AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene029109

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029109.t1 MTR_1g115545 98.347 121 2 0 1 121 1 121 8.33e-81 233
MS.gene029109.t1 MTR_1g067490 92.500 120 9 0 2 121 3 122 1.59e-74 217
MS.gene029109.t1 MTR_4g062410 91.667 120 10 0 2 121 4 123 2.08e-72 211
MS.gene029109.t1 MTR_7g080090 90.000 120 12 0 2 121 4 123 4.69e-71 208
MS.gene029109.t1 MTR_4g072410 85.124 121 18 0 1 121 1 121 2.70e-67 199
MS.gene029109.t1 MTR_1g105880 72.222 90 14 1 9 98 2 80 1.31e-35 117
MS.gene029109.t1 MTR_5g045540 88.571 35 4 0 65 99 2 36 5.06e-14 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene029109.t1 AT2G39390 88.235 119 14 0 2 120 4 122 4.36e-70 206
MS.gene029109.t1 AT3G09500 87.395 119 15 0 2 120 4 122 1.19e-68 202
MS.gene029109.t1 AT5G02610 87.395 119 15 0 2 120 4 122 1.82e-68 202
MS.gene029109.t1 AT3G55170 85.714 119 17 0 2 120 4 122 4.19e-67 198
MS.gene029109.t1 AT3G55170 85.714 119 17 0 2 120 4 122 4.19e-67 198
MS.gene029109.t1 AT3G55170 85.714 119 17 0 2 120 4 122 4.19e-67 198
MS.gene029109.t1 AT5G02610 73.239 142 15 1 2 120 4 145 9.02e-63 188
MS.gene029109.t1 AT3G55170 86.458 96 13 0 2 97 4 99 4.75e-52 159
MS.gene029109.t1 AT3G55170 86.458 96 13 0 2 97 4 99 4.75e-52 159

Find 32 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAATGGCCCTGGTCTTCTT+TGG 0.171363 1.3:+78726365 None:intergenic
TCAAAGCAGCCTTCTGCTTC+TGG 0.210134 1.3:+78726432 None:intergenic
TTGATAGCATATTTCCTCAT+TGG 0.349490 1.3:+78725485 None:intergenic
GAATGGCCCTGGTCTTCTTT+GGG 0.358511 1.3:+78726366 None:intergenic
GACCGAGAGGGAGAAGAAAA+AGG 0.368054 1.3:-78725519 MS.gene029109:CDS
TGATAGCATATTTCCTCATT+GGG 0.379576 1.3:+78725486 None:intergenic
GAAGCAGAAGGCTGCTTTGA+GGG 0.418273 1.3:-78726429 MS.gene029109:CDS
CAAAGCAGCCTTCTGCTTCT+GGG 0.419055 1.3:+78726433 None:intergenic
GAGCCTTCTGCGAATGGCCC+TGG 0.419374 1.3:+78726355 None:intergenic
CTCCGTGTTGCTAAGGTCAC+TGG 0.447113 1.3:-78726830 MS.gene029109:CDS
GTAAAGCAAGTTCAGCTTTG+AGG 0.452854 1.3:+78726852 None:intergenic
CTTGGTGAGCCTTCTGCGAA+TGG 0.472202 1.3:+78726349 None:intergenic
AATGAGGAAATATGCTATCA+AGG 0.472756 1.3:-78725483 MS.gene029109:CDS
TGCTTTACTCCGTGTTGCTA+AGG 0.473685 1.3:-78726837 MS.gene029109:CDS
GAAATATGCTATCAAGGCAT+AGG 0.504384 1.3:-78725477 None:intergenic
AGGGTTTAATACCTGGTGCT+TGG 0.515451 1.3:+78726331 None:intergenic
CAGTGAAGGTTCACGAGTTG+AGG 0.518240 1.3:-78726913 MS.gene029109:CDS
ATCTCCGCCCAAAGAAGACC+AGG 0.531518 1.3:-78726373 MS.gene029109:CDS
CAGAAGGCTCACCAAGCACC+AGG 0.535404 1.3:-78726342 MS.gene029109:intron
TTCTTTGGGCGGAGATCAAG+TGG 0.553377 1.3:+78726380 None:intergenic
GGTGAGGTTGTCGATTGCTC+AGG 0.570678 1.3:-78726471 MS.gene029109:CDS
TGGCCCTGGTCTTCTTTGGG+CGG 0.571866 1.3:+78726369 None:intergenic
AAATATGCTATCAAGGCATA+GGG 0.572355 1.3:-78725476 None:intergenic
AGAAGCAGAAGGCTGCTTTG+AGG 0.576045 1.3:-78726430 MS.gene029109:CDS
AGACCAGGGCCATTCGCAGA+AGG 0.591558 1.3:-78726358 MS.gene029109:CDS
AGGAGACATATTTCCCAATG+AGG 0.613250 1.3:-78725499 MS.gene029109:CDS
AGTGATTTCCCAGAAGCAGA+AGG 0.617415 1.3:-78726441 MS.gene029109:CDS
CACCAGTGACCTTAGCAACA+CGG 0.624056 1.3:+78726828 None:intergenic
GTCTTCGCTGAAGACCGAGA+GGG 0.684722 1.3:-78725531 MS.gene029109:CDS
CGTGTTGCTAAGGTCACTGG+TGG 0.692805 1.3:-78726827 MS.gene029109:CDS
TCTCCGCCCAAAGAAGACCA+GGG 0.718890 1.3:-78726372 MS.gene029109:CDS
AGTCTTCGCTGAAGACCGAG+AGG 0.727322 1.3:-78725532 MS.gene029109:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTTTTGATTATTTTATTT+GGG - chr1.3:78725983-78726002 MS.gene029109:intron 10.0%
!!! TTGAATTTTTATTTACATTT+TGG + chr1.3:78725707-78725726 None:intergenic 10.0%
!!! TTGTTTTTGATTATTTTATT+TGG - chr1.3:78725982-78726001 MS.gene029109:intron 10.0%
!! AAATTTCAGTTTGTATATAT+AGG + chr1.3:78726862-78726881 None:intergenic 15.0%
!! AACATGAATTATACATTAAA+AGG + chr1.3:78726183-78726202 None:intergenic 15.0%
!! ACATGAATTATACATTAAAA+GGG + chr1.3:78726182-78726201 None:intergenic 15.0%
!!! ACATTCAATTTTATGTTTTA+AGG + chr1.3:78726618-78726637 None:intergenic 15.0%
!! GAATGAAATCTTAAATAATG+AGG - chr1.3:78726432-78726451 MS.gene029109:CDS 20.0%
!! TAGTGAATTTCATGTAAAAA+TGG + chr1.3:78726647-78726666 None:intergenic 20.0%
!! TTTGTTTAGAAGATAATAAC+TGG - chr1.3:78726695-78726714 MS.gene029109:intron 20.0%
!!! AGTTTTCTTTCTAAAATCAA+AGG - chr1.3:78726531-78726550 MS.gene029109:intron 20.0%
!!! CTTTATTCTTTTATGTCAAT+TGG - chr1.3:78725728-78725747 MS.gene029109:intron 20.0%
!!! TTGTTTGATTTCAGAAATTA+GGG + chr1.3:78725503-78725522 None:intergenic 20.0%
!!! TTTGTTTGATTTCAGAAATT+AGG + chr1.3:78725504-78725523 None:intergenic 20.0%
! AACAATTTATCCTTCAGAAT+TGG + chr1.3:78725864-78725883 None:intergenic 25.0%
! CTTTCAAGGATAACATTTAA+TGG + chr1.3:78726575-78726594 None:intergenic 25.0%
! GATTGTGTGATGATTATAAT+GGG - chr1.3:78725904-78725923 MS.gene029109:intron 25.0%
! TGATTATTACTGTTCTTTCA+AGG + chr1.3:78726589-78726608 None:intergenic 25.0%
! TGATTGTGTGATGATTATAA+TGG - chr1.3:78725903-78725922 MS.gene029109:intron 25.0%
! TTAGAAGATAATAACTGGAT+TGG - chr1.3:78726700-78726719 MS.gene029109:intron 25.0%
AACAACCAATATGGTGTAAA+AGG + chr1.3:78726749-78726768 None:intergenic 30.0%
AATGAGGAAATATGCTATCA+AGG - chr1.3:78727008-78727027 MS.gene029109:intron 30.0%
ACATACAAGCAAAGAGAAAA+AGG + chr1.3:78726830-78726849 None:intergenic 30.0%
AGGATAACATTTAATGGTGT+AGG + chr1.3:78726569-78726588 None:intergenic 30.0%
CATTAAAAGGGTTTAATACC+TGG + chr1.3:78726170-78726189 None:intergenic 30.0%
GAAGGATAAATTGTTCCTTT+CGG - chr1.3:78725869-78725888 MS.gene029109:intron 30.0%
TATCCTTCAGAATTGGTAAA+TGG + chr1.3:78725857-78725876 None:intergenic 30.0%
TGATAGCATATTTCCTCATT+GGG + chr1.3:78727008-78727027 None:intergenic 30.0%
TTTCGTCTCAAGTACTATTT+AGG - chr1.3:78726400-78726419 MS.gene029109:CDS 30.0%
! GATCTGTATCATTTGGAATA+AGG + chr1.3:78726469-78726488 None:intergenic 30.0%
! TATAGCCTTTTACACCATAT+TGG - chr1.3:78726741-78726760 MS.gene029109:intron 30.0%
! TTGATAGCATATTTCCTCAT+TGG + chr1.3:78727009-78727028 None:intergenic 30.0%
! TTTGATTTCAGAAATTAGGG+TGG + chr1.3:78725500-78725519 None:intergenic 30.0%
!! GCACGATTGTTCTAAAAATA+AGG + chr1.3:78725784-78725803 None:intergenic 30.0%
!! TAACTGGATTGGTTTATTGT+TGG - chr1.3:78726711-78726730 MS.gene029109:intron 30.0%
!! TTTATTTGGGTTTTGCAGTA+AGG - chr1.3:78725996-78726015 MS.gene029109:intron 30.0%
!! TTTTCAACCTGATTTGTCTT+GGG - chr1.3:78726767-78726786 MS.gene029109:intron 30.0%
!!! GTTTTTGTTTTGTGACTGTA+AGG - chr1.3:78725929-78725948 MS.gene029109:intron 30.0%
AGCAAAAACCACAGATACAT+TGG + chr1.3:78726236-78726255 None:intergenic 35.0%
ATACACCAATCACCAATTGA+TGG + chr1.3:78726333-78726352 None:intergenic 35.0%
GAAAAACAAAGCTGATCTGT+TGG - chr1.3:78725603-78725622 MS.gene029109:intron 35.0%
GCAAAAACCACAGATACATT+GGG + chr1.3:78726235-78726254 None:intergenic 35.0%
GCAAAGAGAAAAAGGTTACA+AGG + chr1.3:78726822-78726841 None:intergenic 35.0%
TATTGTGACCATCCATCAAT+TGG - chr1.3:78726318-78726337 MS.gene029109:intron 35.0%
TCAGAAATTAGGGTGGTTTA+GGG + chr1.3:78725493-78725512 None:intergenic 35.0%
TGAATATCCCAAGACAAATC+AGG + chr1.3:78726777-78726796 None:intergenic 35.0%
TTCAAGCAGAACAGTATGTT+TGG - chr1.3:78726902-78726921 MS.gene029109:CDS 35.0%
TTCAGAAATTAGGGTGGTTT+AGG + chr1.3:78725494-78725513 None:intergenic 35.0%
! AATTGTTCCTTTCGGTGTAA+TGG - chr1.3:78725877-78725896 MS.gene029109:intron 35.0%
! CAGGTTGAAAACAACCAATA+TGG + chr1.3:78726758-78726777 None:intergenic 35.0%
!! AATTGGTGCTATGATCGTAA+AGG - chr1.3:78725745-78725764 MS.gene029109:intron 35.0%
!! GTTTTCAACCTGATTTGTCT+TGG - chr1.3:78726766-78726785 MS.gene029109:intron 35.0%
!! TACATTTTGGAGAGCTTGTT+GGG + chr1.3:78725694-78725713 None:intergenic 35.0%
!! TTACATTTTGGAGAGCTTGT+TGG + chr1.3:78725695-78725714 None:intergenic 35.0%
!!! TGTGTTTTGATTTGCAGTGA+AGG - chr1.3:78725564-78725583 MS.gene029109:intron 35.0%
!!! TTTGTTTTGTGACTGTAAGG+TGG - chr1.3:78725932-78725951 MS.gene029109:intron 35.0%
AAAACCACAGATACATTGGG+AGG + chr1.3:78726232-78726251 None:intergenic 40.0%
ACCAATCACCAATTGATGGA+TGG + chr1.3:78726329-78726348 None:intergenic 40.0%
AGGAGACATATTTCCCAATG+AGG - chr1.3:78726992-78727011 MS.gene029109:intron 40.0%
ATCAAAGCCATTACACCGAA+AGG + chr1.3:78725887-78725906 None:intergenic 40.0%
ATGAAATTCACTACACGACC+AGG - chr1.3:78726654-78726673 MS.gene029109:intron 40.0%
CAGAAAATTGTACAGCAACC+TGG + chr1.3:78726675-78726694 None:intergenic 40.0%
CGTCCATTTACCAATTCTGA+AGG - chr1.3:78725851-78725870 MS.gene029109:intron 40.0%
GTAAAGCAAGTTCAGCTTTG+AGG + chr1.3:78725642-78725661 None:intergenic 40.0%
! ACCATCCATCAATTGGTGAT+TGG - chr1.3:78726325-78726344 MS.gene029109:intron 40.0%
!! ATTTGGGTTTTGCAGTAAGG+TGG - chr1.3:78725999-78726018 MS.gene029109:intron 40.0%
AGGGTTTAATACCTGGTGCT+TGG + chr1.3:78726163-78726182 None:intergenic 45.0%
AGTGATTTCCCAGAAGCAGA+AGG - chr1.3:78726050-78726069 MS.gene029109:intron 45.0%
ATACAGATCCTGCAGGTGTA+GGG - chr1.3:78726480-78726499 MS.gene029109:CDS 45.0%
CCAAATGATACAGATCCTGC+AGG - chr1.3:78726473-78726492 MS.gene029109:CDS 45.0%
CCTGCAGGATCTGTATCATT+TGG + chr1.3:78726476-78726495 None:intergenic 45.0%
TACACCTCCCAATGTATCTG+TGG - chr1.3:78726225-78726244 MS.gene029109:intron 45.0%
! CTCCTTTTTCTTCTCCCTCT+CGG + chr1.3:78726977-78726996 None:intergenic 45.0%
! TGCTTTACTCCGTGTTGCTA+AGG - chr1.3:78725654-78725673 MS.gene029109:intron 45.0%
CAAAGCAGCCTTCTGCTTCT+GGG + chr1.3:78726061-78726080 None:intergenic 50.0%
CACCAGTGACCTTAGCAACA+CGG + chr1.3:78725666-78725685 None:intergenic 50.0%
CAGTGAAGGTTCACGAGTTG+AGG - chr1.3:78725578-78725597 MS.gene029109:intron 50.0%
GACCGAGAGGGAGAAGAAAA+AGG - chr1.3:78726972-78726991 MS.gene029109:intron 50.0%
GATACAGATCCTGCAGGTGT+AGG - chr1.3:78726479-78726498 MS.gene029109:CDS 50.0%
TCAAAGCAGCCTTCTGCTTC+TGG + chr1.3:78726062-78726081 None:intergenic 50.0%
TTCTTTGGGCGGAGATCAAG+TGG + chr1.3:78726114-78726133 None:intergenic 50.0%
! AGAAGCAGAAGGCTGCTTTG+AGG - chr1.3:78726061-78726080 MS.gene029109:intron 50.0%
! GAAGCAGAAGGCTGCTTTGA+GGG - chr1.3:78726062-78726081 MS.gene029109:intron 50.0%
! GAATGGCCCTGGTCTTCTTT+GGG + chr1.3:78726128-78726147 None:intergenic 50.0%
! GGTTTTGCAGTAAGGTGGTG+AGG - chr1.3:78726004-78726023 MS.gene029109:intron 50.0%
AGTCTTCGCTGAAGACCGAG+AGG - chr1.3:78726959-78726978 MS.gene029109:intron 55.0%
ATCCTGCAGGTGTAGGGAGA+AGG - chr1.3:78726486-78726505 MS.gene029109:intron 55.0%
ATCCTTCTCCCTACACCTGC+AGG + chr1.3:78726491-78726510 None:intergenic 55.0%
ATCTCCGCCCAAAGAAGACC+AGG - chr1.3:78726118-78726137 MS.gene029109:intron 55.0%
CTTGGTGAGCCTTCTGCGAA+TGG + chr1.3:78726145-78726164 None:intergenic 55.0%
GTCTTCGCTGAAGACCGAGA+GGG - chr1.3:78726960-78726979 MS.gene029109:intron 55.0%
TCTCCGCCCAAAGAAGACCA+GGG - chr1.3:78726119-78726138 MS.gene029109:intron 55.0%
! CGAATGGCCCTGGTCTTCTT+TGG + chr1.3:78726129-78726148 None:intergenic 55.0%
! CGTGTTGCTAAGGTCACTGG+TGG - chr1.3:78725664-78725683 MS.gene029109:intron 55.0%
! CTCCGTGTTGCTAAGGTCAC+TGG - chr1.3:78725661-78725680 MS.gene029109:intron 55.0%
! GGTGAGGTTGTCGATTGCTC+AGG - chr1.3:78726020-78726039 MS.gene029109:intron 55.0%
AGACCAGGGCCATTCGCAGA+AGG - chr1.3:78726133-78726152 MS.gene029109:intron 60.0%
CAGAAGGCTCACCAAGCACC+AGG - chr1.3:78726149-78726168 MS.gene029109:intron 60.0%
! TGGCCCTGGTCTTCTTTGGG+CGG + chr1.3:78726125-78726144 None:intergenic 60.0%
GAGCCTTCTGCGAATGGCCC+TGG + chr1.3:78726139-78726158 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 78725478 78727035 78725478 ID=MS.gene029109
chr1.3 mRNA 78725478 78727035 78725478 ID=MS.gene029109.t1;Parent=MS.gene029109
chr1.3 exon 78727032 78727035 78727032 ID=MS.gene029109.t1.exon1;Parent=MS.gene029109.t1
chr1.3 CDS 78727032 78727035 78727032 ID=cds.MS.gene029109.t1;Parent=MS.gene029109.t1
chr1.3 exon 78726803 78726932 78726803 ID=MS.gene029109.t1.exon2;Parent=MS.gene029109.t1
chr1.3 CDS 78726803 78726932 78726803 ID=cds.MS.gene029109.t1;Parent=MS.gene029109.t1
chr1.3 exon 78726343 78726499 78726343 ID=MS.gene029109.t1.exon3;Parent=MS.gene029109.t1
chr1.3 CDS 78726343 78726499 78726343 ID=cds.MS.gene029109.t1;Parent=MS.gene029109.t1
chr1.3 exon 78725478 78725552 78725478 ID=MS.gene029109.t1.exon4;Parent=MS.gene029109.t1
chr1.3 CDS 78725478 78725552 78725478 ID=cds.MS.gene029109.t1;Parent=MS.gene029109.t1
Gene Sequence

>MS.gene029109

ATGGGTAAATTTCCCTAAACCACCCTAATTTCTGAAATCAAACAAACAATTTCTCATAATCAATCAATCAATTTCACTAATTAGCATGTGTTTTGATTTGCAGTGAAGGTTCACGAGTTGAGGCAGAAAAACAAAGCTGATCTGTTGGCTCAGCTCAAAGACCTCAAAGCTGAACTTGCTTTACTCCGTGTTGCTAAGGTCACTGGTGGTGCACCCAACAAGCTCTCCAAAATGTAAATAAAAATTCAATCTTTATTCTTTTATGTCAATTGGTGCTATGATCGTAAAGGTGTTTTGACGTGACCTTATTTTTAGAACAATCGTGCAGTTTTGCTCAACAAAGATCACTTGTTGTTGTGTATGTAATGTATTGCGTCCATTTACCAATTCTGAAGGATAAATTGTTCCTTTCGGTGTAATGGCTTTGATTGTGTGATGATTATAATGGGTTGTTTTTGTTTTGTGACTGTAAGGTGGTGTTTGTGTTAATGATTGATTGATGTGTTGTTTTTGATTATTTTATTTGGGTTTTGCAGTAAGGTGGTGAGGTTGTCGATTGCTCAGGTGTTGACAGTGATTTCCCAGAAGCAGAAGGCTGCTTTGAGGGAAGTTTACAAGAACAAGAAGTATTTGCCACTTGATCTCCGCCCAAAGAAGACCAGGGCCATTCGCAGAAGGCTCACCAAGCACCAGGTATTAAACCCTTTTAATGTATAATTCATGTTAAAGTTCATTGTTATAAACATATACACCTCCCAATGTATCTGTGGTTTTTGCTTTTGACTGCATTGATGCATTTCATTGTTTTTTTTTCTTTTTTTTTTTTTTCAATTCATATTTTATTGTGACCATCCATCAATTGGTGATTGGTGTATATTAGCTTTAATGAGATCTCTAATACGATGCTTTAGAGTAATCTGATTTTCGTCTCAAGTACTATTTAGGAGTATGAATGAATGAAATCTTAAATAATGAGGTGCTTCTTGTTCCTTATTCCAAATGATACAGATCCTGCAGGTGTAGGGAGAAGGATTATTGAATTTGACAGTGCTTAGTTTTCTTTCTAAAATCAAAGGATTTCAAGTCGACCTACACCATTAAATGTTATCCTTGAAAGAACAGTAATAATCAGTAGTACCTTAAAACATAAAATTGAATGTCAAAATCCATTTTTACATGAAATTCACTACACGACCAGGTTGCTGTACAATTTTCTGTTTGTTTAGAAGATAATAACTGGATTGGTTTATTGTTGGATGCTATTATAGCCTTTTACACCATATTGGTTGTTTTCAACCTGATTTGTCTTGGGATATTCAATCTTACATGAGTTTAGTCTTTCCTTGTAACCTTTTTCTCTTTGCTTGTATGTCAATCTCTTCCTATATATACAAACTGAAATTTTCTTGTGTAATGATTACATATTCAAGCAGAACAGTATGTTTGGATTGTTACTTATGATATGTTTTACTTGTTCATGCAGTCTTCGCTGAAGACCGAGAGGGAGAAGAAAAAGGAGACATATTTCCCAATGAGGAAATATGCTATCAAGGCATAG
Protein sequence

>MS.gene029109.t1

MVKVHELRQKNKADLLAQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREVYKNKKYLPLDLRPKKTRAIRRRLTKHQSSLKTEREKKKETYFPMRKYAIKA