AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1404850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1404850 MtrunA17_Chr4g0064671 96.429 84 3 0 6 89 169 252 1.85e-57 178
Msa1404850 MtrunA17_Chr1g0149991 54.808 104 43 1 6 109 452 551 4.01e-34 124
Msa1404850 MtrunA17_Chr6g0458441 39.744 78 43 4 10 83 349 426 6.21e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1404850 AT5G10790.2 50.000 92 43 1 3 91 319 410 7.03e-26 100
Msa1404850 AT5G10790.1 50.000 92 43 1 3 91 448 539 1.36e-25 100

Find 23 sgRNAs with CRISPR-Local

Find 134 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTACAAGTGTGATGATTCT+TGG 0.387459 tig0023091:-61109 Msa1404850:CDS
AAACATTGTGAGGGCTGCTC+AGG 0.399967 tig0023091:-61069 Msa1404850:CDS
CATGGATCATTTGAAGCATC+TGG 0.409135 tig0023091:+61221 None:intergenic
AAAATCATGGCATATCATTA+GGG 0.428866 tig0023091:+60913 None:intergenic
AAGCAAAGCAACTGATAAAT+CGG 0.429703 tig0023091:-61007 Msa1404850:CDS
GACATATGATGCCAATGGTT+TGG 0.451918 tig0023091:+60956 None:intergenic
TAAATCGGTCGCCTCATGAT+TGG 0.463129 tig0023091:-60992 Msa1404850:CDS
CTCATGATTGGCACAGGAGA+TGG 0.489277 tig0023091:-60980 Msa1404850:CDS
CACTCTGGTAAGTTAGATGC+TGG 0.512954 tig0023091:-61167 Msa1404850:CDS
GTACAAGTGTGATGATTCTT+GGG 0.516165 tig0023091:-61108 Msa1404850:CDS
AAATTTGCAAAATGGTAAAG+AGG 0.517259 tig0023091:-61746 None:intergenic
TCTGGCTCATCCCCATCAAA+AGG 0.519011 tig0023091:+61239 None:intergenic
CAGGAGATGGTCCAAACCAT+TGG 0.530742 tig0023091:-60967 Msa1404850:CDS
TTTGCTGTCGTCACTCACTC+TGG 0.539742 tig0023091:-61182 Msa1404850:CDS
GGTCGCCTCATGATTGGCAC+AGG 0.544879 tig0023091:-60986 Msa1404850:CDS
ATCTGCGATTAAGCAATCAA+TGG 0.573921 tig0023091:-61130 Msa1404850:CDS
ACCATTGGCATCATATGTCA+TGG 0.588411 tig0023091:-60952 Msa1404850:CDS
AACATTGTGAGGGCTGCTCA+GGG 0.594864 tig0023091:-61068 Msa1404850:CDS
AACAATTCAAACTCAGAACA+TGG 0.598642 tig0023091:+61203 None:intergenic
AAGTTGATGAAAACATTGTG+AGG 0.627661 tig0023091:-61079 Msa1404850:CDS
CATCTCCTGTGCCAATCATG+AGG 0.630249 tig0023091:+60981 None:intergenic
ACCATGACATATGATGCCAA+TGG 0.694643 tig0023091:+60951 None:intergenic
AGTTGATGAAAACATTGTGA+GGG 0.699031 tig0023091:-61078 Msa1404850:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTTTCAAATTATTATTTG+GGG + tig0023091:61062-61081 None:intergenic 15.0%
!! CAACTTTCAAATTATTATTT+GGG + tig0023091:61063-61082 None:intergenic 15.0%
!! TCAACTTTCAAATTATTATT+TGG + tig0023091:61064-61083 None:intergenic 15.0%
!!! AAGTTGAATGATTATTTTTA+TGG - tig0023091:61077-61096 Msa1404850:CDS 15.0%
!! AACTTTCAAATTATTATTTG+GGG + tig0023091:61062-61081 None:intergenic 15.0%
!! CAACTTTCAAATTATTATTT+GGG + tig0023091:61063-61082 None:intergenic 15.0%
!! TCAACTTTCAAATTATTATT+TGG + tig0023091:61064-61083 None:intergenic 15.0%
!!! AAGTTGAATGATTATTTTTA+TGG - tig0023091:61077-61096 Msa1404850:CDS 15.0%
!! ATAGTCATTTAATGTCAAAA+TGG + tig0023091:61104-61123 None:intergenic 20.0%
!! GAAAAAACATGAAAAAAGAA+TGG - tig0023091:61133-61152 Msa1404850:CDS 20.0%
!!! ATAGAATATTTCCTTTTGAT+GGG - tig0023091:61402-61421 Msa1404850:intron 20.0%
!! ATAGTCATTTAATGTCAAAA+TGG + tig0023091:61104-61123 None:intergenic 20.0%
!! GAAAAAACATGAAAAAAGAA+TGG - tig0023091:61133-61152 Msa1404850:CDS 20.0%
!!! ATAGAATATTTCCTTTTGAT+GGG - tig0023091:61402-61421 Msa1404850:intron 20.0%
!! GATAGAATATTTCCTTTTGA+TGG - tig0023091:61401-61420 Msa1404850:intron 25.0%
!! TAGAATATTTCCTTTTGATG+GGG - tig0023091:61403-61422 Msa1404850:intron 25.0%
!! GATAGAATATTTCCTTTTGA+TGG - tig0023091:61401-61420 Msa1404850:intron 25.0%
!! TAGAATATTTCCTTTTGATG+GGG - tig0023091:61403-61422 Msa1404850:intron 25.0%
TAAAGAGGTTAGTGAAATAG+AGG - tig0023091:60921-60940 Msa1404850:CDS 30.0%
TTAACGGAAACATTAATGGA+GGG + tig0023091:60965-60984 None:intergenic 30.0%
TTTAACGGAAACATTAATGG+AGG + tig0023091:60966-60985 None:intergenic 30.0%
! CCTTTTAACGGAAACATTAA+TGG + tig0023091:60969-60988 None:intergenic 30.0%
CCATTAATGTTTCCGTTAAA+AGG - tig0023091:60966-60985 Msa1404850:CDS 30.0%
AATGTTTCCGTTAAAAGGTA+TGG - tig0023091:60971-60990 Msa1404850:CDS 30.0%
! AATTATTATTTGGGGCCAAA+TGG + tig0023091:61054-61073 None:intergenic 30.0%
ATTTCTCATCCTCAATCTTA+TGG - tig0023091:61173-61192 Msa1404850:CDS 30.0%
AGAGAAAATGAAATAGCCTT+CGG + tig0023091:61264-61283 None:intergenic 30.0%
AACAATTCAAACTCAGAACA+TGG + tig0023091:61452-61471 None:intergenic 30.0%
!! AAGTTGATGAAAACATTGTG+AGG - tig0023091:61573-61592 Msa1404850:intron 30.0%
!! AGTTGATGAAAACATTGTGA+GGG - tig0023091:61574-61593 Msa1404850:intron 30.0%
AAGCAAAGCAACTGATAAAT+CGG - tig0023091:61645-61664 Msa1404850:intron 30.0%
TAAAGAGGTTAGTGAAATAG+AGG - tig0023091:60921-60940 Msa1404850:CDS 30.0%
TTAACGGAAACATTAATGGA+GGG + tig0023091:60965-60984 None:intergenic 30.0%
TTTAACGGAAACATTAATGG+AGG + tig0023091:60966-60985 None:intergenic 30.0%
! CCTTTTAACGGAAACATTAA+TGG + tig0023091:60969-60988 None:intergenic 30.0%
CCATTAATGTTTCCGTTAAA+AGG - tig0023091:60966-60985 Msa1404850:CDS 30.0%
AATGTTTCCGTTAAAAGGTA+TGG - tig0023091:60971-60990 Msa1404850:CDS 30.0%
! AATTATTATTTGGGGCCAAA+TGG + tig0023091:61054-61073 None:intergenic 30.0%
ATTTCTCATCCTCAATCTTA+TGG - tig0023091:61173-61192 Msa1404850:CDS 30.0%
AGAGAAAATGAAATAGCCTT+CGG + tig0023091:61264-61283 None:intergenic 30.0%
AACAATTCAAACTCAGAACA+TGG + tig0023091:61452-61471 None:intergenic 30.0%
!! AAGTTGATGAAAACATTGTG+AGG - tig0023091:61573-61592 Msa1404850:intron 30.0%
!! AGTTGATGAAAACATTGTGA+GGG - tig0023091:61574-61593 Msa1404850:intron 30.0%
AAGCAAAGCAACTGATAAAT+CGG - tig0023091:61645-61664 Msa1404850:intron 30.0%
!! TAATGGAGGGACTATTTTGA+TGG + tig0023091:60952-60971 None:intergenic 35.0%
GAGAAAATGAAATAGCCTTC+GGG + tig0023091:61263-61282 None:intergenic 35.0%
CAATCACAATAAAGCTTGTG+CGG + tig0023091:61322-61341 None:intergenic 35.0%
ATCTGCGATTAAGCAATCAA+TGG - tig0023091:61522-61541 Msa1404850:intron 35.0%
GTACAAGTGTGATGATTCTT+GGG - tig0023091:61544-61563 Msa1404850:intron 35.0%
!! TAATGGAGGGACTATTTTGA+TGG + tig0023091:60952-60971 None:intergenic 35.0%
GAGAAAATGAAATAGCCTTC+GGG + tig0023091:61263-61282 None:intergenic 35.0%
CAATCACAATAAAGCTTGTG+CGG + tig0023091:61322-61341 None:intergenic 35.0%
ATCTGCGATTAAGCAATCAA+TGG - tig0023091:61522-61541 Msa1404850:intron 35.0%
GTACAAGTGTGATGATTCTT+GGG - tig0023091:61544-61563 Msa1404850:intron 35.0%
! TTCCGTTAAAAGGTATGGAG+TGG - tig0023091:60976-60995 Msa1404850:CDS 40.0%
! TGCCACTCCATACCTTTTAA+CGG + tig0023091:60981-61000 None:intergenic 40.0%
! CACATCAGTATCGAACCATT+TGG - tig0023091:61036-61055 Msa1404850:CDS 40.0%
CATCCTCAATCTTATGGAGT+CGG - tig0023091:61179-61198 Msa1404850:CDS 40.0%
! AAACCGACTCCATAAGATTG+AGG + tig0023091:61185-61204 None:intergenic 40.0%
TCTCTCAGGACAGTTTGTAT+CGG + tig0023091:61238-61257 None:intergenic 40.0%
TAAAGCTTGTGCGGAATTCA+CGG + tig0023091:61313-61332 None:intergenic 40.0%
!! CGCACAAGCTTTATTGTGAT+TGG - tig0023091:61320-61339 Msa1404850:intron 40.0%
! CATGGATCATTTGAAGCATC+TGG + tig0023091:61434-61453 None:intergenic 40.0%
GGTACAAGTGTGATGATTCT+TGG - tig0023091:61543-61562 Msa1404850:intron 40.0%
GACATATGATGCCAATGGTT+TGG + tig0023091:61699-61718 None:intergenic 40.0%
ACCATTGGCATCATATGTCA+TGG - tig0023091:61700-61719 Msa1404850:intron 40.0%
ACCATGACATATGATGCCAA+TGG + tig0023091:61704-61723 None:intergenic 40.0%
! TTCCGTTAAAAGGTATGGAG+TGG - tig0023091:60976-60995 Msa1404850:CDS 40.0%
! TGCCACTCCATACCTTTTAA+CGG + tig0023091:60981-61000 None:intergenic 40.0%
! CACATCAGTATCGAACCATT+TGG - tig0023091:61036-61055 Msa1404850:CDS 40.0%
CATCCTCAATCTTATGGAGT+CGG - tig0023091:61179-61198 Msa1404850:CDS 40.0%
! AAACCGACTCCATAAGATTG+AGG + tig0023091:61185-61204 None:intergenic 40.0%
TCTCTCAGGACAGTTTGTAT+CGG + tig0023091:61238-61257 None:intergenic 40.0%
TAAAGCTTGTGCGGAATTCA+CGG + tig0023091:61313-61332 None:intergenic 40.0%
!! CGCACAAGCTTTATTGTGAT+TGG - tig0023091:61320-61339 Msa1404850:intron 40.0%
! CATGGATCATTTGAAGCATC+TGG + tig0023091:61434-61453 None:intergenic 40.0%
GGTACAAGTGTGATGATTCT+TGG - tig0023091:61543-61562 Msa1404850:intron 40.0%
GACATATGATGCCAATGGTT+TGG + tig0023091:61699-61718 None:intergenic 40.0%
ACCATTGGCATCATATGTCA+TGG - tig0023091:61700-61719 Msa1404850:intron 40.0%
ACCATGACATATGATGCCAA+TGG + tig0023091:61704-61723 None:intergenic 40.0%
GGTATGGAGTGGCACATTAA+CGG - tig0023091:60987-61006 Msa1404850:CDS 45.0%
AGTGGCACATTAACGGTTTG+TGG - tig0023091:60994-61013 Msa1404850:CDS 45.0%
GTTTGTGGTGACACTCAACT+TGG - tig0023091:61009-61028 Msa1404850:CDS 45.0%
CTCTCAGGACAGTTTGTATC+GGG + tig0023091:61237-61256 None:intergenic 45.0%
AAAGCTTGTGCGGAATTCAC+GGG + tig0023091:61312-61331 None:intergenic 45.0%
! GCTTTATTGTGATTGGCTGC+TGG - tig0023091:61327-61346 Msa1404850:intron 45.0%
! TGATTGGCTGCTGGTGATTT+CGG - tig0023091:61336-61355 Msa1404850:intron 45.0%
TGGTGATTTCGGGATAAGCT+CGG - tig0023091:61347-61366 Msa1404850:intron 45.0%
! AAGCTCGGGACGTTTTCTTT+CGG - tig0023091:61362-61381 Msa1404850:intron 45.0%
CACTCTGGTAAGTTAGATGC+TGG - tig0023091:61485-61504 Msa1404850:intron 45.0%
TAAATCGGTCGCCTCATGAT+TGG - tig0023091:61660-61679 Msa1404850:intron 45.0%
GGTATGGAGTGGCACATTAA+CGG - tig0023091:60987-61006 Msa1404850:CDS 45.0%
AGTGGCACATTAACGGTTTG+TGG - tig0023091:60994-61013 Msa1404850:CDS 45.0%
GTTTGTGGTGACACTCAACT+TGG - tig0023091:61009-61028 Msa1404850:CDS 45.0%
CTCTCAGGACAGTTTGTATC+GGG + tig0023091:61237-61256 None:intergenic 45.0%
AAAGCTTGTGCGGAATTCAC+GGG + tig0023091:61312-61331 None:intergenic 45.0%
! GCTTTATTGTGATTGGCTGC+TGG - tig0023091:61327-61346 Msa1404850:intron 45.0%
! TGATTGGCTGCTGGTGATTT+CGG - tig0023091:61336-61355 Msa1404850:intron 45.0%
TGGTGATTTCGGGATAAGCT+CGG - tig0023091:61347-61366 Msa1404850:intron 45.0%
! AAGCTCGGGACGTTTTCTTT+CGG - tig0023091:61362-61381 Msa1404850:intron 45.0%
CACTCTGGTAAGTTAGATGC+TGG - tig0023091:61485-61504 Msa1404850:intron 45.0%
TAAATCGGTCGCCTCATGAT+TGG - tig0023091:61660-61679 Msa1404850:intron 45.0%
ATAGCCTTCGGGAATCTCTC+AGG + tig0023091:61252-61271 None:intergenic 50.0%
CGGGAGAGAGAGGGATAAAA+CGG + tig0023091:61293-61312 None:intergenic 50.0%
! GATTGGCTGCTGGTGATTTC+GGG - tig0023091:61337-61356 Msa1404850:intron 50.0%
GGTGATTTCGGGATAAGCTC+GGG - tig0023091:61348-61367 Msa1404850:intron 50.0%
! AGCTCGGGACGTTTTCTTTC+GGG - tig0023091:61363-61382 Msa1404850:intron 50.0%
! TCTGGCTCATCCCCATCAAA+AGG + tig0023091:61416-61435 None:intergenic 50.0%
! TTTGCTGTCGTCACTCACTC+TGG - tig0023091:61470-61489 Msa1404850:intron 50.0%
AAACATTGTGAGGGCTGCTC+AGG - tig0023091:61583-61602 Msa1404850:intron 50.0%
AACATTGTGAGGGCTGCTCA+GGG - tig0023091:61584-61603 Msa1404850:intron 50.0%
CATCTCCTGTGCCAATCATG+AGG + tig0023091:61674-61693 None:intergenic 50.0%
CTCATGATTGGCACAGGAGA+TGG - tig0023091:61672-61691 Msa1404850:intron 50.0%
CAGGAGATGGTCCAAACCAT+TGG - tig0023091:61685-61704 Msa1404850:intron 50.0%
ATAGCCTTCGGGAATCTCTC+AGG + tig0023091:61252-61271 None:intergenic 50.0%
CGGGAGAGAGAGGGATAAAA+CGG + tig0023091:61293-61312 None:intergenic 50.0%
! GATTGGCTGCTGGTGATTTC+GGG - tig0023091:61337-61356 Msa1404850:intron 50.0%
GGTGATTTCGGGATAAGCTC+GGG - tig0023091:61348-61367 Msa1404850:intron 50.0%
! AGCTCGGGACGTTTTCTTTC+GGG - tig0023091:61363-61382 Msa1404850:intron 50.0%
! TCTGGCTCATCCCCATCAAA+AGG + tig0023091:61416-61435 None:intergenic 50.0%
! TTTGCTGTCGTCACTCACTC+TGG - tig0023091:61470-61489 Msa1404850:intron 50.0%
AAACATTGTGAGGGCTGCTC+AGG - tig0023091:61583-61602 Msa1404850:intron 50.0%
AACATTGTGAGGGCTGCTCA+GGG - tig0023091:61584-61603 Msa1404850:intron 50.0%
CATCTCCTGTGCCAATCATG+AGG + tig0023091:61674-61693 None:intergenic 50.0%
CTCATGATTGGCACAGGAGA+TGG - tig0023091:61672-61691 Msa1404850:intron 50.0%
CAGGAGATGGTCCAAACCAT+TGG - tig0023091:61685-61704 Msa1404850:intron 50.0%
CTGTCCTGAGAGATTCCCGA+AGG - tig0023091:61245-61264 Msa1404850:CDS 55.0%
CGGAATTCACGGGAGAGAGA+GGG + tig0023091:61302-61321 None:intergenic 55.0%
CTGTCCTGAGAGATTCCCGA+AGG - tig0023091:61245-61264 Msa1404850:CDS 55.0%
CGGAATTCACGGGAGAGAGA+GGG + tig0023091:61302-61321 None:intergenic 55.0%
GCGGAATTCACGGGAGAGAG+AGG + tig0023091:61303-61322 None:intergenic 60.0%
GGTCGCCTCATGATTGGCAC+AGG - tig0023091:61666-61685 Msa1404850:intron 60.0%
GCGGAATTCACGGGAGAGAG+AGG + tig0023091:61303-61322 None:intergenic 60.0%
GGTCGCCTCATGATTGGCAC+AGG - tig0023091:61666-61685 Msa1404850:intron 60.0%
Chromosome Type Strat End Strand Name
tig0023091 gene 60917 61757 60917 ID=Msa1404850;Name=Msa1404850
tig0023091 mRNA 60917 61757 60917 ID=Msa1404850-mRNA-1;Parent=Msa1404850;Name=Msa1404850-mRNA-1;_AED=0.54;_eAED=0.54;_QI=0|0|0|0.5|0|0|2|0|124
tig0023091 exon 61747 61757 61747 ID=Msa1404850-mRNA-1:exon:23843;Parent=Msa1404850-mRNA-1
tig0023091 exon 60917 61280 60917 ID=Msa1404850-mRNA-1:exon:23842;Parent=Msa1404850-mRNA-1
tig0023091 CDS 61747 61757 61747 ID=Msa1404850-mRNA-1:cds;Parent=Msa1404850-mRNA-1
tig0023091 CDS 60917 61280 60917 ID=Msa1404850-mRNA-1:cds;Parent=Msa1404850-mRNA-1
Gene Sequence

>Msa1404850

ATGGTAAAGAGCACAGCTGATAGAATATTTCCTTTTGATGGGGATGAGCCAGATGCTTCAAATGATCCATGTTCTGAGTTTGAATTGTTTGCTGTCGTCACTCACTCTGGTAAGTTAGATGCTGGTCATTATGTGACATATCTGCGATTAAGCAATCAATGGTACAAGTGTGATGATTCTTGGGTTACTCAAGTTGATGAAAACATTGTGAGGGCTGCTCAGGGTTACATGATGTTCTATGTACAGAAGATGCTTTACTATAAAGCAAAGCAACTGATAAATCGGTCGCCTCATGATTGGCACAGGAGATGGTCCAAACCATTGGCATCATATGTCATGGTCAATATCAGTTTTCACCCTAATGATATGCCATGA

Protein sequence

>Msa1404850

MVKSTADRIFPFDGDEPDASNDPCSEFELFAVVTHSGKLDAGHYVTYLRLSNQWYKCDDSWVTQVDENIVRAAQGYMMFYVQKMLYYKAKQLINRSPHDWHRRWSKPLASYVMVNISFHPNDMP*