AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40882


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40882.t1 MTR_1g083350 92.857 168 2 1 1 158 1 168 2.29e-110 311
MS.gene40882.t1 MTR_1g083380 92.262 168 3 1 1 158 1 168 2.48e-109 308
MS.gene40882.t1 MTR_2g436620 80.357 168 22 2 1 158 1 167 1.39e-92 266
MS.gene40882.t1 MTR_1g083340 84.713 157 4 2 1 137 1 157 1.51e-87 253
MS.gene40882.t1 MTR_6g071090 75.776 161 28 2 1 151 1 160 3.57e-80 234
MS.gene40882.t1 MTR_2g436620 78.169 142 20 2 27 158 1 141 1.31e-73 217
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40882.t1 AT3G16640 72.619 168 36 1 1 158 1 168 1.07e-85 248
MS.gene40882.t1 AT3G05540 75.740 169 29 3 1 158 1 168 3.79e-79 232

Find 38 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTGTAGGTCTTTGAGTTT+AGG 0.257674 1.4:+67425779 None:intergenic
ATTGTAGGTCTTTGAGTTTA+GGG 0.290821 1.4:+67425780 None:intergenic
CGCAACCATGCTTGTTTACC+AGG 0.349778 1.4:-67427015 None:intergenic
GATGAAACACATACAATTGT+AGG 0.370851 1.4:+67425765 None:intergenic
CTACTTTGCCTATGGCTTGA+AGG 0.378916 1.4:-67425566 MS.gene40882:CDS
GTTTACCAGGATCTTCTTAC+GGG 0.390880 1.4:-67427002 MS.gene40882:intron
TGTTTACCAGGATCTTCTTA+CGG 0.395300 1.4:-67427003 MS.gene40882:CDS
CCATTCTGAATTTCCTTGTA+GGG 0.421805 1.4:+67426214 None:intergenic
TCCATTCTGAATTTCCTTGT+AGG 0.427172 1.4:+67426213 None:intergenic
AATTGCTTCTTATCAAAAGC+TGG 0.428621 1.4:+67425908 None:intergenic
GAATGGAATGTTGTGGGAAG+TGG 0.443613 1.4:-67426197 MS.gene40882:CDS
CCTTGTGTTTGCTTACTACA+AGG 0.455642 1.4:-67425614 MS.gene40882:CDS
TAGGCAAAGTAGAGAAAAGT+TGG 0.474181 1.4:+67425577 None:intergenic
TATTTGCAGTGGGTTGTTCA+AGG 0.483236 1.4:-67426052 MS.gene40882:intron
CTCTGACTCATTCCCCTACA+AGG 0.486361 1.4:-67426227 MS.gene40882:CDS
GGTCTTTGAGTTTAGGGAGA+AGG 0.500494 1.4:+67425786 None:intergenic
GGAGCAGTGGATGTGAATAT+TGG 0.501116 1.4:-67426031 MS.gene40882:CDS
GGTGCTAACCCTTCTGCTGA+GGG 0.509671 1.4:-67426010 MS.gene40882:CDS
CTTGATTTCCTTCAAGCCAT+AGG 0.517168 1.4:+67425558 None:intergenic
AATTCAGAATGGAATGTTGT+GGG 0.534489 1.4:-67426203 MS.gene40882:CDS
TCGTCACCACCCTCAGCAGA+AGG 0.538139 1.4:+67426001 None:intergenic
GTGTTTGCTTACTACAAGGA+TGG 0.538874 1.4:-67425610 MS.gene40882:CDS
CCCTACAAGGAAATTCAGAA+TGG 0.541188 1.4:-67426214 MS.gene40882:CDS
CATTCTGAATTTCCTTGTAG+GGG 0.549656 1.4:+67426215 None:intergenic
TGGTGCTAACCCTTCTGCTG+AGG 0.553542 1.4:-67426011 MS.gene40882:CDS
GTTGTGGGAAGTGGAAGGAA+AGG 0.560660 1.4:-67426188 MS.gene40882:intron
GTTTACCCGTAAGAAGATCC+TGG 0.562606 1.4:+67426997 None:intergenic
GGGGAGAGCATGCATGATGA+TGG 0.565967 1.4:-67425640 MS.gene40882:CDS
AAATTCAGAATGGAATGTTG+TGG 0.574500 1.4:-67426204 MS.gene40882:CDS
TTCTGCTGAGGGTGGTGACG+AGG 0.592413 1.4:-67425999 MS.gene40882:CDS
AAGATCCTGGTAAACAAGCA+TGG 0.602746 1.4:+67427010 None:intergenic
GTAGAGAAAAGTTGGATCAG+TGG 0.605758 1.4:+67425585 None:intergenic
GCTAACCCTTCTGCTGAGGG+TGG 0.615863 1.4:-67426007 MS.gene40882:CDS
CGTCACCACCCTCAGCAGAA+GGG 0.628440 1.4:+67426002 None:intergenic
CCTTGTAGTAAGCAAACACA+AGG 0.635355 1.4:+67425614 None:intergenic
GTGGGTTGTTCAAGGAGCAG+TGG 0.636439 1.4:-67426044 MS.gene40882:CDS
GAGGGTGGTGACGAGGATGA+CGG 0.661706 1.4:-67425992 MS.gene40882:CDS
GGAATGTTGTGGGAAGTGGA+AGG 0.687071 1.4:-67426193 MS.gene40882:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATTTATGATCATATATT+TGG + chr1.4:67426459-67426478 None:intergenic 10.0%
!!! TTTAATTTAATAGAATTTGT+TGG - chr1.4:67426040-67426059 MS.gene40882:CDS 10.0%
!! AAAACAAAAATTCATTCAAA+TGG - chr1.4:67426257-67426276 MS.gene40882:intron 15.0%
!!! TTATATATTAACCTTTTGTA+AGG - chr1.4:67425829-67425848 MS.gene40882:CDS 15.0%
!! AAAAGTAAAAGAAACCTAAT+TGG + chr1.4:67425624-67425643 None:intergenic 20.0%
!! AAAGTAAAAGAAACCTAATT+GGG + chr1.4:67425623-67425642 None:intergenic 20.0%
!! GATAATAATGAAAAACCTAA+AGG + chr1.4:67426014-67426033 None:intergenic 20.0%
!! TAATCTTAAATATTAGTAGC+AGG + chr1.4:67426207-67426226 None:intergenic 20.0%
!! TTATCATTCATCGTAATATT+TGG + chr1.4:67425702-67425721 None:intergenic 20.0%
!!! ACAAGGTTAAAATACTTTTT+TGG - chr1.4:67425895-67425914 MS.gene40882:CDS 20.0%
!!! ATTAAGTTTTCTCTTTTTTG+TGG - chr1.4:67426845-67426864 MS.gene40882:intron 20.0%
!!! ATTATCTTTCATCTCTTTTT+TGG - chr1.4:67426818-67426837 MS.gene40882:intron 20.0%
!!! GTTTTTTTTTTTTTGACACA+AGG - chr1.4:67425878-67425897 MS.gene40882:CDS 20.0%
!!! TTTTACATAAACTTCACTTT+TGG - chr1.4:67425777-67425796 MS.gene40882:intron 20.0%
! AAAATCCTCAATCAAGTATT+AGG + chr1.4:67426167-67426186 None:intergenic 25.0%
! AAATATTACTTAGCAGTTTG+TGG + chr1.4:67426118-67426137 None:intergenic 25.0%
! AAATTCATTCACTAAACACA+GGG + chr1.4:67425734-67425753 None:intergenic 25.0%
! AATCTTAACAACCTTACAAA+AGG + chr1.4:67425843-67425862 None:intergenic 25.0%
! ACTATTATAGATCAAACTTG+TGG - chr1.4:67425949-67425968 MS.gene40882:intron 25.0%
! CAAAATCCTATGAAAAACAA+TGG + chr1.4:67425649-67425668 None:intergenic 25.0%
! TGGAAAACCTTAAATTTCTT+GGG - chr1.4:67425915-67425934 MS.gene40882:CDS 25.0%
! TTGGAAAACCTTAAATTTCT+TGG - chr1.4:67425914-67425933 MS.gene40882:CDS 25.0%
!!! TTTTCTCCATTGTTTTTCAT+AGG - chr1.4:67425640-67425659 MS.gene40882:CDS 25.0%
AAATTCAGAATGGAATGTTG+TGG - chr1.4:67426356-67426375 MS.gene40882:intron 30.0%
AATTCAGAATGGAATGTTGT+GGG - chr1.4:67426357-67426376 MS.gene40882:intron 30.0%
AATTGCTTCTTATCAAAAGC+TGG + chr1.4:67426655-67426674 None:intergenic 30.0%
ACAAAAAACTCAAAGATGCA+AGG + chr1.4:67425588-67425607 None:intergenic 30.0%
CACATCACACAATAAACTTT+AGG + chr1.4:67426486-67426505 None:intergenic 30.0%
GAAATTCATTCACTAAACAC+AGG + chr1.4:67425735-67425754 None:intergenic 30.0%
GATCTATAATAGTGTGTGTT+TGG + chr1.4:67425942-67425961 None:intergenic 30.0%
GATGAAACACATACAATTGT+AGG + chr1.4:67426798-67426817 None:intergenic 30.0%
! AATTGTAGGTCTTTGAGTTT+AGG + chr1.4:67426784-67426803 None:intergenic 30.0%
! ATTGTAGGTCTTTGAGTTTA+GGG + chr1.4:67426783-67426802 None:intergenic 30.0%
! CTTTGTTGATGAATTTGTCT+AGG - chr1.4:67426298-67426317 MS.gene40882:intron 30.0%
! TTTTACTTTACCACCCAATT+AGG - chr1.4:67425607-67425626 MS.gene40882:CDS 30.0%
!! AGTTTTATGTTTGTGTTCTG+TGG - chr1.4:67425983-67426002 MS.gene40882:CDS 30.0%
!!! ATCAATGTTGCAGTTTTGTT+GGG - chr1.4:67426900-67426919 MS.gene40882:intron 30.0%
CATTCTGAATTTCCTTGTAG+GGG + chr1.4:67426348-67426367 None:intergenic 35.0%
CCATTCTGAATTTCCTTGTA+GGG + chr1.4:67426349-67426368 None:intergenic 35.0%
CCTAACCTAATACTTGATTG+AGG - chr1.4:67426159-67426178 MS.gene40882:intron 35.0%
CCTCAATCAAGTATTAGGTT+AGG + chr1.4:67426162-67426181 None:intergenic 35.0%
GTAAAAGAAACCTAATTGGG+TGG + chr1.4:67425620-67425639 None:intergenic 35.0%
GTGATGTGATTATTTGCAGT+GGG - chr1.4:67426498-67426517 MS.gene40882:intron 35.0%
GTTAGGCTAATCGTGTTTAA+GGG + chr1.4:67426145-67426164 None:intergenic 35.0%
GTTTGGTCCCAAGAAATTTA+AGG + chr1.4:67425925-67425944 None:intergenic 35.0%
TAGGCAAAGTAGAGAAAAGT+TGG + chr1.4:67426986-67427005 None:intergenic 35.0%
TCCATTCTGAATTTCCTTGT+AGG + chr1.4:67426350-67426369 None:intergenic 35.0%
TGTGATGTGATTATTTGCAG+TGG - chr1.4:67426497-67426516 MS.gene40882:intron 35.0%
TGTTCTGTGGTTTAACCTTT+AGG - chr1.4:67425996-67426015 MS.gene40882:CDS 35.0%
TGTTTACCAGGATCTTCTTA+CGG - chr1.4:67425557-67425576 MS.gene40882:CDS 35.0%
TTGACATTGTTGACACTTTC+AGG - chr1.4:67426617-67426636 MS.gene40882:intron 35.0%
! ACTTTTCTCTACTTTGCCTA+TGG - chr1.4:67426986-67427005 MS.gene40882:intron 35.0%
!! CATCAATGTTGCAGTTTTGT+TGG - chr1.4:67426899-67426918 MS.gene40882:intron 35.0%
!! TTGAACAACTCTTGCTTTTC+TGG + chr1.4:67426727-67426746 None:intergenic 35.0%
!!! TCAATGTTGCAGTTTTGTTG+GGG - chr1.4:67426901-67426920 MS.gene40882:intron 35.0%
AGTTGTTGTGTTTGTGACAG+AGG - chr1.4:67426074-67426093 MS.gene40882:intron 40.0%
CCCTACAAGGAAATTCAGAA+TGG - chr1.4:67426346-67426365 MS.gene40882:intron 40.0%
CCTTGTAGTAAGCAAACACA+AGG + chr1.4:67426949-67426968 None:intergenic 40.0%
CCTTGTGTTTGCTTACTACA+AGG - chr1.4:67426946-67426965 MS.gene40882:intron 40.0%
CTTGATTTCCTTCAAGCCAT+AGG + chr1.4:67427005-67427024 None:intergenic 40.0%
GGTTAGGCTAATCGTGTTTA+AGG + chr1.4:67426146-67426165 None:intergenic 40.0%
GTAGAGAAAAGTTGGATCAG+TGG + chr1.4:67426978-67426997 None:intergenic 40.0%
GTGTTTGCTTACTACAAGGA+TGG - chr1.4:67426950-67426969 MS.gene40882:intron 40.0%
GTTTACCAGGATCTTCTTAC+GGG - chr1.4:67425558-67425577 MS.gene40882:CDS 40.0%
!! TATTTGCAGTGGGTTGTTCA+AGG - chr1.4:67426508-67426527 MS.gene40882:intron 40.0%
CTACTTTGCCTATGGCTTGA+AGG - chr1.4:67426994-67427013 MS.gene40882:intron 45.0%
GAATGGAATGTTGTGGGAAG+TGG - chr1.4:67426363-67426382 MS.gene40882:intron 45.0%
GGAGCAGTGGATGTGAATAT+TGG - chr1.4:67426529-67426548 MS.gene40882:intron 45.0%
GTTTACCCGTAAGAAGATCC+TGG + chr1.4:67425566-67425585 None:intergenic 45.0%
TGTTGACACTTTCAGGCTTC+AGG - chr1.4:67426624-67426643 MS.gene40882:intron 45.0%
! GGTCTTTGAGTTTAGGGAGA+AGG + chr1.4:67426777-67426796 None:intergenic 45.0%
!!! ATTCTATTAAATTAAAATTT+TGG + chr1.4:67426036-67426055 None:intergenic 5.0%
CTCTGACTCATTCCCCTACA+AGG - chr1.4:67426333-67426352 MS.gene40882:intron 50.0%
GGAATGTTGTGGGAAGTGGA+AGG - chr1.4:67426367-67426386 MS.gene40882:intron 50.0%
GGGAAGTGGAAGGAAAGGTT+TGG - chr1.4:67426377-67426396 MS.gene40882:intron 50.0%
GTTGTGGGAAGTGGAAGGAA+AGG - chr1.4:67426372-67426391 MS.gene40882:intron 50.0%
GGTGCTAACCCTTCTGCTGA+GGG - chr1.4:67426550-67426569 MS.gene40882:intron 55.0%
! GGGGAGAGCATGCATGATGA+TGG - chr1.4:67426920-67426939 MS.gene40882:intron 55.0%
! GTGGGTTGTTCAAGGAGCAG+TGG - chr1.4:67426516-67426535 MS.gene40882:intron 55.0%
! TGGTGCTAACCCTTCTGCTG+AGG - chr1.4:67426549-67426568 MS.gene40882:intron 55.0%
CGTCACCACCCTCAGCAGAA+GGG + chr1.4:67426561-67426580 None:intergenic 60.0%
GCTAACCCTTCTGCTGAGGG+TGG - chr1.4:67426553-67426572 MS.gene40882:intron 60.0%
TCGTCACCACCCTCAGCAGA+AGG + chr1.4:67426562-67426581 None:intergenic 60.0%
! GAGGGTGGTGACGAGGATGA+CGG - chr1.4:67426568-67426587 MS.gene40882:intron 60.0%
! TTCTGCTGAGGGTGGTGACG+AGG - chr1.4:67426561-67426580 MS.gene40882:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 67425552 67427030 67425552 ID=MS.gene40882
chr1.4 mRNA 67425552 67427030 67425552 ID=MS.gene40882.t1;Parent=MS.gene40882
chr1.4 exon 67427003 67427030 67427003 ID=MS.gene40882.t1.exon1;Parent=MS.gene40882.t1
chr1.4 CDS 67427003 67427030 67427003 ID=cds.MS.gene40882.t1;Parent=MS.gene40882.t1
chr1.4 exon 67426189 67426262 67426189 ID=MS.gene40882.t1.exon2;Parent=MS.gene40882.t1
chr1.4 CDS 67426189 67426262 67426189 ID=cds.MS.gene40882.t1;Parent=MS.gene40882.t1
chr1.4 exon 67425967 67426065 67425967 ID=MS.gene40882.t1.exon3;Parent=MS.gene40882.t1
chr1.4 CDS 67425967 67426065 67425967 ID=cds.MS.gene40882.t1;Parent=MS.gene40882.t1
chr1.4 exon 67425779 67425936 67425779 ID=MS.gene40882.t1.exon4;Parent=MS.gene40882.t1
chr1.4 CDS 67425779 67425936 67425779 ID=cds.MS.gene40882.t1;Parent=MS.gene40882.t1
chr1.4 exon 67425552 67425669 67425552 ID=MS.gene40882.t1.exon5;Parent=MS.gene40882.t1
chr1.4 CDS 67425552 67425669 67425552 ID=cds.MS.gene40882.t1;Parent=MS.gene40882.t1
Gene Sequence

>MS.gene40882

ATGCTTGTTTACCAGGATCTTCTTACGGGTAAACCTTGCATCTTTGAGTTTTTTGTTTTACTTTACCACCCAATTAGGTTTCTTTTACTTTTCTCCATTGTTTTTCATAGGATTTTGATAGCATAATGAATGCTTTTTATTTTTTAACCAAATATTACGATGAATGATAAATACTTGTTCCCTGTGTTTAGTGAATGAATTTCTTGTTATGCTTTTATGCACGCGTTTTACATAAACTTCACTTTTGGTTTTAAATAATTCTTCTTTAGAGTTATATTTATATATTAACCTTTTGTAAGGTTGTTAAGATTTTTTTTAGCTTTAGAGTTTTTTTTTTTTTGACACAAGGTTAAAATACTTTTTTGGAAAACCTTAAATTTCTTGGGACCAAACACACACTATTATAGATCAAACTTGTGGCAAAAGTATGAAGTTTTATGTTTGTGTTCTGTGGTTTAACCTTTAGGTTTTTCATTATTATCCAAAATTTTAATTTAATAGAATTTGTTGGTCTAATTTAAAAGTTGTTGTGTTTGTGACAGAGGATTAAATTTACGACTTTACCACAAACTGCTAAGTAATATTTTCTACCCTTAAACACGATTAGCCTAACCTAATACTTGATTGAGGATTTTAGTTTGTGAGATTACTACCTGCTACTAATATTTAAGATTATTTGTTTTTTATTATGAGTTTTACTTATTAAAAACAAAAATTCATTCAAATGGTTTTACTTATGAACTTTACTTTGTTGATGAATTTGTCTAGGTGATGAGCTTCTCTCTGACTCATTCCCCTACAAGGAAATTCAGAATGGAATGTTGTGGGAAGTGGAAGGAAAGGTTTGGAACAAATTTCTTTATTTTATAATAATGTTTCTTTCTATGCTTTATTTTTTATGTCACCAAATATATGATCATAAATAAATTAGCCTAAAGTTTATTGTGTGATGTGATTATTTGCAGTGGGTTGTTCAAGGAGCAGTGGATGTGAATATTGGTGCTAACCCTTCTGCTGAGGGTGGTGACGAGGATGACGGTGTTGATGATCAAGCTGTCAAAGTTGTTGACATTGTTGACACTTTCAGGCTTCAGGAGCAACCAGCTTTTGATAAGAAGCAATTTGTTACTTATATGAAGAGATATATTAAGTTGCTGACATCTAAATTAGAGCCAGAAAAGCAAGAGTTGTTCAAGAAGCACATTGAAGCAGCAACTAAGTTCCTTCTCCCTAAACTCAAAGACCTACAATTGTATGTGTTTCATCATTATCTTTCATCTCTTTTTTGGTTTTATTAAGTTTTCTCTTTTTTGTGGATAAATGATCATTACTGATTGATTAATTATTCATCAATGTTGCAGTTTTGTTGGGGAGAGCATGCATGATGATGGAAGCCTTGTGTTTGCTTACTACAAGGATGGTGCCACTGATCCAACTTTTCTCTACTTTGCCTATGGCTTGAAGGAAATCAAGTGTTAA

Protein sequence

>MS.gene40882.t1

MLVYQDLLTGDELLSDSFPYKEIQNGMLWEVEGKWVVQGAVDVNIGANPSAEGGDEDDGVDDQAVKVEQPAFDKKQFVTYMKRYIKLLTSKLEPEKQELFKKHIEAATKFLLPKLKDLQFFVGESMHDDGSLVFAYYKDGATDPTFLYFAYGLKEIKC