AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0208000


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0208000 MtrunA17_Chr2g0307061 97.468 79 2 0 1 79 1 79 3.95e-48 157
Msa0208000 MtrunA17_Chr2g0295821 39.189 74 44 1 1 73 1 74 5.77e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0208000 AT3G57340.1 61.905 84 25 1 1 77 1 84 7.42e-26 100
Msa0208000 AT3G57340.2 61.905 84 25 1 1 77 1 84 7.42e-26 100
Msa0208000 AT5G05750.1 56.627 83 30 1 1 77 1 83 5.48e-23 91.3
Msa0208000 AT5G49060.2 47.761 67 34 1 1 66 1 67 2.10e-13 65.9
Msa0208000 AT5G49060.1 47.761 67 34 1 1 66 1 67 2.10e-13 65.9

Find 26 sgRNAs with CRISPR-Local

Find 148 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGTTACAAAGTTTGATAAA+TGG 0.193846 2_1:+42040706 None:intergenic
TTGTCGCGAAAATTTGATTT+TGG 0.247425 2_1:+42040827 None:intergenic
GGTAAAGAAGCTTTGGAAAA+AGG 0.294145 2_1:-42041835 Msa0208000:CDS
GGTTACAAAGTTTGATAAAT+GGG 0.353032 2_1:+42040707 None:intergenic
ATCACCTGCATCGCTGTTTA+CGG 0.362410 2_1:+42041732 None:intergenic
GAAAATCGGTAAAGAAGCTT+TGG 0.398563 2_1:-42041842 Msa0208000:CDS
ATTCGGTAAAATGAAAGTAT+TGG 0.425287 2_1:+42040796 None:intergenic
CCTTCAATTCGTCGAAGGAC+TGG 0.449513 2_1:-42041664 Msa0208000:CDS
TGCCACATCAGCTGAGGAGC+CGG 0.449582 2_1:-42041707 Msa0208000:CDS
CCAGTCCTTCGACGAATTGA+AGG 0.463851 2_1:+42041664 None:intergenic
GCATTGAAATCATTGAAAAT+CGG 0.472275 2_1:-42041856 Msa0208000:CDS
CGCCGGCTCCTCAGCTGATG+TGG 0.473969 2_1:+42041705 None:intergenic
ATCCGTTATTGCAAAATGGA+TGG 0.495759 2_1:-42041892 None:intergenic
TCCACCGTAAACAGCGATGC+AGG 0.523350 2_1:-42041736 Msa0208000:CDS
CGATCGGAAGAGACGGGTCG+AGG 0.526213 2_1:+42041770 None:intergenic
TCGACGAATTGAAGGCTGAT+CGG 0.542496 2_1:+42041672 None:intergenic
GATCATCGATCGGAAGAGAC+GGG 0.559925 2_1:+42041764 None:intergenic
GTAAAATGAAAGTATTGGAA+TGG 0.562968 2_1:+42040801 None:intergenic
TCCGTTATTGCAAAATGGAT+GGG 0.563453 2_1:-42041891 None:intergenic
AGATCATCGATCGGAAGAGA+CGG 0.568914 2_1:+42041763 None:intergenic
ATCAGCCTTCAATTCGTCGA+AGG 0.614022 2_1:-42041669 Msa0208000:CDS
TGATCGGATGAATTCTTCGC+CGG 0.631527 2_1:+42041688 None:intergenic
ACCTGCATCGCTGTTTACGG+TGG 0.632948 2_1:+42041735 None:intergenic
TGATCATGCCACATCAGCTG+AGG 0.636133 2_1:-42041713 Msa0208000:CDS
TCGGAAGAGACGGGTCGAGG+CGG 0.656270 2_1:+42041773 None:intergenic
GTGGACAGCAGATCATCGAT+CGG 0.673169 2_1:+42041754 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACCAAATTTAAAACAAAAT+AGG - chr2_1:42041142-42041161 Msa0208000:intron 15.0%
!!! AACCTATTTTGTTTTAAATT+TGG + chr2_1:42041147-42041166 None:intergenic 15.0%
!! TTAAAGTTTGATAAATATGA+AGG + chr2_1:42041215-42041234 None:intergenic 15.0%
!!! TACATAATTTAAAACCAAAT+AGG - chr2_1:42041431-42041450 Msa0208000:intron 15.0%
!! ATATGATATATGAAACTATT+TGG + chr2_1:42041598-42041617 None:intergenic 15.0%
!!! TACCAAATTTAAAACAAAAT+AGG - chr2_1:42041142-42041161 Msa0208000:intron 15.0%
!!! AACCTATTTTGTTTTAAATT+TGG + chr2_1:42041147-42041166 None:intergenic 15.0%
!! TTAAAGTTTGATAAATATGA+AGG + chr2_1:42041215-42041234 None:intergenic 15.0%
!!! TACATAATTTAAAACCAAAT+AGG - chr2_1:42041431-42041450 Msa0208000:intron 15.0%
!! ATATGATATATGAAACTATT+TGG + chr2_1:42041598-42041617 None:intergenic 15.0%
!!! TATTCGTAAAATGAAAGTAT+TGG + chr2_1:42041278-42041297 None:intergenic 20.0%
!! TACAAGTTTGATAAATATGA+AGG + chr2_1:42041356-42041375 None:intergenic 20.0%
!! AACATAATATTGAACCTATT+TGG + chr2_1:42041448-42041467 None:intergenic 20.0%
!! TAGAAGTTTGATAAATATGA+AGG + chr2_1:42041503-42041522 None:intergenic 20.0%
!!! AAACTATTTGGTTTTGTATT+CGG + chr2_1:42041586-42041605 None:intergenic 20.0%
!!! ATATATCATATTTTGCATCA+AGG - chr2_1:42041607-42041626 Msa0208000:intron 20.0%
!!! TATATCATATTTTGCATCAA+GGG - chr2_1:42041608-42041627 Msa0208000:intron 20.0%
!!! AACCTATTTGTTTTTGTATT+CGG + chr2_1:42041810-42041829 None:intergenic 20.0%
!!! TATTCGTAAAATGAAAGTAT+TGG + chr2_1:42041278-42041297 None:intergenic 20.0%
!! TACAAGTTTGATAAATATGA+AGG + chr2_1:42041356-42041375 None:intergenic 20.0%
!! AACATAATATTGAACCTATT+TGG + chr2_1:42041448-42041467 None:intergenic 20.0%
!! TAGAAGTTTGATAAATATGA+AGG + chr2_1:42041503-42041522 None:intergenic 20.0%
!!! AAACTATTTGGTTTTGTATT+CGG + chr2_1:42041586-42041605 None:intergenic 20.0%
!!! ATATATCATATTTTGCATCA+AGG - chr2_1:42041607-42041626 Msa0208000:intron 20.0%
!!! TATATCATATTTTGCATCAA+GGG - chr2_1:42041608-42041627 Msa0208000:intron 20.0%
!!! AACCTATTTGTTTTTGTATT+CGG + chr2_1:42041810-42041829 None:intergenic 20.0%
! GCATTGAAATCATTGAAAAT+CGG - chr2_1:42040730-42040749 Msa0208000:CDS 25.0%
!!! AATGAAGGTTTTAGCATTTA+TGG + chr2_1:42041063-42041082 None:intergenic 25.0%
! TTATCAAACTTTAACCATAC+AGG - chr2_1:42041221-42041240 Msa0208000:intron 25.0%
! TTACGAATATGAAACCAAAT+AGG - chr2_1:42041289-42041308 Msa0208000:intron 25.0%
! ACATATCATGTTTACATCAA+GGG - chr2_1:42041315-42041334 Msa0208000:intron 25.0%
! AATATTATGTTACGCATCAA+AGG - chr2_1:42041457-42041476 Msa0208000:intron 25.0%
! TATCAAACTTCTAACCATAT+AGG - chr2_1:42041510-42041529 Msa0208000:intron 25.0%
!!! AAATGAGATTTTAGCCTATA+TGG + chr2_1:42041527-42041546 None:intergenic 25.0%
!!! AAAATCTCATTTTTGTGACA+AGG - chr2_1:42041535-42041554 Msa0208000:intron 25.0%
!!! AAATCTCATTTTTGTGACAA+GGG - chr2_1:42041536-42041555 Msa0208000:intron 25.0%
! TATGGTTAGAAGTTTGATAA+AGG + chr2_1:42041509-42041528 None:intergenic 25.0%
! TATCAAACTTCTAACCATAT+AGG - chr2_1:42041510-42041529 Msa0208000:intron 25.0%
!!! AAATGAGATTTTAGCCTATA+TGG + chr2_1:42041527-42041546 None:intergenic 25.0%
! TTCTCATTTATCAAACTTGT+AGG - chr2_1:42041728-42041747 Msa0208000:CDS 25.0%
!!! GTAAAATGAAAGTATTGGAA+TGG + chr2_1:42041273-42041292 None:intergenic 25.0%
!! ATTCGGTAAAATGAAAGTAT+TGG + chr2_1:42041793-42041812 None:intergenic 25.0%
! TACCGAATACAAAAACAAAT+AGG - chr2_1:42041805-42041824 Msa0208000:CDS 25.0%
! GCATTGAAATCATTGAAAAT+CGG - chr2_1:42040730-42040749 Msa0208000:CDS 25.0%
!!! AATGAAGGTTTTAGCATTTA+TGG + chr2_1:42041063-42041082 None:intergenic 25.0%
! TTATCAAACTTTAACCATAC+AGG - chr2_1:42041221-42041240 Msa0208000:intron 25.0%
! TTACGAATATGAAACCAAAT+AGG - chr2_1:42041289-42041308 Msa0208000:intron 25.0%
! ACATATCATGTTTACATCAA+GGG - chr2_1:42041315-42041334 Msa0208000:intron 25.0%
! AATATTATGTTACGCATCAA+AGG - chr2_1:42041457-42041476 Msa0208000:intron 25.0%
! TATCAAACTTCTAACCATAT+AGG - chr2_1:42041510-42041529 Msa0208000:intron 25.0%
!!! AAATGAGATTTTAGCCTATA+TGG + chr2_1:42041527-42041546 None:intergenic 25.0%
!!! AAAATCTCATTTTTGTGACA+AGG - chr2_1:42041535-42041554 Msa0208000:intron 25.0%
!!! AAATCTCATTTTTGTGACAA+GGG - chr2_1:42041536-42041555 Msa0208000:intron 25.0%
! TATGGTTAGAAGTTTGATAA+AGG + chr2_1:42041509-42041528 None:intergenic 25.0%
! TATCAAACTTCTAACCATAT+AGG - chr2_1:42041510-42041529 Msa0208000:intron 25.0%
!!! AAATGAGATTTTAGCCTATA+TGG + chr2_1:42041527-42041546 None:intergenic 25.0%
! TTCTCATTTATCAAACTTGT+AGG - chr2_1:42041728-42041747 Msa0208000:CDS 25.0%
!!! GTAAAATGAAAGTATTGGAA+TGG + chr2_1:42041273-42041292 None:intergenic 25.0%
!! ATTCGGTAAAATGAAAGTAT+TGG + chr2_1:42041793-42041812 None:intergenic 25.0%
! TACCGAATACAAAAACAAAT+AGG - chr2_1:42041805-42041824 Msa0208000:CDS 25.0%
AAATATCATGTTTCGCATGA+AGG - chr2_1:42041168-42041187 Msa0208000:intron 30.0%
AATATCATGTTTCGCATGAA+GGG - chr2_1:42041169-42041188 Msa0208000:intron 30.0%
ACATGATATGTGAACCTATT+TGG + chr2_1:42041306-42041325 None:intergenic 30.0%
CACATATCATGTTTACATCA+AGG - chr2_1:42041314-42041333 Msa0208000:intron 30.0%
! TCGGTAAAATGAAAGTGTAT+TGG + chr2_1:42041567-42041586 None:intergenic 30.0%
!! TTGTCGCGAAAATTTGATTT+TGG + chr2_1:42041762-42041781 None:intergenic 30.0%
! AAAATCAAATTTTCGCGACA+AGG - chr2_1:42041761-42041780 Msa0208000:CDS 30.0%
! AAATCAAATTTTCGCGACAA+GGG - chr2_1:42041762-42041781 Msa0208000:CDS 30.0%
AAATATCATGTTTCGCATGA+AGG - chr2_1:42041168-42041187 Msa0208000:intron 30.0%
AATATCATGTTTCGCATGAA+GGG - chr2_1:42041169-42041188 Msa0208000:intron 30.0%
ACATGATATGTGAACCTATT+TGG + chr2_1:42041306-42041325 None:intergenic 30.0%
CACATATCATGTTTACATCA+AGG - chr2_1:42041314-42041333 Msa0208000:intron 30.0%
! TCGGTAAAATGAAAGTGTAT+TGG + chr2_1:42041567-42041586 None:intergenic 30.0%
!! TTGTCGCGAAAATTTGATTT+TGG + chr2_1:42041762-42041781 None:intergenic 30.0%
! AAAATCAAATTTTCGCGACA+AGG - chr2_1:42041761-42041780 Msa0208000:CDS 30.0%
! AAATCAAATTTTCGCGACAA+GGG - chr2_1:42041762-42041781 Msa0208000:CDS 30.0%
GAAAATCGGTAAAGAAGCTT+TGG - chr2_1:42040744-42040763 Msa0208000:CDS 35.0%
!! GGTAAAGAAGCTTTGGAAAA+AGG - chr2_1:42040751-42040770 Msa0208000:CDS 35.0%
GTCATCGAGAAACATATGAT+AGG - chr2_1:42041095-42041114 Msa0208000:intron 35.0%
!! AAACGAGATTTTAGCCTGTA+TGG + chr2_1:42041238-42041257 None:intergenic 35.0%
! TAAAATTCGTTTTCGCAGCA+AGG - chr2_1:42041387-42041406 Msa0208000:intron 35.0%
GAAAATCGGTAAAGAAGCTT+TGG - chr2_1:42040744-42040763 Msa0208000:CDS 35.0%
!! GGTAAAGAAGCTTTGGAAAA+AGG - chr2_1:42040751-42040770 Msa0208000:CDS 35.0%
GTCATCGAGAAACATATGAT+AGG - chr2_1:42041095-42041114 Msa0208000:intron 35.0%
!! AAACGAGATTTTAGCCTGTA+TGG + chr2_1:42041238-42041257 None:intergenic 35.0%
! TAAAATTCGTTTTCGCAGCA+AGG - chr2_1:42041387-42041406 Msa0208000:intron 35.0%
GACTCTTGTCGCAAAAATGA+AGG + chr2_1:42041078-42041097 None:intergenic 40.0%
TTTCGCATGAAGGGATATAG+AGG - chr2_1:42041178-42041197 Msa0208000:intron 40.0%
TTCGCATGAAGGGATATAGA+GGG - chr2_1:42041179-42041198 Msa0208000:intron 40.0%
! AAAATCTCGTTTTCGCGACA+AGG - chr2_1:42041246-42041265 Msa0208000:intron 40.0%
TGTTACGCATCAAAGGACAT+CGG - chr2_1:42041464-42041483 Msa0208000:intron 40.0%
GACTCTTGTCGCAAAAATGA+AGG + chr2_1:42041078-42041097 None:intergenic 40.0%
TTTCGCATGAAGGGATATAG+AGG - chr2_1:42041178-42041197 Msa0208000:intron 40.0%
TTCGCATGAAGGGATATAGA+GGG - chr2_1:42041179-42041198 Msa0208000:intron 40.0%
! AAAATCTCGTTTTCGCGACA+AGG - chr2_1:42041246-42041265 Msa0208000:intron 40.0%
TGTTACGCATCAAAGGACAT+CGG - chr2_1:42041464-42041483 Msa0208000:intron 40.0%
AGATCATCGATCGGAAGAGA+CGG + chr2_1:42040826-42040845 None:intergenic 45.0%
ATCACCTGCATCGCTGTTTA+CGG + chr2_1:42040857-42040876 None:intergenic 45.0%
TGATCGGATGAATTCTTCGC+CGG + chr2_1:42040901-42040920 None:intergenic 45.0%
TCGACGAATTGAAGGCTGAT+CGG + chr2_1:42040917-42040936 None:intergenic 45.0%
ATCAGCCTTCAATTCGTCGA+AGG - chr2_1:42040917-42040936 Msa0208000:intron 45.0%
TTTACATCAAGGGCCATCGA+GGG - chr2_1:42041325-42041344 Msa0208000:intron 45.0%
TATGAAGGTTGAACCCTCGA+TGG + chr2_1:42041341-42041360 None:intergenic 45.0%
GTTACGCATCAAAGGACATC+GGG - chr2_1:42041465-42041484 Msa0208000:intron 45.0%
TTACGCATCAAAGGACATCG+GGG - chr2_1:42041466-42041485 Msa0208000:intron 45.0%
! TTTTGCATCAAGGGACATCG+AGG - chr2_1:42041617-42041636 Msa0208000:intron 45.0%
TTTGCATCAAGGGACATCGA+GGG - chr2_1:42041618-42041637 Msa0208000:intron 45.0%
GACCATTGATGCGAAACATG+AGG + chr2_1:42041698-42041717 None:intergenic 45.0%
AGATCATCGATCGGAAGAGA+CGG + chr2_1:42040826-42040845 None:intergenic 45.0%
ATCACCTGCATCGCTGTTTA+CGG + chr2_1:42040857-42040876 None:intergenic 45.0%
TGATCGGATGAATTCTTCGC+CGG + chr2_1:42040901-42040920 None:intergenic 45.0%
TCGACGAATTGAAGGCTGAT+CGG + chr2_1:42040917-42040936 None:intergenic 45.0%
ATCAGCCTTCAATTCGTCGA+AGG - chr2_1:42040917-42040936 Msa0208000:intron 45.0%
TTTACATCAAGGGCCATCGA+GGG - chr2_1:42041325-42041344 Msa0208000:intron 45.0%
TATGAAGGTTGAACCCTCGA+TGG + chr2_1:42041341-42041360 None:intergenic 45.0%
GTTACGCATCAAAGGACATC+GGG - chr2_1:42041465-42041484 Msa0208000:intron 45.0%
TTACGCATCAAAGGACATCG+GGG - chr2_1:42041466-42041485 Msa0208000:intron 45.0%
! TTTTGCATCAAGGGACATCG+AGG - chr2_1:42041617-42041636 Msa0208000:intron 45.0%
TTTGCATCAAGGGACATCGA+GGG - chr2_1:42041618-42041637 Msa0208000:intron 45.0%
GACCATTGATGCGAAACATG+AGG + chr2_1:42041698-42041717 None:intergenic 45.0%
GATCATCGATCGGAAGAGAC+GGG + chr2_1:42040825-42040844 None:intergenic 50.0%
GTGGACAGCAGATCATCGAT+CGG + chr2_1:42040835-42040854 None:intergenic 50.0%
TGATCATGCCACATCAGCTG+AGG - chr2_1:42040873-42040892 Msa0208000:intron 50.0%
CCAGTCCTTCGACGAATTGA+AGG + chr2_1:42040925-42040944 None:intergenic 50.0%
CCTTCAATTCGTCGAAGGAC+TGG - chr2_1:42040922-42040941 Msa0208000:intron 50.0%
GTTTACATCAAGGGCCATCG+AGG - chr2_1:42041324-42041343 Msa0208000:intron 50.0%
TACGCATCAAAGGACATCGG+GGG - chr2_1:42041467-42041486 Msa0208000:intron 50.0%
CGCCTCATGTTTCGCATCAA+TGG - chr2_1:42041693-42041712 Msa0208000:CDS 50.0%
GATCATCGATCGGAAGAGAC+GGG + chr2_1:42040825-42040844 None:intergenic 50.0%
GTGGACAGCAGATCATCGAT+CGG + chr2_1:42040835-42040854 None:intergenic 50.0%
TGATCATGCCACATCAGCTG+AGG - chr2_1:42040873-42040892 Msa0208000:intron 50.0%
CCAGTCCTTCGACGAATTGA+AGG + chr2_1:42040925-42040944 None:intergenic 50.0%
CCTTCAATTCGTCGAAGGAC+TGG - chr2_1:42040922-42040941 Msa0208000:intron 50.0%
GTTTACATCAAGGGCCATCG+AGG - chr2_1:42041324-42041343 Msa0208000:intron 50.0%
TACGCATCAAAGGACATCGG+GGG - chr2_1:42041467-42041486 Msa0208000:intron 50.0%
CGCCTCATGTTTCGCATCAA+TGG - chr2_1:42041693-42041712 Msa0208000:CDS 50.0%
TCCACCGTAAACAGCGATGC+AGG - chr2_1:42040850-42040869 Msa0208000:intron 55.0%
ACCTGCATCGCTGTTTACGG+TGG + chr2_1:42040854-42040873 None:intergenic 55.0%
TCCACCGTAAACAGCGATGC+AGG - chr2_1:42040850-42040869 Msa0208000:intron 55.0%
ACCTGCATCGCTGTTTACGG+TGG + chr2_1:42040854-42040873 None:intergenic 55.0%
TGCCACATCAGCTGAGGAGC+CGG - chr2_1:42040879-42040898 Msa0208000:intron 60.0%
TGCCACATCAGCTGAGGAGC+CGG - chr2_1:42040879-42040898 Msa0208000:intron 60.0%
TCGGAAGAGACGGGTCGAGG+CGG + chr2_1:42040816-42040835 None:intergenic 65.0%
CGATCGGAAGAGACGGGTCG+AGG + chr2_1:42040819-42040838 None:intergenic 65.0%
TCGGAAGAGACGGGTCGAGG+CGG + chr2_1:42040816-42040835 None:intergenic 65.0%
CGATCGGAAGAGACGGGTCG+AGG + chr2_1:42040819-42040838 None:intergenic 65.0%
!! CGCCGGCTCCTCAGCTGATG+TGG + chr2_1:42040884-42040903 None:intergenic 70.0%
!! CGCCGGCTCCTCAGCTGATG+TGG + chr2_1:42040884-42040903 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 42040709 42041899 42040709 ID=Msa0208000;Name=Msa0208000
chr2_1 mRNA 42040709 42041899 42040709 ID=Msa0208000-mRNA-1;Parent=Msa0208000;Name=Msa0208000-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0|0|0.5|1|1|2|0|129
chr2_1 exon 42041660 42041899 42041660 ID=Msa0208000-mRNA-1:exon:12657;Parent=Msa0208000-mRNA-1
chr2_1 exon 42040709 42040858 42040709 ID=Msa0208000-mRNA-1:exon:12656;Parent=Msa0208000-mRNA-1
chr2_1 CDS 42041660 42041899 42041660 ID=Msa0208000-mRNA-1:cds;Parent=Msa0208000-mRNA-1
chr2_1 CDS 42040709 42040858 42040709 ID=Msa0208000-mRNA-1:cds;Parent=Msa0208000-mRNA-1
Gene Sequence

>Msa0208000

ATGGATGGGAACAAAGACGATGCATTGAAATCATTGAAAATCGGTAAAGAAGCTTTGGAAAAAGGCGATCGTAATCGCGCTTTGAAGTTTCTCAACAAAGCTCGCCGCCTCGACCCGTCTCTTCCGATCGATGATCTGCTGTCCACCGTAAACAGCGATGCAGGTGATCATGCCACATCAGCTGAGGAGCCGGCGAAGAATTCATCCGATCAGCCTTCAATTCGTCGAAGGACTGGCTCCGCATATATACCAAAATCAAATTTTCGCGACAAGGGCCATTCCAATACTTTCATTTTACCGAATACAAAAACAAATAGGTTCACATATCATGTTTCACATCAAGCGACATCAAGAGACAATTTCAAACTTCCCATTTATCAAACTTTGTAA

Protein sequence

>Msa0208000

MDGNKDDALKSLKIGKEALEKGDRNRALKFLNKARRLDPSLPIDDLLSTVNSDAGDHATSAEEPAKNSSDQPSIRRRTGSAYIPKSNFRDKGHSNTFILPNTKTNRFTYHVSHQATSRDNFKLPIYQTL*