AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1374100


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1374100 MtrunA17_Chr1g0155331 96.296 27 1 0 27 53 135 161 2.80e-12 59.3
Msa1374100 MtrunA17_Chr2g0298841 96.296 27 1 0 27 53 135 161 2.80e-12 59.3
Msa1374100 MtrunA17_Chr4g0002321 92.593 27 2 0 27 53 134 160 8.41e-12 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 154 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTATTCAATGACAGGTTCT+TGG 0.316176 tig0019465:-101605 Msa1374100:intron
CCCTGACGCTCTTCAGATTA+GGG 0.318959 tig0019465:+101834 None:intergenic
AATAATTACTGAAATCCTTA+TGG 0.356825 tig0019465:+102879 None:intergenic
TCTTCAAATAAAGGTTCAAC+TGG 0.368005 tig0019465:+102856 None:intergenic
TCCCTGACGCTCTTCAGATT+AGG 0.391787 tig0019465:+101833 None:intergenic
ACCCTAATCTGAAGAGCGTC+AGG 0.410603 tig0019465:-101835 Msa1374100:CDS
ACAAGCAGATTTCATCGAAC+AGG 0.426738 tig0019465:-101778 Msa1374100:intron
TTATTCAATGACAGGTTCTT+GGG 0.454218 tig0019465:-101604 Msa1374100:intron
TTGATCTACAAGAGGGGATA+CGG 0.470817 tig0019465:-101809 Msa1374100:CDS
GGAATTGCTTATGTTACATA+CGG 0.485132 tig0019465:-101860 Msa1374100:CDS
GTTCGATGATGAATGCCATA+AGG 0.503644 tig0019465:-102894 None:intergenic
TATTTGAAGAATGTGAAAAG+AGG 0.510086 tig0019465:-102843 Msa1374100:intron
GAATTGCTTATGTTACATAC+GGG 0.584032 tig0019465:-101859 Msa1374100:CDS
TGACAGGTTCTTGGGAAGCA+CGG 0.610853 tig0019465:-101596 Msa1374100:intron
CAGGGAATTGATCTACAAGA+GGG 0.612367 tig0019465:-101816 Msa1374100:CDS
TCAGGGAATTGATCTACAAG+AGG 0.639447 tig0019465:-101817 Msa1374100:CDS
CCCTAATCTGAAGAGCGTCA+GGG 0.672345 tig0019465:-101834 Msa1374100:CDS
AGGGAATTGATCTACAAGAG+GGG 0.716288 tig0019465:-101815 Msa1374100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGTAAATTAGAAACTAATT+TGG + tig0019465:101660-101679 None:intergenic 15.0%
!!! TTTTTTACAATAAGTTAGAT+TGG + tig0019465:102220-102239 None:intergenic 15.0%
!! AATCTAACTTATTGTAAAAA+AGG - tig0019465:102219-102238 Msa1374100:intron 15.0%
!!! TGAATATTTTAACCATTAAT+AGG - tig0019465:102492-102511 Msa1374100:intron 15.0%
!! ATGTAAATTAGAAACTAATT+TGG + tig0019465:101660-101679 None:intergenic 15.0%
!!! TTTTTTACAATAAGTTAGAT+TGG + tig0019465:102220-102239 None:intergenic 15.0%
!! AATCTAACTTATTGTAAAAA+AGG - tig0019465:102219-102238 Msa1374100:intron 15.0%
!!! TGAATATTTTAACCATTAAT+AGG - tig0019465:102492-102511 Msa1374100:intron 15.0%
!! AATAATTACTGAAATCCTTA+TGG + tig0019465:101583-101602 None:intergenic 20.0%
!!! TTTTCACATTCTTCAAATAA+AGG + tig0019465:101615-101634 None:intergenic 20.0%
!! CAATCATAAAAACTTTCATA+GGG + tig0019465:101926-101945 None:intergenic 20.0%
!! ATTCATAAAAACTTTGCATA+GGG + tig0019465:101958-101977 None:intergenic 20.0%
!! AAACAAAAACTATTGAACAT+TGG - tig0019465:102106-102125 Msa1374100:intron 20.0%
!! ATAAGTTTACAAAACAACAA+AGG + tig0019465:102245-102264 None:intergenic 20.0%
!! AATAATTACTGAAATCCTTA+TGG + tig0019465:101583-101602 None:intergenic 20.0%
!!! TTTTCACATTCTTCAAATAA+AGG + tig0019465:101615-101634 None:intergenic 20.0%
!! CAATCATAAAAACTTTCATA+GGG + tig0019465:101926-101945 None:intergenic 20.0%
!! ATTCATAAAAACTTTGCATA+GGG + tig0019465:101958-101977 None:intergenic 20.0%
!! AAACAAAAACTATTGAACAT+TGG - tig0019465:102106-102125 Msa1374100:intron 20.0%
!! ATAAGTTTACAAAACAACAA+AGG + tig0019465:102245-102264 None:intergenic 20.0%
! TATTTGAAGAATGTGAAAAG+AGG - tig0019465:101616-101635 Msa1374100:intron 25.0%
! TGTGAATACATCTATTCTTT+AGG - tig0019465:101746-101765 Msa1374100:intron 25.0%
!!! TACATCTATTCTTTAGGATT+AGG - tig0019465:101752-101771 Msa1374100:intron 25.0%
! AACAGCATTATGTAATACAT+AGG + tig0019465:101784-101803 None:intergenic 25.0%
! GCAATCATAAAAACTTTCAT+AGG + tig0019465:101927-101946 None:intergenic 25.0%
! CATTCATAAAAACTTTGCAT+AGG + tig0019465:101959-101978 None:intergenic 25.0%
!! CTATGCAAAGTTTTTATGAA+TGG - tig0019465:101957-101976 Msa1374100:intron 25.0%
! CATTAATGCACTATTGTTAA+TGG + tig0019465:102178-102197 None:intergenic 25.0%
!! TGTTATTTGTGACAATGATT+AGG - tig0019465:102340-102359 Msa1374100:intron 25.0%
! TACAACATTTAGTGATTGTA+GGG + tig0019465:102724-102743 None:intergenic 25.0%
! TATTTGAAGAATGTGAAAAG+AGG - tig0019465:101616-101635 Msa1374100:intron 25.0%
! TGTGAATACATCTATTCTTT+AGG - tig0019465:101746-101765 Msa1374100:intron 25.0%
!!! TACATCTATTCTTTAGGATT+AGG - tig0019465:101752-101771 Msa1374100:intron 25.0%
! AACAGCATTATGTAATACAT+AGG + tig0019465:101784-101803 None:intergenic 25.0%
! GCAATCATAAAAACTTTCAT+AGG + tig0019465:101927-101946 None:intergenic 25.0%
! CATTCATAAAAACTTTGCAT+AGG + tig0019465:101959-101978 None:intergenic 25.0%
!! CTATGCAAAGTTTTTATGAA+TGG - tig0019465:101957-101976 Msa1374100:intron 25.0%
! CATTAATGCACTATTGTTAA+TGG + tig0019465:102178-102197 None:intergenic 25.0%
!! TGTTATTTGTGACAATGATT+AGG - tig0019465:102340-102359 Msa1374100:intron 25.0%
! TACAACATTTAGTGATTGTA+GGG + tig0019465:102724-102743 None:intergenic 25.0%
TCTTCAAATAAAGGTTCAAC+TGG + tig0019465:101606-101625 None:intergenic 30.0%
! GCTTGAACAAAGAATTTTGT+TGG + tig0019465:101715-101734 None:intergenic 30.0%
TGAACTCATAATCAGAATGT+GGG + tig0019465:101870-101889 None:intergenic 30.0%
TTGAACTCATAATCAGAATG+TGG + tig0019465:101871-101890 None:intergenic 30.0%
ACAAATGACACCTGAATATT+TGG + tig0019465:102053-102072 None:intergenic 30.0%
!! AAATATTCAGGTGTCATTTG+TGG - tig0019465:102052-102071 Msa1374100:intron 30.0%
CAATAGTGCATTAATGTCAT+TGG - tig0019465:102182-102201 Msa1374100:intron 30.0%
TATTTGTGACAATGATTAGG+AGG - tig0019465:102343-102362 Msa1374100:intron 30.0%
ATTTGTGACAATGATTAGGA+GGG - tig0019465:102344-102363 Msa1374100:intron 30.0%
!! ATAAATCTTTGCTGGTTTGA+AGG - tig0019465:102419-102438 Msa1374100:intron 30.0%
ACACAAAGAAAGCCTATTAA+TGG + tig0019465:102507-102526 None:intergenic 30.0%
! CTTTATTTCACTTCCTTCTT+TGG + tig0019465:102575-102594 None:intergenic 30.0%
CAAAGAAGGAAGTGAAATAA+AGG - tig0019465:102573-102592 Msa1374100:intron 30.0%
AAGGAAGTGAAATAAAGGAA+AGG - tig0019465:102578-102597 Msa1374100:intron 30.0%
GGAATTGCTTATGTTACATA+CGG - tig0019465:102599-102618 Msa1374100:intron 30.0%
GAATTGCTTATGTTACATAC+GGG - tig0019465:102600-102619 Msa1374100:intron 30.0%
CTACAACATTTAGTGATTGT+AGG + tig0019465:102725-102744 None:intergenic 30.0%
CAATCACTAAATGTTGTAGT+CGG - tig0019465:102726-102745 Msa1374100:intron 30.0%
ATCTTTCTATTTGCTCAAGT+TGG - tig0019465:102751-102770 Msa1374100:intron 30.0%
ATTATTCAATGACAGGTTCT+TGG - tig0019465:102854-102873 Msa1374100:CDS 30.0%
TTATTCAATGACAGGTTCTT+GGG - tig0019465:102855-102874 Msa1374100:CDS 30.0%
TCTTCAAATAAAGGTTCAAC+TGG + tig0019465:101606-101625 None:intergenic 30.0%
! GCTTGAACAAAGAATTTTGT+TGG + tig0019465:101715-101734 None:intergenic 30.0%
TGAACTCATAATCAGAATGT+GGG + tig0019465:101870-101889 None:intergenic 30.0%
TTGAACTCATAATCAGAATG+TGG + tig0019465:101871-101890 None:intergenic 30.0%
ACAAATGACACCTGAATATT+TGG + tig0019465:102053-102072 None:intergenic 30.0%
!! AAATATTCAGGTGTCATTTG+TGG - tig0019465:102052-102071 Msa1374100:intron 30.0%
CAATAGTGCATTAATGTCAT+TGG - tig0019465:102182-102201 Msa1374100:intron 30.0%
TATTTGTGACAATGATTAGG+AGG - tig0019465:102343-102362 Msa1374100:intron 30.0%
ATTTGTGACAATGATTAGGA+GGG - tig0019465:102344-102363 Msa1374100:intron 30.0%
!! ATAAATCTTTGCTGGTTTGA+AGG - tig0019465:102419-102438 Msa1374100:intron 30.0%
ACACAAAGAAAGCCTATTAA+TGG + tig0019465:102507-102526 None:intergenic 30.0%
! CTTTATTTCACTTCCTTCTT+TGG + tig0019465:102575-102594 None:intergenic 30.0%
CAAAGAAGGAAGTGAAATAA+AGG - tig0019465:102573-102592 Msa1374100:intron 30.0%
AAGGAAGTGAAATAAAGGAA+AGG - tig0019465:102578-102597 Msa1374100:intron 30.0%
GGAATTGCTTATGTTACATA+CGG - tig0019465:102599-102618 Msa1374100:intron 30.0%
GAATTGCTTATGTTACATAC+GGG - tig0019465:102600-102619 Msa1374100:intron 30.0%
CTACAACATTTAGTGATTGT+AGG + tig0019465:102725-102744 None:intergenic 30.0%
CAATCACTAAATGTTGTAGT+CGG - tig0019465:102726-102745 Msa1374100:intron 30.0%
ATCTTTCTATTTGCTCAAGT+TGG - tig0019465:102751-102770 Msa1374100:intron 30.0%
ATTATTCAATGACAGGTTCT+TGG - tig0019465:102854-102873 Msa1374100:CDS 30.0%
TTATTCAATGACAGGTTCTT+GGG - tig0019465:102855-102874 Msa1374100:CDS 30.0%
CAGATATGTTGTGGAATGAA+TGG - tig0019465:101819-101838 Msa1374100:CDS 35.0%
AAACTTCAATCTGCCATGTT+TGG - tig0019465:102002-102021 Msa1374100:intron 35.0%
CATTGAACATGCTTGTAACT+TGG - tig0019465:102298-102317 Msa1374100:intron 35.0%
GTTAGCTGATAAATCTTTGC+TGG - tig0019465:102411-102430 Msa1374100:intron 35.0%
GATTCATTGTTCATGGAAAG+AGG + tig0019465:102551-102570 None:intergenic 35.0%
! CTTTGGAGATTCATTGTTCA+TGG + tig0019465:102558-102577 None:intergenic 35.0%
GAACAATGAATCTCCAAAGA+AGG - tig0019465:102559-102578 Msa1374100:intron 35.0%
!! TATTTGCTCAAGTTGGAACA+AGG - tig0019465:102758-102777 Msa1374100:intron 35.0%
!! ATTTGCTCAAGTTGGAACAA+GGG - tig0019465:102759-102778 Msa1374100:intron 35.0%
CACTGACATTATTCAATGAC+AGG - tig0019465:102847-102866 Msa1374100:CDS 35.0%
CAGATATGTTGTGGAATGAA+TGG - tig0019465:101819-101838 Msa1374100:CDS 35.0%
AAACTTCAATCTGCCATGTT+TGG - tig0019465:102002-102021 Msa1374100:intron 35.0%
CATTGAACATGCTTGTAACT+TGG - tig0019465:102298-102317 Msa1374100:intron 35.0%
GTTAGCTGATAAATCTTTGC+TGG - tig0019465:102411-102430 Msa1374100:intron 35.0%
GATTCATTGTTCATGGAAAG+AGG + tig0019465:102551-102570 None:intergenic 35.0%
! CTTTGGAGATTCATTGTTCA+TGG + tig0019465:102558-102577 None:intergenic 35.0%
GAACAATGAATCTCCAAAGA+AGG - tig0019465:102559-102578 Msa1374100:intron 35.0%
!! TATTTGCTCAAGTTGGAACA+AGG - tig0019465:102758-102777 Msa1374100:intron 35.0%
!! ATTTGCTCAAGTTGGAACAA+GGG - tig0019465:102759-102778 Msa1374100:intron 35.0%
CACTGACATTATTCAATGAC+AGG - tig0019465:102847-102866 Msa1374100:CDS 35.0%
TGCTTGTGTCAGATATGTTG+TGG - tig0019465:101810-101829 Msa1374100:CDS 40.0%
! TTCATAGGGCTTTTGCTTTC+TGG + tig0019465:101912-101931 None:intergenic 40.0%
CTCCATGTCTCCAAATATTC+AGG - tig0019465:102040-102059 Msa1374100:intron 40.0%
CACCTGAATATTTGGAGACA+TGG + tig0019465:102045-102064 None:intergenic 40.0%
! ACTGCAAACTTGTTCTCCAA+GGG + tig0019465:102377-102396 None:intergenic 40.0%
TCAGGGAATTGATCTACAAG+AGG - tig0019465:102642-102661 Msa1374100:intron 40.0%
CAGGGAATTGATCTACAAGA+GGG - tig0019465:102643-102662 Msa1374100:intron 40.0%
AGGGAATTGATCTACAAGAG+GGG - tig0019465:102644-102663 Msa1374100:intron 40.0%
TTGATCTACAAGAGGGGATA+CGG - tig0019465:102650-102669 Msa1374100:intron 40.0%
ACAAGCAGATTTCATCGAAC+AGG - tig0019465:102681-102700 Msa1374100:intron 40.0%
TCGAACAGGTTTGTCTGATT+TGG - tig0019465:102695-102714 Msa1374100:intron 40.0%
TGCTTGTGTCAGATATGTTG+TGG - tig0019465:101810-101829 Msa1374100:CDS 40.0%
! TTCATAGGGCTTTTGCTTTC+TGG + tig0019465:101912-101931 None:intergenic 40.0%
CTCCATGTCTCCAAATATTC+AGG - tig0019465:102040-102059 Msa1374100:intron 40.0%
CACCTGAATATTTGGAGACA+TGG + tig0019465:102045-102064 None:intergenic 40.0%
! ACTGCAAACTTGTTCTCCAA+GGG + tig0019465:102377-102396 None:intergenic 40.0%
TCAGGGAATTGATCTACAAG+AGG - tig0019465:102642-102661 Msa1374100:intron 40.0%
CAGGGAATTGATCTACAAGA+GGG - tig0019465:102643-102662 Msa1374100:intron 40.0%
AGGGAATTGATCTACAAGAG+GGG - tig0019465:102644-102663 Msa1374100:intron 40.0%
TTGATCTACAAGAGGGGATA+CGG - tig0019465:102650-102669 Msa1374100:intron 40.0%
ACAAGCAGATTTCATCGAAC+AGG - tig0019465:102681-102700 Msa1374100:intron 40.0%
TCGAACAGGTTTGTCTGATT+TGG - tig0019465:102695-102714 Msa1374100:intron 40.0%
! CAATCTGCCATGTTTGGTGA+AGG - tig0019465:102008-102027 Msa1374100:intron 45.0%
AAGAGGACCTTCACCAAACA+TGG + tig0019465:102018-102037 None:intergenic 45.0%
TTTGGAGACATGGAGTCAAG+AGG + tig0019465:102035-102054 None:intergenic 45.0%
TTAGGAGGGAACTTATCCCT+TGG - tig0019465:102358-102377 Msa1374100:intron 45.0%
! GACTGCAAACTTGTTCTCCA+AGG + tig0019465:102378-102397 None:intergenic 45.0%
TGGAGAACAAGTTTGCAGTC+AGG - tig0019465:102378-102397 Msa1374100:intron 45.0%
! CAATCTGCCATGTTTGGTGA+AGG - tig0019465:102008-102027 Msa1374100:intron 45.0%
AAGAGGACCTTCACCAAACA+TGG + tig0019465:102018-102037 None:intergenic 45.0%
TTTGGAGACATGGAGTCAAG+AGG + tig0019465:102035-102054 None:intergenic 45.0%
TTAGGAGGGAACTTATCCCT+TGG - tig0019465:102358-102377 Msa1374100:intron 45.0%
! GACTGCAAACTTGTTCTCCA+AGG + tig0019465:102378-102397 None:intergenic 45.0%
TGGAGAACAAGTTTGCAGTC+AGG - tig0019465:102378-102397 Msa1374100:intron 45.0%
!! AAGAAATATTTAAATTTAAA+CGG - tig0019465:102141-102160 Msa1374100:intron 5.0%
!! AAGAAATATTTAAATTTAAA+CGG - tig0019465:102141-102160 Msa1374100:intron 5.0%
! TGTTTCTGACCTCTGCGAGA+AGG - tig0019465:101843-101862 Msa1374100:CDS 50.0%
!! ACCCTAATCTGAAGAGCGTC+AGG - tig0019465:102624-102643 Msa1374100:intron 50.0%
CCCTGACGCTCTTCAGATTA+GGG + tig0019465:102628-102647 None:intergenic 50.0%
!! CCCTAATCTGAAGAGCGTCA+GGG - tig0019465:102625-102644 Msa1374100:intron 50.0%
TCCCTGACGCTCTTCAGATT+AGG + tig0019465:102629-102648 None:intergenic 50.0%
TGACAGGTTCTTGGGAAGCA+CGG - tig0019465:102863-102882 Msa1374100:CDS 50.0%
! TGTTTCTGACCTCTGCGAGA+AGG - tig0019465:101843-101862 Msa1374100:CDS 50.0%
!! ACCCTAATCTGAAGAGCGTC+AGG - tig0019465:102624-102643 Msa1374100:intron 50.0%
CCCTGACGCTCTTCAGATTA+GGG + tig0019465:102628-102647 None:intergenic 50.0%
!! CCCTAATCTGAAGAGCGTCA+GGG - tig0019465:102625-102644 Msa1374100:intron 50.0%
TCCCTGACGCTCTTCAGATT+AGG + tig0019465:102629-102648 None:intergenic 50.0%
TGACAGGTTCTTGGGAAGCA+CGG - tig0019465:102863-102882 Msa1374100:CDS 50.0%
AATGTGGGACCTTCTCGCAG+AGG + tig0019465:101855-101874 None:intergenic 55.0%
CAGTCAGCGTACACGCAATC+TGG + tig0019465:102808-102827 None:intergenic 55.0%
AATGTGGGACCTTCTCGCAG+AGG + tig0019465:101855-101874 None:intergenic 55.0%
CAGTCAGCGTACACGCAATC+TGG + tig0019465:102808-102827 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0019465 gene 101573 102908 101573 ID=Msa1374100;Name=Msa1374100
tig0019465 mRNA 101573 102908 101573 ID=Msa1374100-mRNA-1;Parent=Msa1374100;Name=Msa1374100-mRNA-1;_AED=0.56;_eAED=0.69;_QI=0|0|0|1|0|0|3|0|70
tig0019465 exon 102844 102908 102844 ID=Msa1374100-mRNA-1:exon:3763;Parent=Msa1374100-mRNA-1
tig0019465 exon 101779 101886 101779 ID=Msa1374100-mRNA-1:exon:3762;Parent=Msa1374100-mRNA-1
tig0019465 exon 101573 101612 101573 ID=Msa1374100-mRNA-1:exon:3761;Parent=Msa1374100-mRNA-1
tig0019465 CDS 102844 102908 102844 ID=Msa1374100-mRNA-1:cds;Parent=Msa1374100-mRNA-1
tig0019465 CDS 101779 101886 101779 ID=Msa1374100-mRNA-1:cds;Parent=Msa1374100-mRNA-1
tig0019465 CDS 101573 101612 101573 ID=Msa1374100-mRNA-1:cds;Parent=Msa1374100-mRNA-1
Gene Sequence

>Msa1374100

ATGAATGCCATAAGGATTTCAGTAATTATTCCAGTTGAACCTTTATTTGAAGAATGTGAAAAGAGGAAAGGAATTGCTTATGTTACATACGGGTACCCTAATCTGAAGAGCGTCAGGGAATTGATCTACAAGAGGGGATACGGCAAAGTTGACAAGCAGATTTCATCGAACAGGTTCTTGGGAAGCACGGTATCATTTGCATTGAAGATCTGA

Protein sequence

>Msa1374100

MNAIRISVIIPVEPLFEECEKRKGIAYVTYGYPNLKSVRELIYKRGYGKVDKQISSNRFLGSTVSFALKI*