AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1410680


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTTGACCATAAAATATTT+TGG 0.261188 tig0023681:+74962 Msa1410680:CDS
TGTATATATCATCATTCAAC+AGG 0.378333 tig0023681:-74988 None:intergenic
AGAACAGTGAAGTTCATGTT+TGG 0.465285 tig0023681:+74312 Msa1410680:CDS
TTCAAGATGGATTGCATGGA+AGG 0.498413 tig0023681:+74345 Msa1410680:CDS
ACAGTGAAGTTCATGTTTGG+TGG 0.503055 tig0023681:+74315 Msa1410680:CDS
AAGGTCTTCAATGTTGACTT+GGG 0.511276 tig0023681:+74287 Msa1410680:CDS
AGGAGCTAGTGGACCGAGTG+TGG 0.529516 tig0023681:+74365 Msa1410680:CDS
GTGGACCGAGTGTGGGAATG+AGG 0.542676 tig0023681:+74373 Msa1410680:CDS
GAAGGTCTTCAATGTTGACT+TGG 0.545743 tig0023681:+74286 Msa1410680:CDS
AGTATTCAAGATGGATTGCA+TGG 0.555407 tig0023681:+74341 Msa1410680:CDS
CAGGTTCAAGATTATGTGGA+AGG 0.557674 tig0023681:+74268 Msa1410680:intron
GTTGCAGGTTCAAGATTATG+TGG 0.558142 tig0023681:+74264 Msa1410680:intron
TGGTGGAAGAGTATTCAAGA+TGG 0.578263 tig0023681:+74332 Msa1410680:CDS
GATTGCATGGAAGGAGCTAG+TGG 0.589977 tig0023681:+74354 Msa1410680:CDS
ACATTCCTCATTCCCACACT+CGG 0.611972 tig0023681:-74378 Msa1410670:CDS
GGAGCTAGTGGACCGAGTGT+GGG 0.616227 tig0023681:+74366 Msa1410680:CDS
AGGTCTTCAATGTTGACTTG+GGG 0.654290 tig0023681:+74288 Msa1410680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAATTCAATTACATATCA+TGG - tig0023681:74511-74530 None:intergenic 20.0%
!! ATATGTAATTGAATTTGAGA+TGG + tig0023681:74513-74532 Msa1410680:intron 20.0%
!!! TAACTAAAGCAATTTTTACT+CGG - tig0023681:74638-74657 None:intergenic 20.0%
!! TTTAGTTAGATTTCAAAGTT+GGG + tig0023681:74650-74669 Msa1410680:intron 20.0%
!! TTCCTTAAAATATTCTTGAA+AGG - tig0023681:74752-74771 None:intergenic 20.0%
!! TAAGGATTTGATATTAATAG+TGG - tig0023681:74907-74926 None:intergenic 20.0%
!! TCAAATTCAATTACATATCA+TGG - tig0023681:74511-74530 None:intergenic 20.0%
!! ATATGTAATTGAATTTGAGA+TGG + tig0023681:74513-74532 Msa1410680:intron 20.0%
!!! TAACTAAAGCAATTTTTACT+CGG - tig0023681:74638-74657 None:intergenic 20.0%
!! TTTAGTTAGATTTCAAAGTT+GGG + tig0023681:74650-74669 Msa1410680:intron 20.0%
!! TTCCTTAAAATATTCTTGAA+AGG - tig0023681:74752-74771 None:intergenic 20.0%
!! TAAGGATTTGATATTAATAG+TGG - tig0023681:74907-74926 None:intergenic 20.0%
! AACAAGATATCTTTGTAAGA+TGG + tig0023681:74545-74564 Msa1410680:intron 25.0%
!!! GATATCTCTTTAATTTGTTG+AGG + tig0023681:74567-74586 Msa1410680:intron 25.0%
!!! TCTTTAATTTGTTGAGGTAA+AGG + tig0023681:74573-74592 Msa1410680:intron 25.0%
! CTTTAGTTAGATTTCAAAGT+TGG + tig0023681:74649-74668 Msa1410680:intron 25.0%
! AACATGCATTCTTGTATAAT+TGG - tig0023681:74708-74727 None:intergenic 25.0%
!! TGCCTTTCAAGAATATTTTA+AGG + tig0023681:74747-74766 Msa1410680:intron 25.0%
! AACTTAGGAACATGTAATAA+TGG + tig0023681:74855-74874 Msa1410680:intron 25.0%
!! TCAAATCCTTATCTTTTTAC+AGG + tig0023681:74916-74935 Msa1410680:intron 25.0%
! ATGAATCCTGTAAAAAGATA+AGG - tig0023681:74925-74944 None:intergenic 25.0%
!! GCTTTGACCATAAAATATTT+TGG + tig0023681:74962-74981 Msa1410680:CDS 25.0%
! TGTATATATCATCATTCAAC+AGG - tig0023681:74991-75010 None:intergenic 25.0%
! AACAAGATATCTTTGTAAGA+TGG + tig0023681:74545-74564 Msa1410680:intron 25.0%
!!! GATATCTCTTTAATTTGTTG+AGG + tig0023681:74567-74586 Msa1410680:intron 25.0%
!!! TCTTTAATTTGTTGAGGTAA+AGG + tig0023681:74573-74592 Msa1410680:intron 25.0%
! CTTTAGTTAGATTTCAAAGT+TGG + tig0023681:74649-74668 Msa1410680:intron 25.0%
! AACATGCATTCTTGTATAAT+TGG - tig0023681:74708-74727 None:intergenic 25.0%
!! TGCCTTTCAAGAATATTTTA+AGG + tig0023681:74747-74766 Msa1410680:intron 25.0%
! AACTTAGGAACATGTAATAA+TGG + tig0023681:74855-74874 Msa1410680:intron 25.0%
!! TCAAATCCTTATCTTTTTAC+AGG + tig0023681:74916-74935 Msa1410680:intron 25.0%
! ATGAATCCTGTAAAAAGATA+AGG - tig0023681:74925-74944 None:intergenic 25.0%
!! GCTTTGACCATAAAATATTT+TGG + tig0023681:74962-74981 Msa1410680:CDS 25.0%
! TGTATATATCATCATTCAAC+AGG - tig0023681:74991-75010 None:intergenic 25.0%
! AATGGTTAATGTCTTTTGGT+AGG - tig0023681:74677-74696 None:intergenic 30.0%
! CTCTAATGGTTAATGTCTTT+TGG - tig0023681:74681-74700 None:intergenic 30.0%
GTATAATTGGTACACTCTAA+TGG - tig0023681:74695-74714 None:intergenic 30.0%
!! CGTATGTGATTGTTTCTATA+AGG + tig0023681:74798-74817 Msa1410680:intron 30.0%
TATCTACTTTGAATGCTCAA+AGG + tig0023681:74831-74850 Msa1410680:intron 30.0%
! TAGGAACATGTAATAATGGA+TGG + tig0023681:74859-74878 Msa1410680:intron 30.0%
! CAGGAGACCAAAATATTTTA+TGG - tig0023681:74972-74991 None:intergenic 30.0%
! AATGGTTAATGTCTTTTGGT+AGG - tig0023681:74677-74696 None:intergenic 30.0%
! CTCTAATGGTTAATGTCTTT+TGG - tig0023681:74681-74700 None:intergenic 30.0%
GTATAATTGGTACACTCTAA+TGG - tig0023681:74695-74714 None:intergenic 30.0%
!! CGTATGTGATTGTTTCTATA+AGG + tig0023681:74798-74817 Msa1410680:intron 30.0%
TATCTACTTTGAATGCTCAA+AGG + tig0023681:74831-74850 Msa1410680:intron 30.0%
! TAGGAACATGTAATAATGGA+TGG + tig0023681:74859-74878 Msa1410680:intron 30.0%
! CAGGAGACCAAAATATTTTA+TGG - tig0023681:74972-74991 None:intergenic 30.0%
ATGAGTTTCATTTGTGTTGC+AGG + tig0023681:74249-74268 Msa1410680:intron 35.0%
!! AAGGTCTTCAATGTTGACTT+GGG + tig0023681:74287-74306 Msa1410680:CDS 35.0%
AGAACAGTGAAGTTCATGTT+TGG + tig0023681:74312-74331 Msa1410680:CDS 35.0%
!! AGTATTCAAGATGGATTGCA+TGG + tig0023681:74341-74360 Msa1410680:CDS 35.0%
! AGTTTTGCAAACTCAACTTG+TGG + tig0023681:74432-74451 Msa1410680:intron 35.0%
ACTCAACTTGTGGAATCAAA+TGG + tig0023681:74442-74461 Msa1410680:intron 35.0%
TGAATGCTCAAAGGTAACTT+AGG + tig0023681:74840-74859 Msa1410680:intron 35.0%
!! ATAGTGGATGATTAGTCATG+AGG - tig0023681:74891-74910 None:intergenic 35.0%
ATGAGTTTCATTTGTGTTGC+AGG + tig0023681:74249-74268 Msa1410680:intron 35.0%
!! AAGGTCTTCAATGTTGACTT+GGG + tig0023681:74287-74306 Msa1410680:CDS 35.0%
AGAACAGTGAAGTTCATGTT+TGG + tig0023681:74312-74331 Msa1410680:CDS 35.0%
!! AGTATTCAAGATGGATTGCA+TGG + tig0023681:74341-74360 Msa1410680:CDS 35.0%
! AGTTTTGCAAACTCAACTTG+TGG + tig0023681:74432-74451 Msa1410680:intron 35.0%
ACTCAACTTGTGGAATCAAA+TGG + tig0023681:74442-74461 Msa1410680:intron 35.0%
TGAATGCTCAAAGGTAACTT+AGG + tig0023681:74840-74859 Msa1410680:intron 35.0%
!! ATAGTGGATGATTAGTCATG+AGG - tig0023681:74891-74910 None:intergenic 35.0%
GTTGCAGGTTCAAGATTATG+TGG + tig0023681:74264-74283 Msa1410680:intron 40.0%
CAGGTTCAAGATTATGTGGA+AGG + tig0023681:74268-74287 Msa1410680:intron 40.0%
! GAAGGTCTTCAATGTTGACT+TGG + tig0023681:74286-74305 Msa1410680:CDS 40.0%
!! AGGTCTTCAATGTTGACTTG+GGG + tig0023681:74288-74307 Msa1410680:CDS 40.0%
ACAGTGAAGTTCATGTTTGG+TGG + tig0023681:74315-74334 Msa1410680:CDS 40.0%
!! TGGTGGAAGAGTATTCAAGA+TGG + tig0023681:74332-74351 Msa1410680:CDS 40.0%
!! TTCAAGATGGATTGCATGGA+AGG + tig0023681:74345-74364 Msa1410680:CDS 40.0%
TGGGAATGAGGAATGTGATA+TGG + tig0023681:74385-74404 Msa1410680:intron 40.0%
TATGGTACTCGTTGTGATGT+TGG + tig0023681:74403-74422 Msa1410680:intron 40.0%
GAACAAGACATGCATTGCTA+TGG - tig0023681:74487-74506 Msa1410670:CDS 40.0%
! ATTTGTTGAGGTAAAGGCTC+TGG + tig0023681:74579-74598 Msa1410680:intron 40.0%
! CTGGTAATCTGAAGTACAGT+CGG + tig0023681:74598-74617 Msa1410680:intron 40.0%
GTTGCAGGTTCAAGATTATG+TGG + tig0023681:74264-74283 Msa1410680:intron 40.0%
CAGGTTCAAGATTATGTGGA+AGG + tig0023681:74268-74287 Msa1410680:intron 40.0%
! GAAGGTCTTCAATGTTGACT+TGG + tig0023681:74286-74305 Msa1410680:CDS 40.0%
!! AGGTCTTCAATGTTGACTTG+GGG + tig0023681:74288-74307 Msa1410680:CDS 40.0%
ACAGTGAAGTTCATGTTTGG+TGG + tig0023681:74315-74334 Msa1410680:CDS 40.0%
!! TGGTGGAAGAGTATTCAAGA+TGG + tig0023681:74332-74351 Msa1410680:CDS 40.0%
!! TTCAAGATGGATTGCATGGA+AGG + tig0023681:74345-74364 Msa1410680:CDS 40.0%
TGGGAATGAGGAATGTGATA+TGG + tig0023681:74385-74404 Msa1410680:intron 40.0%
TATGGTACTCGTTGTGATGT+TGG + tig0023681:74403-74422 Msa1410680:intron 40.0%
GAACAAGACATGCATTGCTA+TGG - tig0023681:74487-74506 Msa1410670:CDS 40.0%
! ATTTGTTGAGGTAAAGGCTC+TGG + tig0023681:74579-74598 Msa1410680:intron 40.0%
! CTGGTAATCTGAAGTACAGT+CGG + tig0023681:74598-74617 Msa1410680:intron 40.0%
ACATTCCTCATTCCCACACT+CGG - tig0023681:74381-74400 Msa1410670:CDS 45.0%
ATTGCTATGGTTCCTTCACC+TGG - tig0023681:74474-74493 Msa1410670:CDS 45.0%
ACATTCCTCATTCCCACACT+CGG - tig0023681:74381-74400 Msa1410670:CDS 45.0%
ATTGCTATGGTTCCTTCACC+TGG - tig0023681:74474-74493 Msa1410670:CDS 45.0%
GATTGCATGGAAGGAGCTAG+TGG + tig0023681:74354-74373 Msa1410680:CDS 50.0%
GGAATCAAATGGCTCAGTCC+AGG + tig0023681:74453-74472 Msa1410680:intron 50.0%
AAATGGCTCAGTCCAGGTGA+AGG + tig0023681:74459-74478 Msa1410680:intron 50.0%
GATTGCATGGAAGGAGCTAG+TGG + tig0023681:74354-74373 Msa1410680:CDS 50.0%
GGAATCAAATGGCTCAGTCC+AGG + tig0023681:74453-74472 Msa1410680:intron 50.0%
AAATGGCTCAGTCCAGGTGA+AGG + tig0023681:74459-74478 Msa1410680:intron 50.0%
! AGGAGCTAGTGGACCGAGTG+TGG + tig0023681:74365-74384 Msa1410680:CDS 60.0%
! GGAGCTAGTGGACCGAGTGT+GGG + tig0023681:74366-74385 Msa1410680:CDS 60.0%
GTGGACCGAGTGTGGGAATG+AGG + tig0023681:74373-74392 Msa1410680:CDS 60.0%
! AGGAGCTAGTGGACCGAGTG+TGG + tig0023681:74365-74384 Msa1410680:CDS 60.0%
! GGAGCTAGTGGACCGAGTGT+GGG + tig0023681:74366-74385 Msa1410680:CDS 60.0%
GTGGACCGAGTGTGGGAATG+AGG + tig0023681:74373-74392 Msa1410680:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0023681 gene 74249 75021 74249 ID=Msa1410680;Name=Msa1410680
tig0023681 mRNA 74249 75021 74249 ID=Msa1410680-mRNA-1;Parent=Msa1410680;Name=Msa1410680-mRNA-1;_AED=0.64;_eAED=0.64;_QI=0|0|0|0.33|1|1|3|0|71
tig0023681 exon 74249 74252 74249 ID=Msa1410680-mRNA-1:exon:26673;Parent=Msa1410680-mRNA-1
tig0023681 exon 74271 74398 74271 ID=Msa1410680-mRNA-1:exon:26674;Parent=Msa1410680-mRNA-1
tig0023681 exon 74938 75021 74938 ID=Msa1410680-mRNA-1:exon:26675;Parent=Msa1410680-mRNA-1
tig0023681 CDS 74249 74252 74249 ID=Msa1410680-mRNA-1:cds;Parent=Msa1410680-mRNA-1
tig0023681 CDS 74271 74398 74271 ID=Msa1410680-mRNA-1:cds;Parent=Msa1410680-mRNA-1
tig0023681 CDS 74938 75021 74938 ID=Msa1410680-mRNA-1:cds;Parent=Msa1410680-mRNA-1
Gene Sequence

>Msa1410680

ATGAGTTCAAGATTATGTGGAAGGTCTTCAATGTTGACTTGGGGAAGAACAGTGAAGTTCATGTTTGGTGGAAGAGTATTCAAGATGGATTGCATGGAAGGAGCTAGTGGACCGAGTGTGGGAATGAGGAATGATTCATCAAACATGTTTGAATGCGCTTTGACCATAAAATATTTTGGTCTCCTGTTGAATGATGATATATACAAAAATTTATGA

Protein sequence

>Msa1410680

MSSRLCGRSSMLTWGRTVKFMFGGRVFKMDCMEGASGPSVGMRNDSSNMFECALTIKYFGLLLNDDIYKNL*