AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052658


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052658.t1 MTR_5g071410 30.469 256 142 3 21 243 19 271 1.32e-30 114
MS.gene052658.t1 MTR_3g082920 49.057 106 38 2 30 133 327 418 1.05e-20 90.5
MS.gene052658.t1 MTR_6g477950 49.412 85 42 1 156 240 61 144 2.44e-19 85.5
MS.gene052658.t1 MTR_7g117585 37.736 106 66 0 138 243 43 148 1.04e-18 80.1
MS.gene052658.t1 MTR_8g069780 41.250 80 47 0 161 240 76 155 9.92e-15 69.7
MS.gene052658.t1 MTR_2g012700 30.508 118 76 2 125 240 6 119 3.29e-13 64.7
MS.gene052658.t1 MTR_3g117130 42.683 82 47 0 159 240 197 278 3.88e-13 67.8
MS.gene052658.t1 MTR_2g062330 35.366 82 52 1 159 240 58 138 1.22e-12 63.9
MS.gene052658.t1 MTR_0010s0310 25.424 236 137 6 20 231 20 240 9.38e-12 63.5
MS.gene052658.t1 MTR_2g437520 39.759 83 47 1 161 240 121 203 9.74e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 55 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCAGAAGTCGTGAAATTT+TGG 0.193946 3.3:+43373955 None:intergenic
GCAAACTTATCACTTCAAAT+AGG 0.238418 3.3:-43373497 MS.gene052658:CDS
AGCCAAAATTTCACGACTTC+TGG 0.271151 3.3:-43373957 MS.gene052658:CDS
TCACCTAAGTATTTCTCATT+TGG 0.308885 3.3:+43373471 None:intergenic
AAACTGCAAAAGTATGATTA+TGG 0.310821 3.3:-43374035 MS.gene052658:CDS
CAAACTTATCACTTCAAATA+GGG 0.313955 3.3:-43373496 MS.gene052658:CDS
ACCTGTGTACGAGTTAAGTT+TGG 0.331180 3.3:-43373990 MS.gene052658:CDS
GCAGTTGATAGATATCTTAT+TGG 0.337824 3.3:+43373581 None:intergenic
CAGGTTCAAGATGATGGTTT+TGG 0.363392 3.3:-43373862 MS.gene052658:CDS
AGTATGATTATGGATGGATT+AGG 0.381484 3.3:-43374025 MS.gene052658:CDS
CAGTTGATAGATATCTTATT+GGG 0.382252 3.3:+43373582 None:intergenic
TCTACTATCCTTCACGAACT+TGG 0.384344 3.3:+43373440 None:intergenic
CGCTTTCCAATGGAATCAAC+CGG 0.384860 3.3:-43374738 None:intergenic
ACAGGAGAGCATTACTTTGC+AGG 0.396717 3.3:-43373547 MS.gene052658:CDS
ACGTCGCAGCTAAATTCAAC+TGG 0.409112 3.3:-43373929 MS.gene052658:CDS
ACTCGTACACAGGTGCCATT+TGG 0.409607 3.3:+43373999 None:intergenic
TAAGTTTGCACTCATATTCT+CGG 0.417716 3.3:+43373511 None:intergenic
AACTATCATTTATCCACAAC+AGG 0.425989 3.3:-43374216 MS.gene052658:intron
GTATGATTATGGATGGATTA+GGG 0.435600 3.3:-43374024 MS.gene052658:CDS
GGTTGTCCGACGTCGTCGTT+AGG 0.436504 3.3:-43373355 None:intergenic
ACCTCCACAAAGAGACGATT+GGG 0.451863 3.3:+43373375 None:intergenic
AGAAATACTTAGGTGAAGAT+TGG 0.462766 3.3:-43373464 MS.gene052658:CDS
TCCTCCCAATCGTCTCTTTG+TGG 0.465471 3.3:-43373379 MS.gene052658:CDS
GTAATGCTCTCCTGTGTGTC+GGG 0.473972 3.3:+43373555 None:intergenic
CAATGGAATCAACCGGGAAA+AGG 0.480353 3.3:-43374731 MS.gene052658:intron
TGGATGAAGTTGGAAGTTCA+AGG 0.497813 3.3:-43373839 MS.gene052658:CDS
CGTGTTAGACTTGAATATAC+TGG 0.498920 3.3:-43373894 MS.gene052658:CDS
CCTGTGTACGAGTTAAGTTT+GGG 0.512909 3.3:-43373989 MS.gene052658:CDS
GGTCCAAATGAGAAATACTT+AGG 0.515401 3.3:-43373474 MS.gene052658:CDS
TGCAAAAGTATGATTATGGA+TGG 0.520237 3.3:-43374031 MS.gene052658:CDS
TGGATAAATGATAGTTTCGA+AGG 0.529484 3.3:+43374223 None:intergenic
CTACTATCCTTCACGAACTT+GGG 0.542504 3.3:+43373441 None:intergenic
AACCTCCACAAAGAGACGAT+TGG 0.547571 3.3:+43373374 None:intergenic
TATTCAAGTCTAACACGTGT+TGG 0.547805 3.3:+43373900 None:intergenic
AAATTTCACGACTTCTGGTA+GGG 0.551367 3.3:-43373952 MS.gene052658:CDS
CAACAAGAGATGTCAAGTAA+TGG 0.551729 3.3:-43373709 MS.gene052658:intron
TTCAAGGGGAAATACAATCA+AGG 0.560197 3.3:-43373823 MS.gene052658:CDS
TCCCAATCGTCTCTTTGTGG+AGG 0.560244 3.3:-43373376 MS.gene052658:CDS
GGATGAAGTTGGAAGTTCAA+GGG 0.560255 3.3:-43373838 MS.gene052658:CDS
AGTAATGCTCTCCTGTGTGT+CGG 0.561176 3.3:+43373554 None:intergenic
TCGTGAAGGATAGTAGACTA+AGG 0.562838 3.3:-43373434 MS.gene052658:CDS
GGATGGATTAGGGATCCAAA+TGG 0.577469 3.3:-43374014 MS.gene052658:CDS
CCCAAACTTAACTCGTACAC+AGG 0.584015 3.3:+43373989 None:intergenic
AAAATTTCACGACTTCTGGT+AGG 0.588749 3.3:-43373953 MS.gene052658:CDS
AAACTTATCACTTCAAATAG+GGG 0.599416 3.3:-43373495 MS.gene052658:CDS
GATGAAGTTGGAAGTTCAAG+GGG 0.628048 3.3:-43373837 MS.gene052658:CDS
CGTCGCAGCTAAATTCAACT+GGG 0.629434 3.3:-43373928 MS.gene052658:CDS
AAGGATAGTAGACTAAGGAA+AGG 0.649294 3.3:-43373429 MS.gene052658:CDS
CAACTGCTTACCCGACACAC+AGG 0.661269 3.3:-43373565 MS.gene052658:CDS
TCCACAAAGAGACGATTGGG+AGG 0.661851 3.3:+43373378 None:intergenic
GCTTTCCAATGGAATCAACC+GGG 0.669471 3.3:-43374737 None:intergenic
TAATATCCTAACGACGACGT+CGG 0.679159 3.3:+43373349 None:intergenic
AGATTGGCCCAAGTTCGTGA+AGG 0.685876 3.3:-43373448 MS.gene052658:CDS
TAGTTTCGAAGGAATTCACG+AGG 0.693574 3.3:+43374234 None:intergenic
AGTTTCGAAGGAATTCACGA+GGG 0.715405 3.3:+43374235 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTCATAAATAATATTAATT+TGG + chr3.3:43374411-43374430 None:intergenic 10.0%
!!! TTTTTATTATATTCTTTCTA+TGG + chr3.3:43373737-43373756 None:intergenic 10.0%
!! ATACATATTTATGATTTAAC+AGG - chr3.3:43373660-43373679 MS.gene052658:intron 15.0%
!! TTTCAGTAACAAAAAAAATT+TGG + chr3.3:43373563-43373582 None:intergenic 15.0%
!!! ATATTTTATCAAATTTCGTA+TGG - chr3.3:43373936-43373955 MS.gene052658:CDS 15.0%
!! TAAAACATAGAAGGTAATAT+GGG - chr3.3:43373476-43373495 MS.gene052658:CDS 20.0%
! AAACTTATCACTTCAAATAG+GGG - chr3.3:43374590-43374609 MS.gene052658:intron 25.0%
! ACATATAAGATGTATAAGTC+AGG + chr3.3:43373964-43373983 None:intergenic 25.0%
! AGGTATTACAAAATATTGCT+TGG - chr3.3:43373889-43373908 MS.gene052658:CDS 25.0%
! ATATAAGATGTATAAGTCAG+GGG + chr3.3:43373962-43373981 None:intergenic 25.0%
! CAAACTTATCACTTCAAATA+GGG - chr3.3:43374589-43374608 MS.gene052658:intron 25.0%
! CACTATTACTATATTTACGA+TGG + chr3.3:43373429-43373448 None:intergenic 25.0%
! CATATAAGATGTATAAGTCA+GGG + chr3.3:43373963-43373982 None:intergenic 25.0%
! CATCGTAAATATAGTAATAG+TGG - chr3.3:43373427-43373446 MS.gene052658:CDS 25.0%
! CTAAAACATAGAAGGTAATA+TGG - chr3.3:43373475-43373494 MS.gene052658:CDS 25.0%
!! AAACTGCAAAAGTATGATTA+TGG - chr3.3:43374050-43374069 MS.gene052658:CDS 25.0%
!! ATATTTTGTAATACCTGTTG+TGG + chr3.3:43373885-43373904 None:intergenic 25.0%
!! TTTTTACATATCCCATGTTA+TGG - chr3.3:43373698-43373717 MS.gene052658:intron 25.0%
!!! CAGTTGATAGATATCTTATT+GGG + chr3.3:43374506-43374525 None:intergenic 25.0%
AACTATCATTTATCCACAAC+AGG - chr3.3:43373869-43373888 MS.gene052658:CDS 30.0%
AGAAATACTTAGGTGAAGAT+TGG - chr3.3:43374621-43374640 MS.gene052658:intron 30.0%
ATATCCCATGTTATGGAATT+CGG - chr3.3:43373705-43373724 MS.gene052658:intron 30.0%
CACATATCCTTATCAAGTTT+AGG - chr3.3:43373585-43373604 MS.gene052658:CDS 30.0%
CTAAACTTGATAAGGATATG+TGG + chr3.3:43373587-43373606 None:intergenic 30.0%
GCAAACTTATCACTTCAAAT+AGG - chr3.3:43374588-43374607 MS.gene052658:intron 30.0%
TAAGTTTGCACTCATATTCT+CGG + chr3.3:43374577-43374596 None:intergenic 30.0%
TCACCTAAGTATTTCTCATT+TGG + chr3.3:43374617-43374636 None:intergenic 30.0%
TGGATAAATGATAGTTTCGA+AGG + chr3.3:43373865-43373884 None:intergenic 30.0%
! ACATGCAATTTTGTAATGAG+TGG - chr3.3:43373620-43373639 MS.gene052658:intron 30.0%
! AGAGTAAAATTACCTTTTCC+CGG + chr3.3:43373369-43373388 None:intergenic 30.0%
! AGTATGATTATGGATGGATT+AGG - chr3.3:43374060-43374079 MS.gene052658:CDS 30.0%
! CTGATTATGATCATTTTGAG+AGG - chr3.3:43374330-43374349 MS.gene052658:intron 30.0%
! GTAATATGGGTTCTTTTCTA+GGG - chr3.3:43373489-43373508 MS.gene052658:CDS 30.0%
! TGCAAAAGTATGATTATGGA+TGG - chr3.3:43374054-43374073 MS.gene052658:CDS 30.0%
! TTTTAACAGGTTCAAGATGA+TGG - chr3.3:43374217-43374236 MS.gene052658:CDS 30.0%
!! GCAGTTGATAGATATCTTAT+TGG + chr3.3:43374507-43374526 None:intergenic 30.0%
!! GTATGATTATGGATGGATTA+GGG - chr3.3:43374061-43374080 MS.gene052658:CDS 30.0%
AAAATTTCACGACTTCTGGT+AGG - chr3.3:43374132-43374151 MS.gene052658:intron 35.0%
AAATTTCACGACTTCTGGTA+GGG - chr3.3:43374133-43374152 MS.gene052658:intron 35.0%
AAGGATAGTAGACTAAGGAA+AGG - chr3.3:43374656-43374675 MS.gene052658:intron 35.0%
CAACAAGAGATGTCAAGTAA+TGG - chr3.3:43374376-43374395 MS.gene052658:intron 35.0%
CGTGTTAGACTTGAATATAC+TGG - chr3.3:43374191-43374210 MS.gene052658:intron 35.0%
GGTCCAAATGAGAAATACTT+AGG - chr3.3:43374611-43374630 MS.gene052658:intron 35.0%
TAAGGTGGCTAAAACATAGA+AGG - chr3.3:43373467-43373486 MS.gene052658:CDS 35.0%
TATTCAAGTCTAACACGTGT+TGG + chr3.3:43374188-43374207 None:intergenic 35.0%
TTCAAGGGGAAATACAATCA+AGG - chr3.3:43374262-43374281 MS.gene052658:CDS 35.0%
! AATATACTGGCGCTTTTAAC+AGG - chr3.3:43374204-43374223 MS.gene052658:intron 35.0%
! GGTAATATGGGTTCTTTTCT+AGG - chr3.3:43373488-43373507 MS.gene052658:CDS 35.0%
! TACCAGAAGTCGTGAAATTT+TGG + chr3.3:43374133-43374152 None:intergenic 35.0%
ACCTGTGTACGAGTTAAGTT+TGG - chr3.3:43374095-43374114 MS.gene052658:intron 40.0%
AGCCAAAATTTCACGACTTC+TGG - chr3.3:43374128-43374147 MS.gene052658:intron 40.0%
AGTTTCGAAGGAATTCACGA+GGG + chr3.3:43373853-43373872 None:intergenic 40.0%
CCTGTGTACGAGTTAAGTTT+GGG - chr3.3:43374096-43374115 MS.gene052658:intron 40.0%
CCTTATCAAGTTTAGGCTGA+CGG - chr3.3:43373592-43373611 MS.gene052658:intron 40.0%
CTACTATCCTTCACGAACTT+GGG + chr3.3:43374647-43374666 None:intergenic 40.0%
GATGAAGTTGGAAGTTCAAG+GGG - chr3.3:43374248-43374267 MS.gene052658:CDS 40.0%
GGATGAAGTTGGAAGTTCAA+GGG - chr3.3:43374247-43374266 MS.gene052658:CDS 40.0%
TAGTTTCGAAGGAATTCACG+AGG + chr3.3:43373854-43373873 None:intergenic 40.0%
TCCACCGAATTCCATAACAT+GGG + chr3.3:43373712-43373731 None:intergenic 40.0%
TCGTGAAGGATAGTAGACTA+AGG - chr3.3:43374651-43374670 MS.gene052658:intron 40.0%
TCTACTATCCTTCACGAACT+TGG + chr3.3:43374648-43374667 None:intergenic 40.0%
TGGATGAAGTTGGAAGTTCA+AGG - chr3.3:43374246-43374265 MS.gene052658:CDS 40.0%
TTCCACCGAATTCCATAACA+TGG + chr3.3:43373713-43373732 None:intergenic 40.0%
!! CAGGTTCAAGATGATGGTTT+TGG - chr3.3:43374223-43374242 MS.gene052658:CDS 40.0%
!!! ATGGTTTTGGTGGATGAAGT+TGG - chr3.3:43374236-43374255 MS.gene052658:CDS 40.0%
!!! GTTCAAGATGATGGTTTTGG+TGG - chr3.3:43374226-43374245 MS.gene052658:CDS 40.0%
AACCTCCACAAAGAGACGAT+TGG + chr3.3:43374714-43374733 None:intergenic 45.0%
ACCTCCACAAAGAGACGATT+GGG + chr3.3:43374713-43374732 None:intergenic 45.0%
ACGTCGCAGCTAAATTCAAC+TGG - chr3.3:43374156-43374175 MS.gene052658:intron 45.0%
AGTAATGCTCTCCTGTGTGT+CGG + chr3.3:43374534-43374553 None:intergenic 45.0%
ATAGTGGTCCCCTATAGTCT+TGG - chr3.3:43373443-43373462 MS.gene052658:CDS 45.0%
CACCTTAGCCAAGACTATAG+GGG + chr3.3:43373454-43373473 None:intergenic 45.0%
CCACCTTAGCCAAGACTATA+GGG + chr3.3:43373455-43373474 None:intergenic 45.0%
CCCAAACTTAACTCGTACAC+AGG + chr3.3:43374099-43374118 None:intergenic 45.0%
CCGTCAGCCTAAACTTGATA+AGG + chr3.3:43373595-43373614 None:intergenic 45.0%
CGTCGCAGCTAAATTCAACT+GGG - chr3.3:43374157-43374176 MS.gene052658:intron 45.0%
TCCCATGTTATGGAATTCGG+TGG - chr3.3:43373708-43373727 MS.gene052658:intron 45.0%
!! ACAGGAGAGCATTACTTTGC+AGG - chr3.3:43374538-43374557 MS.gene052658:intron 45.0%
!! GGATGGATTAGGGATCCAAA+TGG - chr3.3:43374071-43374090 MS.gene052658:CDS 45.0%
GCCACCTTAGCCAAGACTAT+AGG + chr3.3:43373456-43373475 None:intergenic 50.0%
GTAATGCTCTCCTGTGTGTC+GGG + chr3.3:43374533-43374552 None:intergenic 50.0%
TCCACAAAGAGACGATTGGG+AGG + chr3.3:43374710-43374729 None:intergenic 50.0%
TCCCAATCGTCTCTTTGTGG+AGG - chr3.3:43374709-43374728 MS.gene052658:intron 50.0%
TCCTCCCAATCGTCTCTTTG+TGG - chr3.3:43374706-43374725 MS.gene052658:intron 50.0%
! AGATTGGCCCAAGTTCGTGA+AGG - chr3.3:43374637-43374656 MS.gene052658:intron 50.0%
! CCCTATAGTCTTGGCTAAGG+TGG - chr3.3:43373452-43373471 MS.gene052658:CDS 50.0%
! GTCCCCTATAGTCTTGGCTA+AGG - chr3.3:43373449-43373468 MS.gene052658:CDS 50.0%
!! ACTCGTACACAGGTGCCATT+TGG + chr3.3:43374089-43374108 None:intergenic 50.0%
CAACTGCTTACCCGACACAC+AGG - chr3.3:43374520-43374539 MS.gene052658:intron 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 43373356 43374751 43373356 ID=MS.gene052658
chr3.3 mRNA 43373356 43374751 43373356 ID=MS.gene052658.t1;Parent=MS.gene052658
chr3.3 exon 43374732 43374751 43374732 ID=MS.gene052658.t1.exon1;Parent=MS.gene052658.t1
chr3.3 CDS 43374732 43374751 43374732 ID=cds.MS.gene052658.t1;Parent=MS.gene052658.t1
chr3.3 exon 43374217 43374283 43374217 ID=MS.gene052658.t1.exon2;Parent=MS.gene052658.t1
chr3.3 CDS 43374217 43374283 43374217 ID=cds.MS.gene052658.t1;Parent=MS.gene052658.t1
chr3.3 exon 43373710 43374102 43373710 ID=MS.gene052658.t1.exon3;Parent=MS.gene052658.t1
chr3.3 CDS 43373710 43374102 43373710 ID=cds.MS.gene052658.t1;Parent=MS.gene052658.t1
chr3.3 exon 43373356 43373610 43373356 ID=MS.gene052658.t1.exon4;Parent=MS.gene052658.t1
chr3.3 CDS 43373356 43373610 43373356 ID=cds.MS.gene052658.t1;Parent=MS.gene052658.t1
Gene Sequence

>MS.gene052658

ATGGAATCAACCGGGAAAAGGTAATTTTACTCTCTTTTCTTTCATTTTGTCTCTTTCGTCTCTAAGATTTCCATCGTAAATATAGTAATAGTGGTCCCCTATAGTCTTGGCTAAGGTGGCTAAAACATAGAAGGTAATATGGGTTCTTTTCTAGGGTTTGCAAGATATTTTGCATAAATTTGAAGTTAATATGAGTTTTTTCTTCCAAATTTTTTTTGTTACTGAAAACCACATATCCTTATCAAGTTTAGGCTGACGGTTATAACATGCAATTTTGTAATGAGTGGAAATCAATTTTAGTGATATACATATTTATGATTTAACAGGTAGAAGCAATTAGTATTTTTACATATCCCATGTTATGGAATTCGGTGGAAACCATAGAAAGAATATAATAAAAACAGTTTTCTTATAAATATTTAGTTACATGATTTTTGTATGTAATTAACTACAATCAATTGTTTTTAGATTATGCAAAGCAACAAGCTACTATACCCTCGTGAATTCCTTCGAAACTATCATTTATCCACAACAGGTATTACAAAATATTGCTTGGTTGTTATGATATTCTTGTATAATGATATTTTATCAAATTTCGTATGGCCCCTGACTTATACATCTTATATGTGTGTTTTTTTTATCGTTGTAGTCAAAGATACAAGTATGTTCTGTATTCTTCTCATCTTACTTCAAGAAACTGCAAAAGTATGATTATGGATGGATTAGGGATCCAAATGGCACCTGTGTACGAGTTAAGTTTGGGAGAAATTTAAGCCAAAATTTCACGACTTCTGGTAGGGACGTCGCAGCTAAATTCAACTGGGAGAAACCAACACGTGTTAGACTTGAATATACTGGCGCTTTTAACAGGTTCAAGATGATGGTTTTGGTGGATGAAGTTGGAAGTTCAAGGGGAAATACAATCAAGGAAGAAGTTATTGATTCTGATTCTGAAGATGATTGTATAGAAATTGCTGATTATGATCATTTTGAGAGGAATGTCACATATGTCACAGCTAACAACAAGAGATGTCAAGTAATGGTATGTTCAACCAAATTAATATTATTTATGAACATTACAATTATTCATTTAACATTCATTATTTGCATACTAAAGCATGTGAGTTTATAATTTGTTTAGCACTTTCCCAATAAGATATCTATCAACTGCTTACCCGACACACAGGAGAGCATTACTTTGCAGGATGTGCATAATCTCCGAGAATATGAGTGCAAACTTATCACTTCAAATAGGGGTCCAAATGAGAAATACTTAGGTGAAGATTGGCCCAAGTTCGTGAAGGATAGTAGACTAAGGAAAGGTGATAAGTTGATATTTGATCTTTGTGCTCCTCCCAATCGTCTCTTTGTGGAGGTTGTCCGACGTCGTCGTTAG

Protein sequence

>MS.gene052658.t1

MESTGKRLCKATSYYTLVNSFETIIYPQQSKIQVCSVFFSSYFKKLQKYDYGWIRDPNGTCVRVKFGRNLSQNFTTSGRDVAAKFNWEKPTRVRLEYTGAFNRFKMMVLVDEVGSSRGNTIKEEVIDSDSEDDCIEIADYDHFERNVTYVTANNKRCQVMHFPNKISINCLPDTQESITLQDVHNLREYECKLITSNRGPNEKYLGEDWPKFVKDSRLRKGDKLIFDLCAPPNRLFVEVVRRRR