AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene44863

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44863.t1 MTR_3g034200 35.036 137 72 4 4 129 2 132 2.74e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44863.t1 AT5G13780 35.556 135 70 4 4 127 2 130 6.89e-12 60.8

Find 29 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACCTGTTCTAAATCCTTA+TGG 0.223792 5.2:+58969885 None:intergenic
TATCGTAATCCAAGGCCTTT+TGG 0.266555 5.2:+58969556 None:intergenic
CTTATCTTGCCTTTGAGTAC+TGG 0.344775 5.2:-58970091 MS.gene44863:CDS
CGCCCATAAGGATTTAGAAC+AGG 0.402316 5.2:-58969888 MS.gene44863:intron
AACCTGTTCTAAATCCTTAT+GGG 0.412206 5.2:+58969886 None:intergenic
TTTATAAGCCGATGTCTTCT+CGG 0.419946 5.2:-58969497 MS.gene44863:CDS
GCTTGTGACTGCCGCCCATA+AGG 0.446228 5.2:-58969900 MS.gene44863:CDS
GAAGGAGAAGGAGGTTAAGA+AGG 0.449885 5.2:-58969996 MS.gene44863:CDS
TTATAAGCCGATGTCTTCTC+GGG 0.463522 5.2:-58969496 MS.gene44863:CDS
GGAGAAGGAGGTTAAGAAGG+AGG 0.504777 5.2:-58969993 MS.gene44863:CDS
AAGCTGGAATGTTGTACCTC+GGG 0.522913 5.2:+58969589 None:intergenic
CTCGCAACCTATCAGAGACT+TGG 0.530721 5.2:-58969935 MS.gene44863:CDS
CACGTCGCGGTCAGGAATGG+CGG 0.545005 5.2:-58970055 MS.gene44863:CDS
TTTCACGTCGCGGTCAGGAA+TGG 0.551932 5.2:-58970058 MS.gene44863:CDS
TTATGTCTGCTCTATTAAGA+AGG 0.559468 5.2:-58970014 MS.gene44863:CDS
AGCGATACCAAGTCTCTGAT+AGG 0.565478 5.2:+58969928 None:intergenic
TTCATAAATATCGTAATCCA+AGG 0.565491 5.2:+58969548 None:intergenic
CTCTATTAAGAAGGAGAAGG+AGG 0.573692 5.2:-58970005 MS.gene44863:CDS
GCAAGATAAGATCATATTCG+CGG 0.579984 5.2:+58970104 None:intergenic
CTGCTCTATTAAGAAGGAGA+AGG 0.580871 5.2:-58970008 MS.gene44863:CDS
CGCTGAAATCAGTCACGTCG+TGG 0.599192 5.2:-58969960 MS.gene44863:CDS
TGTTCATCTCCAGTACTCAA+AGG 0.610835 5.2:+58970082 None:intergenic
AAAGCTGGAATGTTGTACCT+CGG 0.618480 5.2:+58969588 None:intergenic
ACATCTCAGCGCTCGTCCCG+AGG 0.619758 5.2:-58969605 MS.gene44863:CDS
TTGGTCTCCCGAGAAGACAT+CGG 0.622749 5.2:+58969489 None:intergenic
GGCGGCCGTCGCAATATCGT+CGG 0.629073 5.2:-58970037 MS.gene44863:CDS
ACGAGCGCTGAGATGTACTC+AGG 0.636447 5.2:+58969612 None:intergenic
CTGTTCTAAATCCTTATGGG+CGG 0.665175 5.2:+58969889 None:intergenic
CATAACCGACGATATTGCGA+CGG 0.695901 5.2:+58970032 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACATATAGAATTACAGAACT+AGG + chr5.2:58969867-58969886 None:intergenic 25.0%
! CATATAGAATTACAGAACTA+GGG + chr5.2:58969866-58969885 None:intergenic 25.0%
! GTTCTGTAATTCTATATGTT+AGG - chr5.2:58969868-58969887 MS.gene44863:intron 25.0%
! TTCATAAATATCGTAATCCA+AGG + chr5.2:58970097-58970116 None:intergenic 25.0%
TTATGTCTGCTCTATTAAGA+AGG - chr5.2:58969628-58969647 MS.gene44863:intron 30.0%
! AAACCTGTTCTAAATCCTTA+TGG + chr5.2:58969760-58969779 None:intergenic 30.0%
! AACCTGTTCTAAATCCTTAT+GGG + chr5.2:58969759-58969778 None:intergenic 30.0%
! AGCTTTCATTTTGTTCCAAA+AGG - chr5.2:58970071-58970090 MS.gene44863:CDS 30.0%
!!! TTTTGGAACAAAATGAAAGC+TGG + chr5.2:58970072-58970091 None:intergenic 30.0%
GCAAGATAAGATCATATTCG+CGG + chr5.2:58969541-58969560 None:intergenic 35.0%
TTTATAAGCCGATGTCTTCT+CGG - chr5.2:58970145-58970164 MS.gene44863:CDS 35.0%
AAAGCTGGAATGTTGTACCT+CGG + chr5.2:58970057-58970076 None:intergenic 40.0%
CTCTATTAAGAAGGAGAAGG+AGG - chr5.2:58969637-58969656 MS.gene44863:intron 40.0%
CTGCTCTATTAAGAAGGAGA+AGG - chr5.2:58969634-58969653 MS.gene44863:intron 40.0%
CTTATCTTGCCTTTGAGTAC+TGG - chr5.2:58969551-58969570 MS.gene44863:CDS 40.0%
TGTTCATCTCCAGTACTCAA+AGG + chr5.2:58969563-58969582 None:intergenic 40.0%
TTATAAGCCGATGTCTTCTC+GGG - chr5.2:58970146-58970165 MS.gene44863:CDS 40.0%
! AGATGAACATTTTCACGTCG+CGG - chr5.2:58969574-58969593 MS.gene44863:CDS 40.0%
! CATTTTGTTCCAAAAGGCCT+TGG - chr5.2:58970077-58970096 MS.gene44863:CDS 40.0%
! CTGTTCTAAATCCTTATGGG+CGG + chr5.2:58969756-58969775 None:intergenic 40.0%
! TATCGTAATCCAAGGCCTTT+TGG + chr5.2:58970089-58970108 None:intergenic 40.0%
AAGCTGGAATGTTGTACCTC+GGG + chr5.2:58970056-58970075 None:intergenic 45.0%
AGCGATACCAAGTCTCTGAT+AGG + chr5.2:58969717-58969736 None:intergenic 45.0%
CATAACCGACGATATTGCGA+CGG + chr5.2:58969613-58969632 None:intergenic 45.0%
GAAGGAGAAGGAGGTTAAGA+AGG - chr5.2:58969646-58969665 MS.gene44863:intron 45.0%
! CGCCCATAAGGATTTAGAAC+AGG - chr5.2:58969754-58969773 MS.gene44863:intron 45.0%
CTCGCAACCTATCAGAGACT+TGG - chr5.2:58969707-58969726 MS.gene44863:intron 50.0%
GGAGAAGGAGGTTAAGAAGG+AGG - chr5.2:58969649-58969668 MS.gene44863:intron 50.0%
TTGGTCTCCCGAGAAGACAT+CGG + chr5.2:58970156-58970175 None:intergenic 50.0%
! AACATTTTCACGTCGCGGTC+AGG - chr5.2:58969579-58969598 MS.gene44863:CDS 50.0%
CGCTGAAATCAGTCACGTCG+TGG - chr5.2:58969682-58969701 MS.gene44863:intron 55.0%
TTTCACGTCGCGGTCAGGAA+TGG - chr5.2:58969584-58969603 MS.gene44863:CDS 55.0%
!! ACGAGCGCTGAGATGTACTC+AGG + chr5.2:58970033-58970052 None:intergenic 55.0%
GCTTGTGACTGCCGCCCATA+AGG - chr5.2:58969742-58969761 MS.gene44863:intron 60.0%
ACATCTCAGCGCTCGTCCCG+AGG - chr5.2:58970037-58970056 MS.gene44863:CDS 65.0%
CACGTCGCGGTCAGGAATGG+CGG - chr5.2:58969587-58969606 MS.gene44863:CDS 65.0%
GGCGGCCGTCGCAATATCGT+CGG - chr5.2:58969605-58969624 MS.gene44863:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 58969485 58970179 58969485 ID=MS.gene44863
chr5.2 mRNA 58969485 58970179 58969485 ID=MS.gene44863.t1;Parent=MS.gene44863
chr5.2 exon 58969889 58970179 58969889 ID=MS.gene44863.t1.exon1;Parent=MS.gene44863.t1
chr5.2 CDS 58969889 58970179 58969889 ID=cds.MS.gene44863.t1;Parent=MS.gene44863.t1
chr5.2 exon 58969485 58969643 58969485 ID=MS.gene44863.t1.exon2;Parent=MS.gene44863.t1
chr5.2 CDS 58969485 58969643 58969485 ID=cds.MS.gene44863.t1;Parent=MS.gene44863.t1
Gene Sequence

>MS.gene44863

ATGTCGAACGTGAGCATAAGAGCTGCAACATGCAACGACATGTCTGAGCTTTGCCGCGAATATGATCTTATCTTGCCTTTGAGTACTGGAGATGAACATTTTCACGTCGCGGTCAGGAATGGCGGCCGTCGCAATATCGTCGGTTATGTCTGCTCTATTAAGAAGGAGAAGGAGGTTAAGAAGGAGGTTAAGATTTACGCTGAAATCAGTCACGTCGTGGTTCTCGCAACCTATCAGAGACTTGGTATCGCTACAAAGCTTGTGACTGCCGCCCATAAGGATTTAGAACAGGTTTGTTTGTTATTATAAGATTTTGTTTCAATTACTGTTTGTTATATCACAATGTTTTGCTCTGTCATTGATATATTTGTCACAGATCCCTAGTTCTGTAATTCTATATGTTAGGAGTTAGATTTTGTTCAAAAATATAAAAACATGTTAGAAGCTAGATTTATTCATCAACTTTTGTATAATTAATATGTCTTCAATGTGTGTAAACTTTAATATCGTTGCTGTTACTACTGTGTTTGTCACAGAATTATCATCCTGAGTACATCTCAGCGCTCGTCCCGAGGTACAACATTCCAGCTTTCATTTTGTTCCAAAAGGCCTTGGATTACGATATTTATGAAGATGATTGTACAAAAAACAGTTATCACTTTTATAAGCCGATGTCTTCTCGGGAGACCAAATGA
Protein sequence

>MS.gene44863.t1

MSNVSIRAATCNDMSELCREYDLILPLSTGDEHFHVAVRNGGRRNIVGYVCSIKKEKEVKKEVKIYAEISHVVVLATYQRLGIATKLVTAAHKDLEQNYHPEYISALVPRYNIPAFILFQKALDYDIYEDDCTKNSYHFYKPMSSRETK