AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene047324

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene047324.t1 MTR_2g013920 87.861 173 19 2 1 171 1 173 3.81e-106 301
MS.gene047324.t1 MTR_2g090440 41.667 168 90 3 6 167 12 177 1.05e-37 129
MS.gene047324.t1 MTR_2g090480 39.412 170 93 4 6 167 12 179 1.14e-35 124
MS.gene047324.t1 MTR_2g090425 40.571 175 93 4 6 171 12 184 2.88e-35 125
MS.gene047324.t1 MTR_4g078350 44.134 179 78 8 3 167 7 177 6.28e-35 121
MS.gene047324.t1 MTR_2g090500 36.111 144 86 2 28 167 49 190 3.87e-26 99.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene047324.t1 AT4G20970 41.808 177 91 5 3 167 7 183 8.75e-38 128

Find 27 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTATTTAGGTAGGAGAATT+TGG 0.200977 2.3:-70750854 MS.gene047324:intron
TTAGAGGTTGTTCTAATAAC+TGG 0.223327 2.3:-70751961 MS.gene047324:CDS
AAAATTAAGATACAACAAAT+TGG 0.306857 2.3:-70751991 MS.gene047324:CDS
TTTCTATTCATATTCACATT+TGG 0.306963 2.3:+70752039 None:intergenic
ACAAATTGGTTTAGTCTTAG+AGG 0.319445 2.3:-70751977 MS.gene047324:CDS
TCTGCCTCATCAAACTTCTA+AGG 0.344529 2.3:-70752386 MS.gene047324:intron
CTGTCAACTCTTGATGAACT+AGG 0.359161 2.3:+70752472 None:intergenic
TATTGTCAATGCAAGTTATA+AGG 0.360092 2.3:-70751878 MS.gene047324:CDS
GGTTGTTCTAATAACTGGAT+TGG 0.435753 2.3:-70751956 MS.gene047324:CDS
CTTCGTGTTCTTCATGAAGA+AGG 0.454763 2.3:-70751907 MS.gene047324:CDS
TTTCCATTCAATACACTGCC+AGG 0.478671 2.3:-70751839 MS.gene047324:intron
GAAAAGAAGAACTTTCTACT+AGG 0.532951 2.3:-70752072 MS.gene047324:CDS
TGTCAACTCTTGATGAACTA+GGG 0.540967 2.3:+70752473 None:intergenic
GATCAACTTGGAGAAAATGA+AGG 0.550998 2.3:-70752094 MS.gene047324:CDS
CTAGTTCATCAAGAGTTGAC+AGG 0.559038 2.3:-70752471 MS.gene047324:CDS
TTACCTGGCAGTGTATTGAA+TGG 0.573100 2.3:+70751836 None:intergenic
ACTTTCTACTAGGAATTCAA+AGG 0.595040 2.3:-70752062 MS.gene047324:CDS
AAAGAAATTACAGATCAACT+TGG 0.602314 2.3:-70752106 MS.gene047324:CDS
GAGACCTTAGAAGTTTGATG+AGG 0.624740 2.3:+70752382 None:intergenic
ATGAATAGAAACAAGAACAT+GGG 0.625623 2.3:-70752027 MS.gene047324:CDS
TATGAATAGAAACAAGAACA+TGG 0.630359 2.3:-70752028 MS.gene047324:CDS
TCTGATGCAGGTGATTTCAG+CGG 0.656257 2.3:-70752160 MS.gene047324:intron
GCAGAAATGAGTTGAGCTTG+TGG 0.677546 2.3:+70752404 None:intergenic
CTTCTTCATGAAGAACACGA+AGG 0.679799 2.3:+70751908 None:intergenic
AATTTGGTAATGAAGCTGCA+AGG 0.690882 2.3:-70750838 MS.gene047324:CDS
GAAATGAGTTGAGCTTGTGG+CGG 0.691957 2.3:+70752407 None:intergenic
TTCAGCGGCAGATCAGCTCG+AGG 0.700026 2.3:-70752145 MS.gene047324:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGATAAAAATATGATTATT+TGG - chr2.3:70752317-70752336 MS.gene047324:intron 10.0%
!!! TAATTAGAAGTTTTTTTTTT+TGG + chr2.3:70751768-70751787 None:intergenic 10.0%
!!! TATGATTTTTATAATATTTG+TGG - chr2.3:70752054-70752073 MS.gene047324:CDS 10.0%
!! AAAATTAAGATACAACAAAT+TGG - chr2.3:70751295-70751314 MS.gene047324:intron 15.0%
!! AAAGTTAACTATTTATAGAT+AGG + chr2.3:70752397-70752416 None:intergenic 15.0%
!! TTAATTTCCTTTAATATGAA+CGG - chr2.3:70751488-70751507 MS.gene047324:intron 15.0%
!!! ATTTGTTGTATCTTAATTTT+TGG + chr2.3:70751295-70751314 None:intergenic 15.0%
!!! TTTAGTTATTTTTTTCTTTG+AGG - chr2.3:70751941-70751960 MS.gene047324:CDS 15.0%
!!! TTTTTTTTTTGGAAAATTTG+AGG + chr2.3:70751757-70751776 None:intergenic 15.0%
!! AATTTAGTTGTCATTATAAG+TGG - chr2.3:70751969-70751988 MS.gene047324:CDS 20.0%
!! ATACTTAAATACATGAATCA+GGG + chr2.3:70751919-70751938 None:intergenic 20.0%
!! ATGTTAGTATTGTTAGTATT+TGG - chr2.3:70751087-70751106 MS.gene047324:intron 20.0%
!! GAAAAAAATAGAATTAGTGA+CGG - chr2.3:70750988-70751007 MS.gene047324:intron 20.0%
!! TTCAAACTGATATTTGAATA+CGG - chr2.3:70752368-70752387 MS.gene047324:intron 20.0%
!! TTTCTATTCATATTCACATT+TGG + chr2.3:70751250-70751269 None:intergenic 20.0%
!!! ATTAACTTGTGTCTTAATTA+AGG - chr2.3:70751656-70751675 MS.gene047324:intron 20.0%
!!! TAATTTAATTTATCTGATGC+AGG - chr2.3:70751114-70751133 MS.gene047324:intron 20.0%
! AAAGAAATTACAGATCAACT+TGG - chr2.3:70751180-70751199 MS.gene047324:intron 25.0%
! AGTCAATAACATCAAACTAA+CGG + chr2.3:70752249-70752268 None:intergenic 25.0%
! ATGAATAGAAACAAGAACAT+GGG - chr2.3:70751259-70751278 MS.gene047324:intron 25.0%
! CATACTTAAATACATGAATC+AGG + chr2.3:70751920-70751939 None:intergenic 25.0%
! CTAATTGCATTGTTCTATTT+AGG - chr2.3:70752419-70752438 MS.gene047324:CDS 25.0%
! GTAACAATTTATGATTTACC+TGG + chr2.3:70751468-70751487 None:intergenic 25.0%
! GTTAACTATTTATAGATAGG+AGG + chr2.3:70752394-70752413 None:intergenic 25.0%
! TATGAATAGAAACAAGAACA+TGG - chr2.3:70751258-70751277 MS.gene047324:intron 25.0%
! TATTGTCAATGCAAGTTATA+AGG - chr2.3:70751408-70751427 MS.gene047324:intron 25.0%
!! ATTTCTTCTTTTGCTTTCAA+TGG + chr2.3:70750845-70750864 None:intergenic 25.0%
!! CATTTAGTGAATGATTTTGT+CGG + chr2.3:70751791-70751810 None:intergenic 25.0%
!! TGATGTTATTGACTACAATA+TGG - chr2.3:70752255-70752274 MS.gene047324:intron 25.0%
!!! GTCATTATGTTTTAAAACGA+CGG - chr2.3:70751064-70751083 MS.gene047324:intron 25.0%
ACATGATCCGTTCATATTAA+AGG + chr2.3:70751498-70751517 None:intergenic 30.0%
ACTTTCTACTAGGAATTCAA+AGG - chr2.3:70751224-70751243 MS.gene047324:intron 30.0%
ATATGAAATCAAGTGCAAGA+AGG - chr2.3:70751699-70751718 MS.gene047324:intron 30.0%
CTTGCACTTGATTTCATATT+GGG + chr2.3:70751698-70751717 None:intergenic 30.0%
GAAAAGAAGAACTTTCTACT+AGG - chr2.3:70751214-70751233 MS.gene047324:intron 30.0%
GTCAATAACATCAAACTAAC+GGG + chr2.3:70752248-70752267 None:intergenic 30.0%
TCAATAACATCAAACTAACG+GGG + chr2.3:70752247-70752266 None:intergenic 30.0%
TCTATTTAGGTAGGAGAATT+TGG - chr2.3:70752432-70752451 MS.gene047324:CDS 30.0%
TCTTGCACTTGATTTCATAT+TGG + chr2.3:70751699-70751718 None:intergenic 30.0%
TTAGAGGTTGTTCTAATAAC+TGG - chr2.3:70751325-70751344 MS.gene047324:intron 30.0%
TTGCATTGTTCTATTTAGGT+AGG - chr2.3:70752423-70752442 MS.gene047324:CDS 30.0%
! CTACCGAATATTTTCTCAAA+GGG - chr2.3:70752207-70752226 MS.gene047324:intron 30.0%
! GTCTTACATACTTTTACGTA+TGG + chr2.3:70751822-70751841 None:intergenic 30.0%
! TACCCCTTTGAGAAAATATT+CGG + chr2.3:70752213-70752232 None:intergenic 30.0%
! TACCGAATATTTTCTCAAAG+GGG - chr2.3:70752208-70752227 MS.gene047324:intron 30.0%
! TCTACCGAATATTTTCTCAA+AGG - chr2.3:70752206-70752225 MS.gene047324:intron 30.0%
!! ACAAATTGGTTTAGTCTTAG+AGG - chr2.3:70751309-70751328 MS.gene047324:intron 30.0%
!! GTCAATTATGCTTTGTTTCT+AGG - chr2.3:70751854-70751873 MS.gene047324:CDS 30.0%
!! TTCCTTAACTTGTGTTCTTA+AGG + chr2.3:70751530-70751549 None:intergenic 30.0%
CTAAGAGAAGAAGAGAGTAA+AGG + chr2.3:70750939-70750958 None:intergenic 35.0%
GATCAACTTGGAGAAAATGA+AGG - chr2.3:70751192-70751211 MS.gene047324:intron 35.0%
GGTTGTTCTAATAACTGGAT+TGG - chr2.3:70751330-70751349 MS.gene047324:intron 35.0%
TGCCTTAAGAACACAAGTTA+AGG - chr2.3:70751525-70751544 MS.gene047324:intron 35.0%
TGTCAACTCTTGATGAACTA+GGG + chr2.3:70750816-70750835 None:intergenic 35.0%
! CAAGCTTTAGTTTCACCTAA+GGG + chr2.3:70751894-70751913 None:intergenic 35.0%
! TCAAGCTTTAGTTTCACCTA+AGG + chr2.3:70751895-70751914 None:intergenic 35.0%
!! AATTTGGTAATGAAGCTGCA+AGG - chr2.3:70752448-70752467 MS.gene047324:CDS 35.0%
ACATGACCTCGAAGTTATAG+GGG - chr2.3:70751730-70751749 MS.gene047324:intron 40.0%
CACATGACCTCGAAGTTATA+GGG - chr2.3:70751729-70751748 MS.gene047324:intron 40.0%
CTAGTTCATCAAGAGTTGAC+AGG - chr2.3:70750815-70750834 MS.gene047324:CDS 40.0%
CTGTCAACTCTTGATGAACT+AGG + chr2.3:70750817-70750836 None:intergenic 40.0%
CTTCGTGTTCTTCATGAAGA+AGG - chr2.3:70751379-70751398 MS.gene047324:intron 40.0%
CTTCTTCATGAAGAACACGA+AGG + chr2.3:70751381-70751400 None:intergenic 40.0%
GAGACCTTAGAAGTTTGATG+AGG + chr2.3:70750907-70750926 None:intergenic 40.0%
GTAAATGTCTATGTGCCCTT+AGG - chr2.3:70751876-70751895 MS.gene047324:CDS 40.0%
TCTGCCTCATCAAACTTCTA+AGG - chr2.3:70750900-70750919 MS.gene047324:intron 40.0%
TTACCTGGCAGTGTATTGAA+TGG + chr2.3:70751453-70751472 None:intergenic 40.0%
TTTCCATTCAATACACTGCC+AGG - chr2.3:70751447-70751466 MS.gene047324:intron 40.0%
ACTTCGAGGTCATGTGCTAA+AGG + chr2.3:70751725-70751744 None:intergenic 45.0%
GCACATGACCTCGAAGTTAT+AGG - chr2.3:70751728-70751747 MS.gene047324:intron 45.0%
TCTGATGCAGGTGATTTCAG+CGG - chr2.3:70751126-70751145 MS.gene047324:intron 45.0%
! GAAATGAGTTGAGCTTGTGG+CGG + chr2.3:70750882-70750901 None:intergenic 45.0%
! GCAGAAATGAGTTGAGCTTG+TGG + chr2.3:70750885-70750904 None:intergenic 45.0%
!! TTATTTAATAAACAAAATAA+AGG - chr2.3:70752143-70752162 MS.gene047324:CDS 5.0%
TGAGGTCCCCTATAACTTCG+AGG + chr2.3:70751739-70751758 None:intergenic 50.0%
TTCAGCGGCAGATCAGCTCG+AGG - chr2.3:70751141-70751160 MS.gene047324:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 70750802 70752506 70750802 ID=MS.gene047324
chr2.3 mRNA 70750802 70752506 70750802 ID=MS.gene047324.t1;Parent=MS.gene047324
chr2.3 exon 70752387 70752506 70752387 ID=MS.gene047324.t1.exon1;Parent=MS.gene047324.t1
chr2.3 CDS 70752387 70752506 70752387 ID=cds.MS.gene047324.t1;Parent=MS.gene047324.t1
chr2.3 exon 70751840 70752172 70751840 ID=MS.gene047324.t1.exon2;Parent=MS.gene047324.t1
chr2.3 CDS 70751840 70752172 70751840 ID=cds.MS.gene047324.t1;Parent=MS.gene047324.t1
chr2.3 exon 70750802 70750867 70750802 ID=MS.gene047324.t1.exon3;Parent=MS.gene047324.t1
chr2.3 CDS 70750802 70750867 70750802 ID=cds.MS.gene047324.t1;Parent=MS.gene047324.t1
Gene Sequence

>MS.gene047324

ATGGAGAATAACCCTAGTTCATCAAGAGTTGACAGGAAATCCATTGAAAGCAAAAGAAGAAATCAAATGAAAGCTCTCCGCCACAAGCTCAACTCATTTCTGCCTCATCAAACTTCTAAGGTCTCTCTTAATTTCCTTTACTCTCTTCTTCTCTTAGATGCTTAGTCAATTATATGAATTATACTAGAAAAAAATAGAATTAGTGACGGAAAAAATAAAATTCGTTACAAGTAATTAGAAATGTTCTCTTCTTAAATTTTATGTCATTATGTTTTAAAACGACGGATGTTAGTATTGTTAGTATTTGGTCACTAATTTAATTTATCTGATGCAGGTGATTTCAGCGGCAGATCAGCTCGAGGAAGCAACAAACTACATAAAGAAATTACAGATCAACTTGGAGAAAATGAAGGAAAAGAAGAACTTTCTACTAGGAATTCAAAGGCCAAATGTGAATATGAATAGAAACAAGAACATGGGATTAAAGACTCCAAAAATTAAGATACAACAAATTGGTTTAGTCTTAGAGGTTGTTCTAATAACTGGATTGGATTCTCAGTTTTTGTTCAATGAAATCCTTCGTGTTCTTCATGAAGAAGGAGTTGATATTGTCAATGCAAGTTATAAGGTCAATGAAGATTCAGTTTTCCATTCAATACACTGCCAGGTAAATCATAAATTGTTACTTAATTTCCTTTAATATGAACGGATCATGTTAACTTGTGCCTTAAGAACACAAGTTAAGGAATTTAAAAAAAGAAATAAAAAATAAATTTTATATTGAAAATATAAGTTCTTACACTTTTACATCATTGAATACACAATTTTCAAGAAAAAACTTCTATTTTTAGCTTATTAACTTGTGTCTTAATTAAGGATACAAGTTAGCATTTCCCAATATGAAATCAAGTGCAAGAAGGCCTTTAGCACATGACCTCGAAGTTATAGGGGACCTCAAATTTTCCAAAAAAAAAAACTTCTAATTACCGACAAAATCATTCACTAAATGTCATTTGTCCATACGTAAAAGTATGTAAGACAACAATTTTTATGTCAATTATGCTTTGTTTCTAGGTAAATGTCTATGTGCCCTTAGGTGAAACTAAAGCTTGAACCCTGATTCATGTATTTAAGTATGATTTAGTTATTTTTTTCTTTGAGGAAAACAATTTAGTTGTCATTATAAGTGGTGTTGAAATTTTTTTATATTTTCTTTTTAGATGAAAATCATCAAATGTGAATCAATTTATTTTATGATTTTTATAATATTTGTGGAATATTATTATTATTATTATCATTGTTTTTTTTTTGAAACAATTATTAGCATCATAAGACGTCTATTTATTTAATAAACAAAATAAAGGAGTTTATTTATTTTTTTTAAAATTGTTATTGAATTGTATATCTACCGAATATTTTCTCAAAGGGGTAGAATATGAATACCCCGTTAGTTTGATGTTATTGACTACAATATGGTTCTTGTTTATGTTATTGATGTTATTTAACTACAAGTTATTGATAAAAATATGATTATTTGGTATGACTTGCGTCAAACGATGAAATTTTTTCAAACTGATATTTGAATACGGCCTCCTATCTATAAATAGTTAACTTTAGCTAATTGCATTGTTCTATTTAGGTAGGAGAATTTGGTAATGAAGCTGCAAGGATATCTGAGAGATTGAAGTTTATGCAAGATTGTTAG
Protein sequence

>MS.gene047324.t1

MENNPSSSRVDRKSIESKRRNQMKALRHKLNSFLPHQTSKVISAADQLEEATNYIKKLQINLEKMKEKKNFLLGIQRPNVNMNRNKNMGLKTPKIKIQQIGLVLEVVLITGLDSQFLFNEILRVLHEEGVDIVNASYKVNEDSVFHSIHCQVGEFGNEAARISERLKFMQDC