AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene23197

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene23197.t1 MTR_7g050670 91.275 298 26 0 1 298 1 298 0.0 563
MS.gene23197.t1 MTR_7g076570 69.463 298 89 1 1 298 29 324 3.12e-145 417
MS.gene23197.t1 MTR_7g076760 66.667 300 98 1 1 298 1 300 3.36e-143 412
MS.gene23197.t1 MTR_4g088845 67.450 298 97 0 1 298 1 298 1.61e-141 407
MS.gene23197.t1 MTR_1g021820 25.088 283 165 11 5 274 16 264 1.28e-11 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene23197.t1 AT1G61330 30.000 280 191 4 24 299 15 293 1.72e-32 125
MS.gene23197.t1 AT1G61320 26.014 296 214 5 7 298 9 303 4.37e-28 113

Find 36 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTCTTTCCTCAAGTAAT+TGG 0.148637 7.2:-52009369 None:intergenic
ACTACCAGAGGAAGCAATTT+TGG 0.163512 7.2:-52009392 None:intergenic
CCGATATAGCCAACAAAATT+TGG 0.166151 7.2:+52009555 MS.gene23197:CDS
TTCTCTTTCCTCAAGTAATT+GGG 0.333664 7.2:-52009368 None:intergenic
TTTCCTCAAGTAATTGGGTT+TGG 0.353663 7.2:-52009363 None:intergenic
CACTTGGAACATCTGGTAAC+TGG 0.354434 7.2:-52009813 None:intergenic
CCTTGAGCAATTCGAACAAT+TGG 0.372454 7.2:-52010087 None:intergenic
TGCAAACCACTTGGAACATC+TGG 0.415677 7.2:-52009820 None:intergenic
GTTATAATTGCATGTTTGAT+TGG 0.417480 7.2:-52009454 None:intergenic
AATCGATTGTTGTGAGGACT+TGG 0.438503 7.2:+52010008 MS.gene23197:CDS
CATTTATTCAATTCGCATGA+AGG 0.441661 7.2:+52009592 MS.gene23197:CDS
CAGTTACATATCGATCCTGT+TGG 0.451921 7.2:+52009634 MS.gene23197:CDS
AGCAAAACTTCAATCCCAAC+AGG 0.463500 7.2:-52009649 None:intergenic
CTGCAACAACAGTGTCTCCT+AGG 0.465886 7.2:+52009476 MS.gene23197:CDS
GCTGACATGTGAGAAATCTT+TGG 0.470936 7.2:-52010187 None:intergenic
AGTCTCTATCAAACAAGAAT+CGG 0.472631 7.2:-52009525 None:intergenic
CCAATTGTTCGAATTGCTCA+AGG 0.473509 7.2:+52010087 MS.gene23197:CDS
GAACCCAAAATTGCTTCCTC+TGG 0.478922 7.2:+52009388 MS.gene23197:CDS
TGCAAAAGTTGCAAACCACT+TGG 0.484261 7.2:-52009829 None:intergenic
AGTTACATATCGATCCTGTT+GGG 0.489783 7.2:+52009635 MS.gene23197:CDS
CTCAATAAGTTGAGGTGTAG+TGG 0.510982 7.2:-52010217 None:intergenic
CACTACACCTCAACTTATTG+AGG 0.526106 7.2:+52010218 MS.gene23197:CDS
TTCCTCTGGTAGTCTTTCTG+AGG 0.527967 7.2:+52009402 MS.gene23197:CDS
CTCCTAGGTACAAAAGATCA+TGG 0.530531 7.2:+52009491 MS.gene23197:CDS
CACATCACTGAAGAAATGTC+TGG 0.537374 7.2:+52009874 MS.gene23197:CDS
CAGACATTTCTTCAGTGATG+TGG 0.565836 7.2:-52009873 None:intergenic
CAATTGTTCGAATTGCTCAA+GGG 0.587482 7.2:+52010088 MS.gene23197:CDS
ATGCACTAACAAGGATCTAG+AGG 0.591437 7.2:+52009690 MS.gene23197:CDS
ATTCAATTGTGAAACCAGGT+TGG 0.602985 7.2:-52009732 None:intergenic
TTTGAGAATCGATTGTTGTG+AGG 0.603428 7.2:+52010002 MS.gene23197:CDS
AAACCAAACCCAATTACTTG+AGG 0.614535 7.2:+52009360 MS.gene23197:CDS
GTAAATTCAATTGTGAAACC+AGG 0.629720 7.2:-52009736 None:intergenic
CAGTTACCAGATGTTCCAAG+TGG 0.629758 7.2:+52009814 MS.gene23197:CDS
ATCCTCAGAAAGACTACCAG+AGG 0.635655 7.2:-52009404 None:intergenic
ATATATACCTCAATAAGTTG+AGG 0.643108 7.2:-52010225 None:intergenic
GTTGCAAATATGCACTAACA+AGG 0.665849 7.2:+52009681 MS.gene23197:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAGTTAAAAACACTAAAAT+TGG + chr7.2:52009777-52009796 MS.gene23197:CDS 20.0%
! ATATATACCTCAATAAGTTG+AGG - chr7.2:52010228-52010247 None:intergenic 25.0%
! GTTATAATTGCATGTTTGAT+TGG - chr7.2:52009457-52009476 None:intergenic 25.0%
! TAAAAAATTGAACGAAGAGT+TGG - chr7.2:52010054-52010073 None:intergenic 25.0%
!!! CTTCGTTCAATTTTTTATCA+TGG + chr7.2:52010057-52010076 MS.gene23197:CDS 25.0%
AGTCTCTATCAAACAAGAAT+CGG - chr7.2:52009528-52009547 None:intergenic 30.0%
CATTTATTCAATTCGCATGA+AGG + chr7.2:52009592-52009611 MS.gene23197:CDS 30.0%
GTAAATTCAATTGTGAAACC+AGG - chr7.2:52009739-52009758 None:intergenic 30.0%
TTCTCTTTCCTCAAGTAATT+GGG - chr7.2:52009371-52009390 None:intergenic 30.0%
! GATTGCATGTATTCTTTTGA+TGG - chr7.2:52010147-52010166 None:intergenic 30.0%
! TTGAAGTTTTGCTTAAGAGA+TGG + chr7.2:52009659-52009678 MS.gene23197:CDS 30.0%
!! CCAAATTTTGTTGGCTATAT+CGG - chr7.2:52009558-52009577 None:intergenic 30.0%
!!! TTGGGTTTGGTTTTCAAAAT+TGG - chr7.2:52009353-52009372 None:intergenic 30.0%
AAACCAAACCCAATTACTTG+AGG + chr7.2:52009360-52009379 MS.gene23197:CDS 35.0%
AGTTACATATCGATCCTGTT+GGG + chr7.2:52009635-52009654 MS.gene23197:CDS 35.0%
ATTCAATTGTGAAACCAGGT+TGG - chr7.2:52009735-52009754 None:intergenic 35.0%
CAATTGTTCGAATTGCTCAA+GGG + chr7.2:52010088-52010107 MS.gene23197:CDS 35.0%
CCGATATAGCCAACAAAATT+TGG + chr7.2:52009555-52009574 MS.gene23197:CDS 35.0%
GTTCTCTTTCCTCAAGTAAT+TGG - chr7.2:52009372-52009391 None:intergenic 35.0%
GTTGCAAATATGCACTAACA+AGG + chr7.2:52009681-52009700 MS.gene23197:CDS 35.0%
TTTCCTCAAGTAATTGGGTT+TGG - chr7.2:52009366-52009385 None:intergenic 35.0%
TTTGAGAATCGATTGTTGTG+AGG + chr7.2:52010002-52010021 MS.gene23197:CDS 35.0%
! CTATTGCAGCCAAATTTTGT+TGG - chr7.2:52009567-52009586 None:intergenic 35.0%
! TACCATGATCTTTTGTACCT+AGG - chr7.2:52009496-52009515 None:intergenic 35.0%
AATCGATTGTTGTGAGGACT+TGG + chr7.2:52010008-52010027 MS.gene23197:CDS 40.0%
AGCAAAACTTCAATCCCAAC+AGG - chr7.2:52009652-52009671 None:intergenic 40.0%
ATGCACTAACAAGGATCTAG+AGG + chr7.2:52009690-52009709 MS.gene23197:CDS 40.0%
CACATCACTGAAGAAATGTC+TGG + chr7.2:52009874-52009893 MS.gene23197:CDS 40.0%
CACTACACCTCAACTTATTG+AGG + chr7.2:52010218-52010237 MS.gene23197:CDS 40.0%
CAGACATTTCTTCAGTGATG+TGG - chr7.2:52009876-52009895 None:intergenic 40.0%
CAGTTACATATCGATCCTGT+TGG + chr7.2:52009634-52009653 MS.gene23197:CDS 40.0%
CCAATTGTTCGAATTGCTCA+AGG + chr7.2:52010087-52010106 MS.gene23197:CDS 40.0%
CCTTGAGCAATTCGAACAAT+TGG - chr7.2:52010090-52010109 None:intergenic 40.0%
CTCCTAGGTACAAAAGATCA+TGG + chr7.2:52009491-52009510 MS.gene23197:CDS 40.0%
GCTGACATGTGAGAAATCTT+TGG - chr7.2:52010190-52010209 None:intergenic 40.0%
TGCAAAAGTTGCAAACCACT+TGG - chr7.2:52009832-52009851 None:intergenic 40.0%
! ACTACCAGAGGAAGCAATTT+TGG - chr7.2:52009395-52009414 None:intergenic 40.0%
! CTACCAGAGGAAGCAATTTT+GGG - chr7.2:52009394-52009413 None:intergenic 40.0%
! CTCAATAAGTTGAGGTGTAG+TGG - chr7.2:52010220-52010239 None:intergenic 40.0%
! GAGATGACTTTTTACCAACC+TGG + chr7.2:52009718-52009737 MS.gene23197:CDS 40.0%
ATCCTCAGAAAGACTACCAG+AGG - chr7.2:52009407-52009426 None:intergenic 45.0%
CACTTGGAACATCTGGTAAC+TGG - chr7.2:52009816-52009835 None:intergenic 45.0%
CAGTTACCAGATGTTCCAAG+TGG + chr7.2:52009814-52009833 MS.gene23197:CDS 45.0%
GAACCCAAAATTGCTTCCTC+TGG + chr7.2:52009388-52009407 MS.gene23197:CDS 45.0%
TGCAAACCACTTGGAACATC+TGG - chr7.2:52009823-52009842 None:intergenic 45.0%
TTCCTCTGGTAGTCTTTCTG+AGG + chr7.2:52009402-52009421 MS.gene23197:CDS 45.0%
CTGCAACAACAGTGTCTCCT+AGG + chr7.2:52009476-52009495 MS.gene23197:CDS 50.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 52009346 52010251 52009346 ID=MS.gene23197
chr7.2 mRNA 52009346 52010251 52009346 ID=MS.gene23197.t1;Parent=MS.gene23197
chr7.2 exon 52009346 52010251 52009346 ID=MS.gene23197.t1.exon1;Parent=MS.gene23197.t1
chr7.2 CDS 52009346 52010251 52009346 ID=cds.MS.gene23197.t1;Parent=MS.gene23197.t1
Gene Sequence

>MS.gene23197

ATGGCCAATTTTGAAAACCAAACCCAATTACTTGAGGAAAGAGAACCCAAAATTGCTTCCTCTGGTAGTCTTTCTGAGGATATGATTCAAAACATTTTCACTTTTTTACCAATCAAACATGCAATTATAACTGCAACAACAGTGTCTCCTAGGTACAAAAGATCATGGTATCATAATCGCCGATTCTTGTTTGATAGAGACTTATGTTTCCGATATAGCCAACAAAATTTGGCTGCAATAGTTGATCATTTATTCAATTCGCATGAAGGTGACGAAATTAAAACGTTTCAGTTACATATCGATCCTGTTGGGATTGAAGTTTTGCTTAAGAGATGGTTGCAAATATGCACTAACAAGGATCTAGAGGATCTTGAGATGACTTTTTACCAACCTGGTTTCACAATTGAATTTACTGTTTTTAACGCACTGCACAAGTTAAAAACACTAAAATTGGCTCAATGTGTGATCCAGTTACCAGATGTTCCAAGTGGTTTGCAACTTTTGCAAAAGCTAAAGCTAGCTAACATCCACATCACTGAAGAAATGTCTGGTATGTTGATTGAGCATTGTAAGATGCTTGAAATGATTGTTTTAATTAATTGCTCTACAATTAAGAAATTGAAATTAATTGCTAGACAAAATAAATATTTCAAAAATTTGAGAATCGATTGTTGTGAGGACTTGGAAGAGATTGAAATCGATTCACCAACTCTTCGTTCAATTTTTTATCATGGAAAATTTCCAATTGTTCGAATTGCTCAAGGGATGCAATTGTACGATGCTTTCTTTCGCTTTACACCATCAAAAGAATACATGCAATCTACTCAGCTAGAAGCTCTTGCCAAAGATTTCTCACATGTCAGCATTCTCACCACTACACCTCAACTTATTGAGGTATATATATAA
Protein sequence

>MS.gene23197.t1

MANFENQTQLLEEREPKIASSGSLSEDMIQNIFTFLPIKHAIITATTVSPRYKRSWYHNRRFLFDRDLCFRYSQQNLAAIVDHLFNSHEGDEIKTFQLHIDPVGIEVLLKRWLQICTNKDLEDLEMTFYQPGFTIEFTVFNALHKLKTLKLAQCVIQLPDVPSGLQLLQKLKLANIHITEEMSGMLIEHCKMLEMIVLINCSTIKKLKLIARQNKYFKNLRIDCCEDLEEIEIDSPTLRSIFYHGKFPIVRIAQGMQLYDAFFRFTPSKEYMQSTQLEALAKDFSHVSILTTTPQLIEVYI