AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1040400


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1040400 MtrunA17_Chr7g0271081 98.413 63 1 0 1 63 1 63 3.75e-39 123
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1040400 AT1G73177.1 71.667 60 17 0 1 60 1 60 4.39e-16 65.5

Find 30 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTTAATCGCTTTATATAA+AGG 0.238997 7_1:-77765292 None:intergenic
TTCCCTCCAAATTTCCAAAA+AGG 0.261906 7_1:-77767083 None:intergenic
CTTTAATCGCTTTATATAAA+GGG 0.315095 7_1:-77765291 None:intergenic
TGATAGACATTAAGAAATTT+CGG 0.335030 7_1:+77766877 Msa1040400:three_prime_UTR
TTGTCAACAGTGTTTGGTTT+GGG 0.342904 7_1:+77767020 Msa1040400:three_prime_UTR
TGTTTGGTTTGGGAAATAAA+AGG 0.351855 7_1:+77767030 Msa1040400:three_prime_UTR
GGAGGCACAACAAGTTAATA+AGG 0.370280 7_1:+77766751 Msa1040400:CDS
TGCCTCCAACACTGGTTGTT+CGG 0.370391 7_1:+77766182 Msa1040400:CDS
TTTGTCAACAGTGTTTGGTT+TGG 0.401354 7_1:+77767019 Msa1040400:three_prime_UTR
TTTATTGAAACTTCTACTCT+TGG 0.408151 7_1:-77766799 None:intergenic
GCTTGGCACGATCTTGCCCT+TGG 0.435718 7_1:+77766776 Msa1040400:CDS
AAAATGGCAGAACTGAGTTT+GGG 0.446438 7_1:+77765554 Msa1040400:exon
TTGACATTGTTGATGAGGAT+TGG 0.447381 7_1:+77765585 Msa1040400:CDS
ACAACCAGTGTTGGAGGCAG+TGG 0.463826 7_1:-77766178 None:intergenic
GTAATCTATCATTATGCATA+AGG 0.464340 7_1:-77766968 None:intergenic
TGTCTATCACATACATAGAA+AGG 0.488465 7_1:-77766863 None:intergenic
TCTTCCACTGCCTCCAACAC+TGG 0.491395 7_1:+77766174 Msa1040400:CDS
GAAACTTCTACTCTTGGCCA+AGG 0.510239 7_1:-77766793 None:intergenic
TCTAATTGACATTGTTGATG+AGG 0.512652 7_1:+77765580 Msa1040400:CDS
AACAAGTTAATAAGGATGCT+TGG 0.520232 7_1:+77766759 Msa1040400:CDS
GTCCGAACAACCAGTGTTGG+AGG 0.546833 7_1:-77766184 None:intergenic
TGTCATGCTTAGTAGTAAGT+AGG 0.548709 7_1:+77766834 Msa1040400:three_prime_UTR
AGAGACATTCTTCCTCAAGA+TGG 0.570997 7_1:+77765611 Msa1040400:CDS
TCTGTCCGAACAACCAGTGT+TGG 0.577627 7_1:-77766187 None:intergenic
ATTGTTCTTAATCTGAGTGA+AGG 0.578708 7_1:+77765335 Msa1040400:five_prime_UTR
TATCACATACATAGAAAGGA+AGG 0.591643 7_1:-77766859 None:intergenic
TGGTTTGGGAAATAAAAGGA+TGG 0.592378 7_1:+77767034 Msa1040400:three_prime_UTR
TTGTTGTTAATCAGATCAGG+AGG 0.619606 7_1:+77766733 Msa1040400:intron
AAACTTCTACTCTTGGCCAA+GGG 0.628656 7_1:-77766792 None:intergenic
TGTTCGGACAGATGATACTG+AGG 0.734610 7_1:+77766198 Msa1040400:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTATCAATATACAATAT+AGG - chr7_1:77765956-77765975 None:intergenic 10.0%
!! ACTTTAATCGCTTTATATAA+AGG - chr7_1:77765295-77765314 None:intergenic 20.0%
!! AAAAAAAAAATACCATCTTG+AGG - chr7_1:77765626-77765645 None:intergenic 20.0%
!! TAAAAAACAGTTGCAAAATA+AGG + chr7_1:77765758-77765777 Msa1040400:intron 20.0%
!!! ACTTCTTATTTCATTTACAA+TGG - chr7_1:77765852-77765871 None:intergenic 20.0%
!! CAAATATAACAAAGTATAGA+TGG + chr7_1:77766019-77766038 Msa1040400:intron 20.0%
!! TTTAAAAGAAAATGTGTTCT+TGG + chr7_1:77766426-77766445 Msa1040400:intron 20.0%
!!! ATGTTTTCAAACTTATATGT+CGG + chr7_1:77766606-77766625 Msa1040400:intron 20.0%
!! TGATAGACATTAAGAAATTT+CGG + chr7_1:77766877-77766896 Msa1040400:three_prime_UTR 20.0%
! AATGAAGAGAAAGAAGAATT+TGG - chr7_1:77765436-77765455 None:intergenic 25.0%
!! AACGACAAGAATTAGATTTT+GGG - chr7_1:77765505-77765524 None:intergenic 25.0%
!! AAACGACAAGAATTAGATTT+TGG - chr7_1:77765506-77765525 None:intergenic 25.0%
!!! ATTTTGTGTTATTAACAGTG+TGG + chr7_1:77765527-77765546 Msa1040400:intron 25.0%
! GTAAAATTAGTATACACTGA+CGG - chr7_1:77765698-77765717 None:intergenic 25.0%
! AATCTATTTGTAGTTGAAGT+TGG - chr7_1:77765722-77765741 None:intergenic 25.0%
! GTAAAAATAGTTTACACTGT+CGG + chr7_1:77765819-77765838 Msa1040400:intron 25.0%
! TCAATATACAATATAGGACA+GGG - chr7_1:77765950-77765969 None:intergenic 25.0%
! ATCAATATACAATATAGGAC+AGG - chr7_1:77765951-77765970 None:intergenic 25.0%
! TATAACAAAGTATAGATGGT+TGG + chr7_1:77766023-77766042 Msa1040400:intron 25.0%
!! TGTTTTCAAACTTATATGTC+GGG + chr7_1:77766607-77766626 Msa1040400:intron 25.0%
! ATTGATTATTGTTCATGAGA+TGG + chr7_1:77766652-77766671 Msa1040400:intron 25.0%
! TTGATTATTGTTCATGAGAT+GGG + chr7_1:77766653-77766672 Msa1040400:intron 25.0%
! TTTATTGAAACTTCTACTCT+TGG - chr7_1:77766802-77766821 None:intergenic 25.0%
!!! ATTTTTGCTTTGAACTCTAA+AGG + chr7_1:77766942-77766961 Msa1040400:three_prime_UTR 25.0%
! GTAATCTATCATTATGCATA+AGG - chr7_1:77766971-77766990 None:intergenic 25.0%
!! TAAATTTTGTCAACAGTGTT+TGG + chr7_1:77767014-77767033 Msa1040400:three_prime_UTR 25.0%
!! AATAAAATCTCTTGCCTTTT+TGG + chr7_1:77767069-77767088 Msa1040400:three_prime_UTR 25.0%
ATTGTTCTTAATCTGAGTGA+AGG + chr7_1:77765335-77765354 Msa1040400:five_prime_UTR 30.0%
! GGTTAGGGATAATTTGAAAT+TGG - chr7_1:77765476-77765495 None:intergenic 30.0%
! ACGACAAGAATTAGATTTTG+GGG - chr7_1:77765504-77765523 None:intergenic 30.0%
TTAACAGTGTGGAGAAAAAA+TGG + chr7_1:77765538-77765557 Msa1040400:intron 30.0%
TCTAATTGACATTGTTGATG+AGG + chr7_1:77765580-77765599 Msa1040400:CDS 30.0%
AATAAGGCTACATAGCAAAA+TGG + chr7_1:77765774-77765793 Msa1040400:intron 30.0%
! TTTTTACGCTGTTGTCTAAT+TGG - chr7_1:77765806-77765825 None:intergenic 30.0%
TACGAAGAGAATGTAAGTTT+AGG + chr7_1:77766064-77766083 Msa1040400:intron 30.0%
ACGAAGAGAATGTAAGTTTA+GGG + chr7_1:77766065-77766084 Msa1040400:intron 30.0%
! TTGATAATTGATATCCACGT+GGG + chr7_1:77766119-77766138 Msa1040400:intron 30.0%
TAAACTAAGCTCAAGAAAGA+TGG - chr7_1:77766274-77766293 None:intergenic 30.0%
! CTTTAGAAGTTGCAATTTAG+TGG + chr7_1:77766378-77766397 Msa1040400:intron 30.0%
GAATTGCTTCAATGAAAACA+TGG + chr7_1:77766400-77766419 Msa1040400:intron 30.0%
AACTATATATGTTGCCATGT+TGG + chr7_1:77766551-77766570 Msa1040400:intron 30.0%
! GTTTTCAAACTTATATGTCG+GGG + chr7_1:77766608-77766627 Msa1040400:intron 30.0%
GGCTACAAAACTTATTATAG+TGG + chr7_1:77766629-77766648 Msa1040400:intron 30.0%
CTGATTAACAACAAATCACA+TGG - chr7_1:77766727-77766746 None:intergenic 30.0%
!! GATTTGTTGTTAATCAGATC+AGG + chr7_1:77766730-77766749 Msa1040400:intron 30.0%
AACAAGTTAATAAGGATGCT+TGG + chr7_1:77766759-77766778 Msa1040400:CDS 30.0%
TATCACATACATAGAAAGGA+AGG - chr7_1:77766862-77766881 None:intergenic 30.0%
TGTCTATCACATACATAGAA+AGG - chr7_1:77766866-77766885 None:intergenic 30.0%
!! TGTTTGGTTTGGGAAATAAA+AGG + chr7_1:77767030-77767049 Msa1040400:three_prime_UTR 30.0%
GAATTTGGAGAAGAGAGATA+AGG - chr7_1:77765421-77765440 None:intergenic 35.0%
!! GAATTAGATTTTGGGGGTTA+GGG - chr7_1:77765497-77765516 None:intergenic 35.0%
!! AGAATTAGATTTTGGGGGTT+AGG - chr7_1:77765498-77765517 None:intergenic 35.0%
! CGACAAGAATTAGATTTTGG+GGG - chr7_1:77765503-77765522 None:intergenic 35.0%
AAAAATGGCAGAACTGAGTT+TGG + chr7_1:77765553-77765572 Msa1040400:exon 35.0%
AAAATGGCAGAACTGAGTTT+GGG + chr7_1:77765554-77765573 Msa1040400:exon 35.0%
! TTGACATTGTTGATGAGGAT+TGG + chr7_1:77765585-77765604 Msa1040400:CDS 35.0%
ATACAATATAGGACAGGGAT+GGG - chr7_1:77765945-77765964 None:intergenic 35.0%
TATACAATATAGGACAGGGA+TGG - chr7_1:77765946-77765965 None:intergenic 35.0%
GATAAATTGTCCTGAACTGA+CGG + chr7_1:77765968-77765987 Msa1040400:intron 35.0%
AGAGAATGTAAGTTTAGGGA+TGG + chr7_1:77766069-77766088 Msa1040400:intron 35.0%
AGTTTAGGGATGGATGAAAT+TGG + chr7_1:77766079-77766098 Msa1040400:intron 35.0%
! CTTGATAATTGATATCCACG+TGG + chr7_1:77766118-77766137 Msa1040400:intron 35.0%
ATCATATTTACATTCCCACG+TGG - chr7_1:77766136-77766155 None:intergenic 35.0%
GACTAAAGCAGTTACATTTG+TGG + chr7_1:77766245-77766264 Msa1040400:intron 35.0%
! GTATTAAGCACACGTTGATT+TGG + chr7_1:77766307-77766326 Msa1040400:intron 35.0%
! TTGTTGTTAATCAGATCAGG+AGG + chr7_1:77766733-77766752 Msa1040400:intron 35.0%
TGTCATGCTTAGTAGTAAGT+AGG + chr7_1:77766834-77766853 Msa1040400:three_prime_UTR 35.0%
TTTGTCAACAGTGTTTGGTT+TGG + chr7_1:77767019-77767038 Msa1040400:three_prime_UTR 35.0%
! TTGTCAACAGTGTTTGGTTT+GGG + chr7_1:77767020-77767039 Msa1040400:three_prime_UTR 35.0%
! TGGTTTGGGAAATAAAAGGA+TGG + chr7_1:77767034-77767053 Msa1040400:three_prime_UTR 35.0%
AGAGACATTCTTCCTCAAGA+TGG + chr7_1:77765611-77765630 Msa1040400:CDS 40.0%
CAAATATGTACCGTCAGTTC+AGG - chr7_1:77765981-77766000 None:intergenic 40.0%
!! CACACGTTGATTTGGTTGAT+GGG + chr7_1:77766315-77766334 Msa1040400:intron 40.0%
ACAATGCATTACTGACAGTG+TGG + chr7_1:77766481-77766500 Msa1040400:intron 40.0%
ACAGTGTGGCATGTAAACAA+CGG + chr7_1:77766495-77766514 Msa1040400:intron 40.0%
ATATGTTGCCATGTTGGTGT+CGG + chr7_1:77766557-77766576 Msa1040400:intron 40.0%
! TCATGAGATGGGTCTTATGT+TGG + chr7_1:77766664-77766683 Msa1040400:intron 40.0%
! GGAGGCACAACAAGTTAATA+AGG + chr7_1:77766751-77766770 Msa1040400:CDS 40.0%
AAACTTCTACTCTTGGCCAA+GGG - chr7_1:77766795-77766814 None:intergenic 40.0%
!! CTGAGTGAAGGCAGTTTTAG+TGG + chr7_1:77765347-77765366 Msa1040400:five_prime_UTR 45.0%
!! GATTTTGGGGGTTAGGGTTA+GGG - chr7_1:77765491-77765510 None:intergenic 45.0%
!! AGATTTTGGGGGTTAGGGTT+AGG - chr7_1:77765492-77765511 None:intergenic 45.0%
TGTTCGGACAGATGATACTG+AGG + chr7_1:77766198-77766217 Msa1040400:CDS 45.0%
!! GCACACGTTGATTTGGTTGA+TGG + chr7_1:77766314-77766333 Msa1040400:intron 45.0%
TGTCGGATACAGACACATGT+TGG + chr7_1:77766574-77766593 Msa1040400:intron 45.0%
! TGAGATGGGTCTTATGTTGG+AGG + chr7_1:77766667-77766686 Msa1040400:intron 45.0%
GAAACTTCTACTCTTGGCCA+AGG - chr7_1:77766796-77766815 None:intergenic 45.0%
! TGCCTCCAACACTGGTTGTT+CGG + chr7_1:77766182-77766201 Msa1040400:CDS 50.0%
TCTGTCCGAACAACCAGTGT+TGG - chr7_1:77766190-77766209 None:intergenic 50.0%
GTCTGTATCCGACACCAACA+TGG - chr7_1:77766568-77766587 None:intergenic 50.0%
TCGCTGAGTCTCAGTCAGTC+AGG + chr7_1:77765393-77765412 Msa1040400:five_prime_UTR 55.0%
TCTTCCACTGCCTCCAACAC+TGG + chr7_1:77766174-77766193 Msa1040400:CDS 55.0%
! ACAACCAGTGTTGGAGGCAG+TGG - chr7_1:77766181-77766200 None:intergenic 55.0%
! GTCCGAACAACCAGTGTTGG+AGG - chr7_1:77766187-77766206 None:intergenic 55.0%
GCTTGGCACGATCTTGCCCT+TGG + chr7_1:77766776-77766795 Msa1040400:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 77765292 77767098 77765292 ID=Msa1040400;Name=Msa1040400
chr7_1 mRNA 77765292 77767098 77765292 ID=Msa1040400-mRNA-1;Parent=Msa1040400;Name=Msa1040400-mRNA-1;_AED=0.00;_eAED=0.00;_QI=135|1|1|1|0.66|0.5|4|290|63
chr7_1 exon 77765292 77765414 77765292 ID=Msa1040400-mRNA-1:exon:20519;Parent=Msa1040400-mRNA-1
chr7_1 exon 77765545 77765632 77765545 ID=Msa1040400-mRNA-1:exon:20520;Parent=Msa1040400-mRNA-1
chr7_1 exon 77766173 77766226 77766173 ID=Msa1040400-mRNA-1:exon:20521;Parent=Msa1040400-mRNA-1
chr7_1 exon 77766747 77767098 77766747 ID=Msa1040400-mRNA-1:exon:20522;Parent=Msa1040400-mRNA-1
chr7_1 five_prime_UTR 77765292 77765414 77765292 ID=Msa1040400-mRNA-1:five_prime_utr;Parent=Msa1040400-mRNA-1
chr7_1 five_prime_UTR 77765545 77765556 77765545 ID=Msa1040400-mRNA-1:five_prime_utr;Parent=Msa1040400-mRNA-1
chr7_1 CDS 77765557 77765632 77765557 ID=Msa1040400-mRNA-1:cds;Parent=Msa1040400-mRNA-1
chr7_1 CDS 77766173 77766226 77766173 ID=Msa1040400-mRNA-1:cds;Parent=Msa1040400-mRNA-1
chr7_1 CDS 77766747 77766808 77766747 ID=Msa1040400-mRNA-1:cds;Parent=Msa1040400-mRNA-1
chr7_1 three_prime_UTR 77766809 77767098 77766809 ID=Msa1040400-mRNA-1:three_prime_utr;Parent=Msa1040400-mRNA-1
Gene Sequence

>Msa1040400

ATGGCAGAACTGAGTTTGGGAATTCTAATTGACATTGTTGATGAGGATTGGATGAGAGACATTCTTCCTCAAGATGATCTTCCACTGCCTCCAACACTGGTTGTTCGGACAGATGATACTGAGGACTCAAATCAGGAGGCACAACAAGTTAATAAGGATGCTTGGCACGATCTTGCCCTTGGCCAAGAGTAG

Protein sequence

>Msa1040400

MAELSLGILIDIVDEDWMRDILPQDDLPLPPTLVVRTDDTEDSNQEAQQVNKDAWHDLALGQE*