS 30.0%
!! CAGTGTGTCATTCAAATTTT+GGG + chr8_1:15625608-15625627 Msa1181290:CDS 30.0%
!! AGTGTGTCATTCAAATTTTG+GGG + chr8_1:15625609-15625628 Msa1181290:CDS 30.0%
TTAATCGCATAATTCTCATC+AGG - chr8_1:15625643-15625662 None:intergenic 30.0%
AGCAATTTCAATTTCATCCA+AGG - chr8_1:15625789-15625808 None:intergenic 30.0%
CATATACTCAAGTTTAAGTC+AGG - chr8_1:15625890-15625909 None:intergenic 30.0%
CTGACTTAAACTTGAGTATA+TGG + chr8_1:15625888-15625907 Msa1181290:CDS 30.0%
ATGTGTTCAGTACTCTATTA+AGG - chr8_1:15626078-15626097 None:intergenic 30.0%
!! TTAATAGAGTACTGAACACA+TGG + chr8_1:15626077-15626096 Msa1181290:intron 30.0%
!! TAATAGAGTACTGAACACAT+GGG + chr8_1:15626078-15626097 Msa1181290:intron 30.0%
!! TCAGTGTGTCATTCAAATTT+TGG + chr8_1:15625607-15625626 Msa1181290:CDS 30.0%
!! CAGTGTGTCATTCAAATTTT+GGG + chr8_1:15625608-15625627 Msa1181290:CDS 30.0%
!! AGTGTGTCATTCAAATTTTG+GGG + chr8_1:15625609-15625628 Msa1181290:CDS 30.0%
TTAATCGCATAATTCTCATC+AGG - chr8_1:15625643-15625662 None:intergenic 30.0%
AGCAATTTCAATTTCATCCA+AGG - chr8_1:15625789-15625808 None:intergenic 30.0%
CATATACTCAAGTTTAAGTC+AGG - chr8_1:15625890-15625909 None:intergenic 30.0%
CTGACTTAAACTTGAGTATA+TGG + chr8_1:15625888-15625907 Msa1181290:CDS 30.0%
ATGTGTTCAGTACTCTATTA+AGG - chr8_1:15626078-15626097 None:intergenic 30.0%
!! TTAATAGAGTACTGAACACA+TGG + chr8_1:15626077-15626096 Msa1181290:intron 30.0%
!! TAATAGAGTACTGAACACAT+GGG + chr8_1:15626078-15626097 Msa1181290:intron 30.0%
ATCCAAGGATGTGCTTATTT+GGG - chr8_1:15625774-15625793 None:intergenic 35.0%
ATTCCATGTACTTGTGAAAG+AGG + chr8_1:15626135-15626154 Msa1181290:CDS 35.0%
TGTACACAGTAATCTATCCA+AGG + chr8_1:15626309-15626328 Msa1181290:intron 35.0%
GTACACAGTAATCTATCCAA+GGG + chr8_1:15626310-15626329 Msa1181290:intron 35.0%
AAAGTCTTCATCCTCATTAC+TGG - chr8_1:15626386-15626405 None:intergenic 35.0%
ATCCAAGGATGTGCTTATTT+GGG - chr8_1:15625774-15625793 None:intergenic 35.0%
ATTCCATGTACTTGTGAAAG+AGG + chr8_1:15626135-15626154 Msa1181290:CDS 35.0%
TGTACACAGTAATCTATCCA+AGG + chr8_1:15626309-15626328 Msa1181290:intron 35.0%
GTACACAGTAATCTATCCAA+GGG + chr8_1:15626310-15626329 Msa1181290:intron 35.0%
AAAGTCTTCATCCTCATTAC+TGG - chr8_1:15626386-15626405 None:intergenic 35.0%
TGTGCCAACATATGAGAAGA+AGG + chr8_1:15625528-15625547 Msa1181290:CDS 40.0%
CATGCCTTCTTCTCATATGT+TGG - chr8_1:15625535-15625554 None:intergenic 40.0%
! CATGACACTGACTGTGAATT+TGG + chr8_1:15625551-15625570 Msa1181290:CDS 40.0%
! GTCAATACTTTTCGACCAGT+AGG + chr8_1:15625573-15625592 Msa1181290:CDS 40.0%
GCAACAACTTGTCTTTGATG+TGG - chr8_1:15625671-15625690 None:intergenic 40.0%
! GGGTTTTCTTGAACACCAAT+TGG + chr8_1:15625739-15625758 Msa1181290:CDS 40.0%
CATCCAAGGATGTGCTTATT+TGG - chr8_1:15625775-15625794 None:intergenic 40.0%
AATTTGAGTGCTAGAAGGCA+TGG - chr8_1:15625867-15625886 None:intergenic 40.0%
TCAGGAATTTGAGTGCTAGA+AGG - chr8_1:15625872-15625891 None:intergenic 40.0%
TCTCCTCTTTCACAAGTACA+TGG - chr8_1:15626141-15626160 None:intergenic 40.0%
CTTGTGAAAGAGGAGAATCA+AGG + chr8_1:15626145-15626164 Msa1181290:CDS 40.0%
CAGTAATCTATCCAAGGGAA+TGG + chr8_1:15626315-15626334 Msa1181290:intron 40.0%
TAATCTATCCAAGGGAATGG+TGG + chr8_1:15626318-15626337 Msa1181290:CDS 40.0%
TCTTCATCCTCATTACTGGT+GGG - chr8_1:15626382-15626401 None:intergenic 40.0%
TGTGCCAACATATGAGAAGA+AGG + chr8_1:15625528-15625547 Msa1181290:CDS 40.0%
CATGCCTTCTTCTCATATGT+TGG - chr8_1:15625535-15625554 None:intergenic 40.0%
! CATGACACTGACTGTGAATT+TGG + chr8_1:15625551-15625570 Msa1181290:CDS 40.0%
! GTCAATACTTTTCGACCAGT+AGG + chr8_1:15625573-15625592 Msa1181290:CDS 40.0%
GCAACAACTTGTCTTTGATG+TGG - chr8_1:15625671-15625690 None:intergenic 40.0%
! GGGTTTTCTTGAACACCAAT+TGG + chr8_1:15625739-15625758 Msa1181290:CDS 40.0%
CATCCAAGGATGTGCTTATT+TGG - chr8_1:15625775-15625794 None:intergenic 40.0%
AATTTGAGTGCTAGAAGGCA+TGG - chr8_1:15625867-15625886 None:intergenic 40.0%
TCAGGAATTTGAGTGCTAGA+AGG - chr8_1:15625872-15625891 None:intergenic 40.0%
TCTCCTCTTTCACAAGTACA+TGG - chr8_1:15626141-15626160 None:intergenic 40.0%
CTTGTGAAAGAGGAGAATCA+AGG + chr8_1:15626145-15626164 Msa1181290:CDS 40.0%
CAGTAATCTATCCAAGGGAA+TGG + chr8_1:15626315-15626334 Msa1181290:intron 40.0%
TAATCTATCCAAGGGAATGG+TGG + chr8_1:15626318-15626337 Msa1181290:CDS 40.0%
TCTTCATCCTCATTACTGGT+GGG - chr8_1:15626382-15626401 None:intergenic 40.0%
CTGAAAATCAGCATGCCTAC+TGG - chr8_1:15625591-15625610 None:intergenic 45.0%
TCCTTCTGTGAGAAGCGAAT+CGG - chr8_1:15625693-15625712 None:intergenic 45.0%
TTCTCACAGAAGGAGAAGCT+TGG + chr8_1:15625699-15625718 Msa1181290:CDS 45.0%
CTTGGCGAAGTAACTCAGAT+CGG + chr8_1:15625717-15625736 Msa1181290:CDS 45.0%
TTGGCGAAGTAACTCAGATC+GGG + chr8_1:15625718-15625737 Msa1181290:CDS 45.0%
TCTTGAACACCAATTGGTGC+TGG + chr8_1:15625745-15625764 Msa1181290:CDS 45.0%
! CTTGAACACCAATTGGTGCT+GGG + chr8_1:15625746-15625765 Msa1181290:CDS 45.0%
TGCCCAAATAAGCACATCCT+TGG + chr8_1:15625769-15625788 Msa1181290:CDS 45.0%
TACTGAACACATGGGTGACA+TGG + chr8_1:15626086-15626105 Msa1181290:CDS 45.0%
ATCACGGAACATGACATGCA+AGG + chr8_1:15626111-15626130 Msa1181290:CDS 45.0%
GGAATGGTGGCTGATGAAAA+GGG + chr8_1:15626331-15626350 Msa1181290:CDS 45.0%
GTGGCTGATGAAAAGGGAAA+AGG + chr8_1:15626337-15626356 Msa1181290:CDS 45.0%
GTCTTCATCCTCATTACTGG+TGG - chr8_1:15626383-15626402 None:intergenic 45.0%
CTGAAAATCAGCATGCCTAC+TGG - chr8_1:15625591-15625610 None:intergenic 45.0%
TCCTTCTGTGAGAAGCGAAT+CGG - chr8_1:15625693-15625712 None:intergenic 45.0%
TTCTCACAGAAGGAGAAGCT+TGG + chr8_1:15625699-15625718 Msa1181290:CDS 45.0%
CTTGGCGAAGTAACTCAGAT+CGG + chr8_1:15625717-15625736 Msa1181290:CDS 45.0%
TTGGCGAAGTAACTCAGATC+GGG + chr8_1:15625718-15625737 Msa1181290:CDS 45.0%
TCTTGAACACCAATTGGTGC+TGG + chr8_1:15625745-15625764 Msa1181290:CDS 45.0%
! CTTGAACACCAATTGGTGCT+GGG + chr8_1:15625746-15625765 Msa1181290:CDS 45.0%
TGCCCAAATAAGCACATCCT+TGG + chr8_1:15625769-15625788 Msa1181290:CDS 45.0%
TACTGAACACATGGGTGACA+TGG + chr8_1:15626086-15626105 Msa1181290:CDS 45.0%
ATCACGGAACATGACATGCA+AGG + chr8_1:15626111-15626130 Msa1181290:CDS 45.0%
GGAATGGTGGCTGATGAAAA+GGG + chr8_1:15626331-15626350 Msa1181290:CDS 45.0%
GTGGCTGATGAAAAGGGAAA+AGG + chr8_1:15626337-15626356 Msa1181290:CDS 45.0%
GTCTTCATCCTCATTACTGG+TGG - chr8_1:15626383-15626402 None:intergenic 45.0%
TGGCGAAGTAACTCAGATCG+GGG + chr8_1:15625719-15625738 Msa1181290:CDS 50.0%
! GTGCTAGAAGGCATGGAAGA+AGG - chr8_1:15625860-15625879 None:intergenic 50.0%
CATGGGTGACATGGACATCA+CGG + chr8_1:15626095-15626114 Msa1181290:CDS 50.0%
TTCATCAGCCACCATTCCCT+TGG - chr8_1:15626329-15626348 None:intergenic 50.0%
GGGAATGGTGGCTGATGAAA+AGG + chr8_1:15626330-15626349 Msa1181290:CDS 50.0%
ACAAGGACCCACCAGTAATG+AGG + chr8_1:15626372-15626391 Msa1181290:CDS 50.0%
TGGCGAAGTAACTCAGATCG+GGG + chr8_1:15625719-15625738 Msa1181290:CDS 50.0%
! GTGCTAGAAGGCATGGAAGA+AGG - chr8_1:15625860-15625879 None:intergenic 50.0%
CATGGGTGACATGGACATCA+CGG + chr8_1:15626095-15626114 Msa1181290:CDS 50.0%
TTCATCAGCCACCATTCCCT+TGG - chr8_1:15626329-15626348 None:intergenic 50.0%
GGGAATGGTGGCTGATGAAA+AGG + chr8_1:15626330-15626349 Msa1181290:CDS 50.0%
ACAAGGACCCACCAGTAATG+AGG + chr8_1:15626372-15626391 Msa1181290:CDS 50.0%
!! GCCGATTCGCTTCTCACAGA+AGG + chr8_1:15625689-15625708 Msa1181290:CDS 55.0%
TTTGGGCACCCAGCACCAAT+TGG - chr8_1:15625757-15625776 None:intergenic 55.0%
!! GCCGATTCGCTTCTCACAGA+AGG + chr8_1:15625689-15625708 Msa1181290:CDS 55.0%
TTTGGGCACCCAGCACCAAT+TGG - chr8_1:15625757-15625776 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 15625491 15626417 15625491 ID=Msa1181290;Name=Msa1181290
chr8_1 mRNA 15625491 15626417 15625491 ID=Msa1181290-mRNA-1;Parent=Msa1181290;Name=Msa1181290-mRNA-1;_AED=0.01;_eAED=0.02;_QI=0|0|0|1|1|1|3|0|200
chr8_1 exon 15625491 15625910 15625491 ID=Msa1181290-mRNA-1:exon:5868;Parent=Msa1181290-mRNA-1
chr8_1 exon 15626084 15626166 15626084 ID=Msa1181290-mRNA-1:exon:5869;Parent=Msa1181290-mRNA-1
chr8_1 exon 15626318 15626417 15626318 ID=Msa1181290-mRNA-1:exon:5870;Parent=Msa1181290-mRNA-1
chr8_1 CDS 15625491 15625910 15625491 ID=Msa1181290-mRNA-1:cds;Parent=Msa1181290-mRNA-1
chr8_1 CDS 15626084 15626166 15626084 ID=Msa1181290-mRNA-1:cds;Parent=Msa1181290-mRNA-1
chr8_1 CDS 15626318 15626417 15626318 ID=Msa1181290-mRNA-1:cds;Parent=Msa1181290-mRNA-1
Gene Sequence

>Msa1181290

ATGCATCAGAGAAATACAAGGGCTATTACATGTCTTTTGTGCCAACATATGAGAAGAAGGCATGACACTGACTGTGAATTTGGTCAATACTTTTCGACCAGTAGGCATGCTGATTTTCAGTGTGTCATTCAAATTTTGGGGTTAAGTCGCCTGATGAGAATTATGCGATTAATAGAACCACATCAAAGACAAGTTGTTGCCGATTCGCTTCTCACAGAAGGAGAAGCTTGGCGAAGTAACTCAGATCGGGGTTTTCTTGAACACCAATTGGTGCTGGGTGCCCAAATAAGCACATCCTTGGATGAAATTGAAATTGCTAGAAGACTTTTAGCTTTTTGCATTGATAATGCAAATTCAAACAATGCACCTTCTTCCATGCCTTCTAGCACTCAAATTCCTGACTTAAACTTGAGTATATGGAGTACTGAACACATGGGTGACATGGACATCACGGAACATGACATGCAAGGTATTCCATGTACTTGTGAAAGAGGAGAATCAAGTAATCTATCCAAGGGAATGGTGGCTGATGAAAAGGGAAAAGGAATTCTTAATGAACAAGGACCCACCAGTAATGAGGATGAAGACTTTTCCCCAAAGTAA

Protein sequence

>Msa1181290

MHQRNTRAITCLLCQHMRRRHDTDCEFGQYFSTSRHADFQCVIQILGLSRLMRIMRLIEPHQRQVVADSLLTEGEAWRSNSDRGFLEHQLVLGAQISTSLDEIEIARRLLAFCIDNANSNNAPSSMPSSTQIPDLNLSIWSTEHMGDMDITEHDMQGIPCTCERGESSNLSKGMVADEKGKGILNEQGPTSNEDEDFSPK*