AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01542

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01542.t1 MTR_4g123470 89.024 82 9 0 44 125 142 223 5.55e-51 161
MS.gene01542.t1 MTR_4g123470 82.857 35 6 0 12 46 31 65 1.17e-14 67.8
MS.gene01542.t1 MTR_7g113060 89.189 37 4 0 89 125 3 39 5.68e-18 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGTGCATGTAGAAAATC+AGG 0.323162 2.2:+67693272 MS.gene01542:CDS
AGGAATTTGCCGAAAGTATC+AGG 0.335653 2.2:-67693917 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 2.2:-67693937 None:intergenic
TAGGAACTACCTGATACTTT+CGG 0.400617 2.2:+67693908 MS.gene01542:intron
TCCGAACATCACATTTGGTA+TGG 0.417548 2.2:-67694023 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 2.2:-67694022 None:intergenic
GAGCAATGGCACTTGCTAGA+TGG 0.455163 2.2:+67693517 MS.gene01542:CDS
TTGTGCTGCCAATGGTATTG+AGG 0.463000 2.2:+67694063 MS.gene01542:CDS
CCAAATGTGATGTTCGGAAA+AGG 0.475440 2.2:+67694028 MS.gene01542:CDS
TAAATATTTGTACGAGCTAC+CGG 0.476243 2.2:+67693495 MS.gene01542:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 2.2:+67694022 MS.gene01542:CDS
TGTGCTGCCAATGGTATTGA+GGG 0.501205 2.2:+67694064 MS.gene01542:CDS
ACGGAAATGATATTGTCATA+AGG 0.522697 2.2:-67693977 None:intergenic
TCTAGCAAGTGCCATTGCTC+CGG 0.534587 2.2:-67693514 None:intergenic
CGAACATCACATTTGGTATG+GGG 0.552019 2.2:-67694021 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 2.2:+67694102 MS.gene01542:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 2.2:-67694071 None:intergenic
GTCTGTATATTTGAGTCTCA+CGG 0.587084 2.2:-67693996 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.587936 2.2:+67693523 MS.gene01542:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 2.2:+67694032 MS.gene01542:CDS
GGCACTTGCTAGATGGTGAT+GGG 0.608333 2.2:+67693524 MS.gene01542:CDS
TGTACGAGCTACCGGAGCAA+TGG 0.612121 2.2:+67693503 MS.gene01542:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 2.2:+67694067 MS.gene01542:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAGATTTTTTTATTTTTTTT+AGG + chr2.2:67693889-67693908 MS.gene01542:intron 10.0%
!! GTTTATATATGCTATAATAA+AGG + chr2.2:67693848-67693867 MS.gene01542:intron 15.0%
!! AAAAAACAATAAACAACCTT+CGG - chr2.2:67693809-67693828 None:intergenic 20.0%
!! TTAGACAGTGTATTAAAAAA+AGG - chr2.2:67693437-67693456 None:intergenic 20.0%
!! TTCTATTTAAATACGATGAA+GGG + chr2.2:67693322-67693341 MS.gene01542:intron 20.0%
!! TTTCTATTTAAATACGATGA+AGG + chr2.2:67693321-67693340 MS.gene01542:intron 20.0%
!! ATGTGCATGAAAATAACTTT+TGG + chr2.2:67693361-67693380 MS.gene01542:intron 25.0%
!! TTTTGATGCTATTCATTTAG+AGG + chr2.2:67693826-67693845 MS.gene01542:intron 25.0%
ACGGAAATGATATTGTCATA+AGG - chr2.2:67693980-67693999 None:intergenic 30.0%
TAAATATTTGTACGAGCTAC+CGG + chr2.2:67693495-67693514 MS.gene01542:CDS 30.0%
TAATACACTGTCTAACTTCT+TGG + chr2.2:67693442-67693461 MS.gene01542:intron 30.0%
! GCATGAAAATAACTTTTGGT+TGG + chr2.2:67693365-67693384 MS.gene01542:intron 30.0%
AATCGTGATGTTTCACTCTA+AGG - chr2.2:67693940-67693959 None:intergenic 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr2.2:67693646-67693665 MS.gene01542:intron 35.0%
GTCTGTATATTTGAGTCTCA+CGG - chr2.2:67693999-67694018 None:intergenic 35.0%
TAGGAACTACCTGATACTTT+CGG + chr2.2:67693908-67693927 MS.gene01542:intron 35.0%
TATCCAGATAGGAACTTCAA+AGG - chr2.2:67693770-67693789 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG + chr2.2:67693770-67693789 MS.gene01542:intron 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr2.2:67693666-67693685 None:intergenic 35.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr2.2:67694032-67694051 MS.gene01542:CDS 40.0%
CACAGTGCATGTAGAAAATC+AGG + chr2.2:67693272-67693291 MS.gene01542:CDS 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr2.2:67694028-67694047 MS.gene01542:CDS 40.0%
CCCATACCAAATGTGATGTT+CGG + chr2.2:67694022-67694041 MS.gene01542:CDS 40.0%
CCGAACATCACATTTGGTAT+GGG - chr2.2:67694025-67694044 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr2.2:67694024-67694043 None:intergenic 40.0%
TCCGAACATCACATTTGGTA+TGG - chr2.2:67694026-67694045 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr2.2:67694031-67694050 None:intergenic 40.0%
!! AGGAATTTGCCGAAAGTATC+AGG - chr2.2:67693920-67693939 None:intergenic 40.0%
!! GTACCTTTGAAGTTCCTATC+TGG + chr2.2:67693764-67693783 MS.gene01542:intron 40.0%
ACCCTATCATTCCATGAGTG+CGG + chr2.2:67693726-67693745 MS.gene01542:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr2.2:67693660-67693679 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr2.2:67693649-67693668 MS.gene01542:intron 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr2.2:67693589-67693608 None:intergenic 45.0%
TCGTCGATCCATATCCAGAT+AGG - chr2.2:67693781-67693800 None:intergenic 45.0%
TGATAGGGTGGATAATCAGC+TGG - chr2.2:67693715-67693734 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr2.2:67694063-67694082 MS.gene01542:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr2.2:67694055-67694074 MS.gene01542:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr2.2:67694064-67694083 MS.gene01542:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr2.2:67694102-67694121 MS.gene01542:CDS 45.0%
AGCCGTTGTTGACAGATGGT+TGG + chr2.2:67693584-67693603 MS.gene01542:intron 50.0%
AGTCAGCCGTTGTTGACAGA+TGG + chr2.2:67693580-67693599 MS.gene01542:intron 50.0%
GCACTCATGGAATGATAGGG+TGG - chr2.2:67693727-67693746 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr2.2:67693730-67693749 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr2.2:67693731-67693750 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG + chr2.2:67693790-67693809 MS.gene01542:intron 50.0%
! GAGCAATGGCACTTGCTAGA+TGG + chr2.2:67693517-67693536 MS.gene01542:CDS 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr2.2:67693524-67693543 MS.gene01542:CDS 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG - chr2.2:67693517-67693536 None:intergenic 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr2.2:67693523-67693542 MS.gene01542:CDS 50.0%
GTCTCCGCCCTCAATACCAT+TGG - chr2.2:67694074-67694093 None:intergenic 55.0%
TGTACGAGCTACCGGAGCAA+TGG + chr2.2:67693503-67693522 MS.gene01542:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr2.2:67694067-67694086 MS.gene01542:CDS 55.0%
ACACGATGCTGCCGCACTCA+TGG - chr2.2:67693740-67693759 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 67693260 67694150 67693260 ID=MS.gene01542
chr2.2 mRNA 67693260 67694150 67693260 ID=MS.gene01542.t1;Parent=MS.gene01542
chr2.2 exon 67693260 67693293 67693260 ID=MS.gene01542.t1.exon1;Parent=MS.gene01542.t1
chr2.2 CDS 67693260 67693293 67693260 ID=cds.MS.gene01542.t1;Parent=MS.gene01542.t1
chr2.2 exon 67693473 67693576 67693473 ID=MS.gene01542.t1.exon2;Parent=MS.gene01542.t1
chr2.2 CDS 67693473 67693576 67693473 ID=cds.MS.gene01542.t1;Parent=MS.gene01542.t1
chr2.2 exon 67693911 67694150 67693911 ID=MS.gene01542.t1.exon3;Parent=MS.gene01542.t1
chr2.2 CDS 67693911 67694150 67693911 ID=cds.MS.gene01542.t1;Parent=MS.gene01542.t1
Gene Sequence

>MS.gene01542

ATGTTCGTTCTTCACAGTGCATGTAGAAAATCAGGTTTGTTTCACTTGATGATTTAATCTTTTTCTATTTAAATACGATGAAGGGAGTCAGTTAACTTATTATGTGCATGAAAATAACTTTTGGTTGGATTTAATATTTTTTGTTGTTGTTAAAATCAGCTTGCAGTTGTTTTTCCTTTTTTTAATACACTGTCTAACTTCTTGGATGTCTAGAACTACAACAATTATTCGTTGCTAAATATTTGTACGAGCTACCGGAGCAATGGCACTTGCTAGATGGTGATGGGAATACTCATAACGTCATGTTCAACAAATCAGTTAGTCAGCCGTTGTTGACAGATGGTTGGAGTGCATTGTGATTATTCTACGAGTTTAGTAGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTGCTCCAGCTGATTATCCACCCTATCATTCCATGAGTGCGGCAGCATCGTGTTATTGTACCTTTGAAGTTCCTATCTGGATATGGATCGACGAAATCACCGAAGGTTGTTTATTGTTTTTTTGATGCTATTCATTTAGAGGTTTATATATGCTATAATAAAGGATTTATGTATGTCATTAACAGATTTTTTTATTTTTTTTAGGAACTACCTGATACTTTCGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCAGACCTTATGACAATATCATTTCCGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCTAG
Protein sequence

>MS.gene01542.t1

MFVLHSACRKSELQQLFVAKYLYELPEQWHLLDGDGNTHNVMFNKSELPDTFGKFLRVKHHDYVMLCRPYDNIISVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVS