AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1161190

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1161190 MtrunA17_Chr7g0255511 90.598 234 18 2 1 230 1 234 7.61e-150 416
Msa1161190 MtrunA17_Chr7g0225091 80.342 234 28 3 1 230 1 220 2.72e-131 369
Msa1161190 MtrunA17_Chr7g0225121 77.350 234 27 3 1 230 1 212 6.05e-126 355
Msa1161190 MtrunA17_Chr7g0222361 79.208 202 40 2 31 230 1 202 1.64e-117 333
Msa1161190 MtrunA17_Chr7g0222371 76.033 121 24 3 19 134 1 121 5.24e-62 190
Msa1161190 MtrunA17_Chr1g0149811 33.140 172 96 6 76 230 93 262 1.65e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1161190 AT1G66140.1 29.121 182 99 4 76 230 82 260 4.56e-11 61.2

Find 45 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATATATTAATTAAAGCTTA+AGG 0.307958 7_4:-51421999 None:intergenic
AAGAAATGGAGAAATTTCTT+TGG 0.320928 7_4:-51421485 None:intergenic
TCCAAGCATTGTTAAAAGCT+TGG 0.375606 7_4:-51421651 None:intergenic
CTTAAGGGTCAAATCAATCT+TGG 0.381650 7_4:-51421983 None:intergenic
CACCATCTCTCCATTCCATA+TGG 0.384400 7_4:+51421711 Msa1161190:CDS
ATTGATATCCACACCCCATA+TGG 0.402297 7_4:-51421726 None:intergenic
AGAAATTTCTTTGGAAGAAT+CGG 0.402846 7_4:-51421476 None:intergenic
ATATATTAATTAAAGCTTAA+GGG 0.407582 7_4:-51421998 None:intergenic
AATTACTCAAATGGTGATCA+AGG 0.411277 7_4:+51421676 Msa1161190:CDS
CTCCTTCCCCTTGTTACACA+TGG 0.419504 7_4:-51421317 None:intergenic
AACAATATGATTCAGCATGC+AGG 0.425567 7_4:+51421760 Msa1161190:CDS
GCTTGGATAAATTACTCAAA+TGG 0.450589 7_4:+51421667 Msa1161190:CDS
AGTAGCCAATTTGAAGATGA+TGG 0.452167 7_4:+51421357 Msa1161190:CDS
TGTTAGTGATGAAGTTGATC+AGG 0.458285 7_4:+51421930 Msa1161190:CDS
ATGTTGAAACTCAGAATTCA+AGG 0.460149 7_4:+51421422 Msa1161190:CDS
AATATGTCTGAGATTGAAGT+TGG 0.464395 7_4:+51421886 Msa1161190:CDS
ACCATCTCTCCATTCCATAT+GGG 0.464694 7_4:+51421712 Msa1161190:CDS
TTCACTAGTCCACAGGCATT+AGG 0.474635 7_4:+51421580 Msa1161190:CDS
TTGGATTCATTGTTGATCAC+AGG 0.479894 7_4:+51421512 Msa1161190:CDS
CTCTGATGCCATGTGTAACA+AGG 0.493194 7_4:+51421309 None:intergenic
CAAGAGAAAGGCAATCGTGC+TGG 0.504921 7_4:+51421390 Msa1161190:CDS
TCACAGGAAAGGAATTCAAA+AGG 0.505285 7_4:+51421528 Msa1161190:CDS
TGAAGTTGGTTCAGTTTCAG+AGG 0.508093 7_4:+51421900 Msa1161190:CDS
TCTCCATTCCATATGGGGTG+TGG 0.536840 7_4:+51421718 Msa1161190:CDS
GGAAAATCAGAACAAGAGAA+AGG 0.539450 7_4:+51421378 Msa1161190:CDS
TTCATTGTTGATCACAGGAA+AGG 0.555662 7_4:+51421517 Msa1161190:CDS
ACAATATGATTCAGCATGCA+GGG 0.561522 7_4:+51421761 Msa1161190:CDS
CCCCATATGGAATGGAGAGA+TGG 0.561790 7_4:-51421713 None:intergenic
GGGTGTGGATATCAATATTG+TGG 0.571463 7_4:+51421733 Msa1161190:CDS
GTTGGTTCAGTTTCAGAGGG+AGG 0.572183 7_4:+51421904 Msa1161190:CDS
CAGAAAGTTCACTAGTCCAC+AGG 0.575345 7_4:+51421573 Msa1161190:CDS
GTGTAACAAGGGGAAGGAGA+AGG 0.590077 7_4:+51421321 Msa1161190:CDS
GAAGTTGGTTCAGTTTCAGA+GGG 0.592457 7_4:+51421901 Msa1161190:CDS
TATCCACACCCCATATGGAA+TGG 0.594771 7_4:-51421721 None:intergenic
TTGAATTCTGAGTTTCAACA+TGG 0.596792 7_4:-51421420 None:intergenic
CCATCTCTCCATTCCATATG+GGG 0.598148 7_4:+51421713 Msa1161190:CDS
ATTACTCAAATGGTGATCAA+GGG 0.605537 7_4:+51421677 Msa1161190:CDS
TGCCATGTGTAACAAGGGGA+AGG 0.606759 7_4:+51421315 None:intergenic
TCTGATGCCATGTGTAACAA+GGG 0.620861 7_4:+51421310 None:intergenic
GGAAGACAAAGAGACTCAAG+AGG 0.634668 7_4:+51421951 Msa1161190:CDS
TGATGACCACCTAATGCCTG+TGG 0.637178 7_4:-51421589 None:intergenic
TGAATTCTGAGTTTCAACAT+GGG 0.637539 7_4:-51421419 None:intergenic
CTGATGCCATGTGTAACAAG+GGG 0.655959 7_4:+51421311 None:intergenic
ACTAGTCCACAGGCATTAGG+TGG 0.661075 7_4:+51421583 Msa1161190:CDS
AGACAAAGAGACTCAAGAGG+AGG 0.673262 7_4:+51421954 Msa1161190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTTCCATCATCTTCAAAT+TGG - chr7_4:51421365-51421384 None:intergenic 25.0%
!! TTCTTCTTCAACATCTTTTT+GGG - chr7_4:51421452-51421471 None:intergenic 25.0%
!! ATTCTTCTTCAACATCTTTT+TGG - chr7_4:51421453-51421472 None:intergenic 25.0%
!! AGAAATTTCTTTGGAAGAAT+CGG - chr7_4:51421479-51421498 None:intergenic 25.0%
! AAGAAATGGAGAAATTTCTT+TGG - chr7_4:51421488-51421507 None:intergenic 25.0%
!! ATTTCTCCATTTCTTCTTTT+TGG + chr7_4:51421493-51421512 Msa1161190:CDS 25.0%
! ATGAATCCAAAAAGAAGAAA+TGG - chr7_4:51421502-51421521 None:intergenic 25.0%
TGAATTCTGAGTTTCAACAT+GGG - chr7_4:51421422-51421441 None:intergenic 30.0%
TTGAATTCTGAGTTTCAACA+TGG - chr7_4:51421423-51421442 None:intergenic 30.0%
ATGTTGAAACTCAGAATTCA+AGG + chr7_4:51421422-51421441 Msa1161190:CDS 30.0%
! TCTTCTTCAACATCTTTTTG+GGG - chr7_4:51421451-51421470 None:intergenic 30.0%
TAGAGAGAAGTCTCAAAAAA+AGG + chr7_4:51421626-51421645 Msa1161190:CDS 30.0%
GCTTGGATAAATTACTCAAA+TGG + chr7_4:51421667-51421686 Msa1161190:CDS 30.0%
AATTACTCAAATGGTGATCA+AGG + chr7_4:51421676-51421695 Msa1161190:CDS 30.0%
ATTACTCAAATGGTGATCAA+GGG + chr7_4:51421677-51421696 Msa1161190:CDS 30.0%
! TTTTATGCAGGGAATTTGTA+TGG + chr7_4:51421793-51421812 Msa1161190:CDS 30.0%
! AATATGTCTGAGATTGAAGT+TGG + chr7_4:51421886-51421905 Msa1161190:CDS 30.0%
AGTAGCCAATTTGAAGATGA+TGG + chr7_4:51421357-51421376 Msa1161190:CDS 35.0%
GGAAAATCAGAACAAGAGAA+AGG + chr7_4:51421378-51421397 Msa1161190:CDS 35.0%
TTGGATTCATTGTTGATCAC+AGG + chr7_4:51421512-51421531 Msa1161190:CDS 35.0%
TTCATTGTTGATCACAGGAA+AGG + chr7_4:51421517-51421536 Msa1161190:CDS 35.0%
TCACAGGAAAGGAATTCAAA+AGG + chr7_4:51421528-51421547 Msa1161190:CDS 35.0%
! TCCAAGCTTTTAACAATGCT+TGG + chr7_4:51421650-51421669 Msa1161190:CDS 35.0%
! TCCAAGCATTGTTAAAAGCT+TGG - chr7_4:51421654-51421673 None:intergenic 35.0%
AACAATATGATTCAGCATGC+AGG + chr7_4:51421760-51421779 Msa1161190:CDS 35.0%
ACAATATGATTCAGCATGCA+GGG + chr7_4:51421761-51421780 Msa1161190:CDS 35.0%
! GGTCATCAAACTTTTATGCA+GGG + chr7_4:51421782-51421801 Msa1161190:CDS 35.0%
! TGTTAGTGATGAAGTTGATC+AGG + chr7_4:51421930-51421949 Msa1161190:CDS 35.0%
CTTAAGGGTCAAATCAATCT+TGG - chr7_4:51421986-51422005 None:intergenic 35.0%
ACCATCTCTCCATTCCATAT+GGG + chr7_4:51421712-51421731 Msa1161190:CDS 40.0%
ATTGATATCCACACCCCATA+TGG - chr7_4:51421729-51421748 None:intergenic 40.0%
GGGTGTGGATATCAATATTG+TGG + chr7_4:51421733-51421752 Msa1161190:CDS 40.0%
! GGGTCATCAAACTTTTATGC+AGG + chr7_4:51421781-51421800 Msa1161190:CDS 40.0%
! TGAAGTTGGTTCAGTTTCAG+AGG + chr7_4:51421900-51421919 Msa1161190:CDS 40.0%
! GAAGTTGGTTCAGTTTCAGA+GGG + chr7_4:51421901-51421920 Msa1161190:CDS 40.0%
CAGAAAGTTCACTAGTCCAC+AGG + chr7_4:51421573-51421592 Msa1161190:CDS 45.0%
TTCACTAGTCCACAGGCATT+AGG + chr7_4:51421580-51421599 Msa1161190:CDS 45.0%
CACCATCTCTCCATTCCATA+TGG + chr7_4:51421711-51421730 Msa1161190:CDS 45.0%
CCATCTCTCCATTCCATATG+GGG + chr7_4:51421713-51421732 Msa1161190:CDS 45.0%
TATCCACACCCCATATGGAA+TGG - chr7_4:51421724-51421743 None:intergenic 45.0%
GGAAGACAAAGAGACTCAAG+AGG + chr7_4:51421951-51421970 Msa1161190:CDS 45.0%
AGACAAAGAGACTCAAGAGG+AGG + chr7_4:51421954-51421973 Msa1161190:CDS 45.0%
GTGTAACAAGGGGAAGGAGA+AGG + chr7_4:51421321-51421340 Msa1161190:CDS 50.0%
CAAGAGAAAGGCAATCGTGC+TGG + chr7_4:51421390-51421409 Msa1161190:CDS 50.0%
ACTAGTCCACAGGCATTAGG+TGG + chr7_4:51421583-51421602 Msa1161190:CDS 50.0%
TGATGACCACCTAATGCCTG+TGG - chr7_4:51421592-51421611 None:intergenic 50.0%
CCCCATATGGAATGGAGAGA+TGG - chr7_4:51421716-51421735 None:intergenic 50.0%
TCTCCATTCCATATGGGGTG+TGG + chr7_4:51421718-51421737 Msa1161190:CDS 50.0%
! GTTGGTTCAGTTTCAGAGGG+AGG + chr7_4:51421904-51421923 Msa1161190:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 51421319 51422011 51421319 ID=Msa1161190;Name=Msa1161190
chr7_4 mRNA 51421319 51422011 51421319 ID=Msa1161190-mRNA-1;Parent=Msa1161190;Name=Msa1161190-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|230
chr7_4 exon 51421319 51422011 51421319 ID=Msa1161190-mRNA-1:exon:14512;Parent=Msa1161190-mRNA-1
chr7_4 CDS 51421319 51422011 51421319 ID=Msa1161190-mRNA-1:cds;Parent=Msa1161190-mRNA-1
Gene Sequence

>Msa1161190

ATGTGTAACAAGGGGAAGGAGAAGGTGAATGAAGAATCAGTAGCCAATTTGAAGATGATGGAAAATCAGAACAAGAGAAAGGCAATCGTGCTGGAAGAATCCCATGTTGAAACTCAGAATTCAAGGACTCCCCAAAAAGATGTTGAAGAAGAATCAACCGATTCTTCCAAAGAAATTTCTCCATTTCTTCTTTTTGGATTCATTGTTGATCACAGGAAAGGAATTCAAAAGGCTTACTCGTGCAAATTTTGTAGCAGAAAGTTCACTAGTCCACAGGCATTAGGTGGTCATCAAAATTCTCACAAATTAGAGAGAAGTCTCAAAAAAAGGATCCAAGCTTTTAACAATGCTTGGATAAATTACTCAAATGGTGATCAAGGGATAAGTCTAAACACCATCTCTCCATTCCATATGGGGTGTGGATATCAATATTGTGGATTTAACAATATGATTCAGCATGCAGGGTCATCAAACTTTTATGCAGGGAATTTGTATGGTGCATTGCAGCATATTTCAGAGATAGATGAAGCAGATGAAGCTAATCAAAGCATAATGAGTCAAAAAGTTAATATGTCTGAGATTGAAGTTGGTTCAGTTTCAGAGGGAGGAGCTGTTAGTGATGAAGTTGATCAGGAAGACAAAGAGACTCAAGAGGAGGAAGCAACCAAGATTGATTTGACCCTTAAGCTTTAA
Protein sequence

>Msa1161190

MCNKGKEKVNEESVANLKMMENQNKRKAIVLEESHVETQNSRTPQKDVEEESTDSSKEISPFLLFGFIVDHRKGIQKAYSCKFCSRKFTSPQALGGHQNSHKLERSLKKRIQAFNNAWINYSNGDQGISLNTISPFHMGCGYQYCGFNNMIQHAGSSNFYAGNLYGALQHISEIDEADEANQSIMSQKVNMSEIEVGSVSEGGAVSDEVDQEDKETQEEEATKIDLTLKL*