AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene20050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20050.t1 MTR_7g100905 100.000 73 0 0 1 73 1 73 9.50e-47 143
MS.gene20050.t1 MTR_7g100905 100.000 66 0 0 8 73 3 68 3.29e-41 129
MS.gene20050.t1 MTR_7g100880 85.897 78 6 1 1 73 7 84 2.78e-18 71.6
MS.gene20050.t1 MTR_7g100890 90.411 73 6 1 1 73 426 497 2.80e-16 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene20050.t1 AT2G37120 76.190 63 15 0 11 73 14 76 5.32e-15 63.2
MS.gene20050.t1 AT3G53370 80.000 60 12 0 14 73 17 76 1.71e-12 57.0

Find 16 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATTGTTCTCCTGGTTAT+TGG 0.231388 7.2:+11296313 MS.gene20050:CDS
CCCAGGCTTGATTGTTCTCC+TGG 0.358351 7.2:+11296306 MS.gene20050:CDS
TGGGGAAATGTTTAGAATGC+TGG 0.422488 7.2:+11296268 MS.gene20050:intron
GTTTAGAATGCTGGATCTCA+AGG 0.468079 7.2:+11296277 MS.gene20050:intron
ACCAGGAGAACAATCAAGCC+TGG 0.470447 7.2:-11296307 None:intergenic
ATTGTTCTCCTGGTTATTGG+TGG 0.489076 7.2:+11296316 MS.gene20050:CDS
TTGCTGTTGACATTTCTCAT+TGG 0.497549 7.2:+11296340 MS.gene20050:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.518649 7.2:+11296454 MS.gene20050:CDS
ATACAGTGCCTCTACTCTCC+AGG 0.531169 7.2:-11296472 None:intergenic
TTGTTCTCCTGGTTATTGGT+GGG 0.546594 7.2:+11296317 MS.gene20050:CDS
GCTCTACGTTTATGCACAGA+AGG 0.594297 7.2:+11296372 MS.gene20050:CDS
ACAGCAACCCACCAATAACC+AGG 0.598951 7.2:-11296324 None:intergenic
CCAGGAGAACAATCAAGCCT+GGG 0.608678 7.2:-11296306 None:intergenic
GGATCTCAAGGGTTCAACCC+AGG 0.613072 7.2:+11296289 MS.gene20050:CDS
TTTAGAATGCTGGATCTCAA+GGG 0.619147 7.2:+11296278 MS.gene20050:intron
TCTCTGCACCTGGAGAGTAG+AGG 0.653251 7.2:+11296464 MS.gene20050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAACACTTAAATA+AGG - chr7.2:11296240-11296259 None:intergenic 10.0%
!! AAAATAAATAATGAAGAATG+TGG - chr7.2:11295226-11295245 None:intergenic 15.0%
!! AAATAAATAATGAAGAATGT+GGG - chr7.2:11295225-11295244 None:intergenic 15.0%
!! CAATAAAAAAATATTTCCAA+AGG - chr7.2:11296197-11296216 None:intergenic 15.0%
!! GATCTATTCATAATTAAATT+AGG + chr7.2:11295409-11295428 MS.gene20050:intron 15.0%
!! TTATTTGAGAATAACAATAA+GGG - chr7.2:11295790-11295809 None:intergenic 15.0%
!!! ATTTTTTTTTATTCACATTC+AGG + chr7.2:11295432-11295451 MS.gene20050:intron 15.0%
!! AATCAAAAAATACAAACAAG+CGG - chr7.2:11295672-11295691 None:intergenic 20.0%
!! AGATTCTACTTTGAATATAA+TGG + chr7.2:11296011-11296030 MS.gene20050:intron 20.0%
!! CATATTACTATTTGTATACA+TGG + chr7.2:11296129-11296148 MS.gene20050:intron 20.0%
!! CTTATTTGAGAATAACAATA+AGG - chr7.2:11295791-11295810 None:intergenic 20.0%
!! GATTCTACTTTGAATATAAT+GGG + chr7.2:11296012-11296031 MS.gene20050:intron 20.0%
!!! TTAATTTGAGAATGTTTTTG+TGG - chr7.2:11295950-11295969 None:intergenic 20.0%
! AAAGACATAGAATATGAGAA+AGG - chr7.2:11295288-11295307 None:intergenic 25.0%
! AAGACATAGAATATGAGAAA+GGG - chr7.2:11295287-11295306 None:intergenic 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr7.2:11296423-11296442 MS.gene20050:CDS 25.0%
! GGTTACAAATAACATCAATA+TGG - chr7.2:11295769-11295788 None:intergenic 25.0%
!! TTTACATGTCAATTTTCCTT+TGG + chr7.2:11296178-11296197 MS.gene20050:intron 25.0%
!!! GGAATTGATTTGAAGAAAAT+CGG - chr7.2:11295204-11295223 None:intergenic 25.0%
!!! GTTTTTTTTTTGTTGCTCTT+GGG + chr7.2:11296249-11296268 MS.gene20050:intron 25.0%
!!! TGCTTTATTAGACACTTTTA+AGG + chr7.2:11295511-11295530 MS.gene20050:intron 25.0%
!!! TGTTTTTTTTTTGTTGCTCT+TGG + chr7.2:11296248-11296267 MS.gene20050:intron 25.0%
!!! TTTTATTCACATTCAGGTTA+AGG + chr7.2:11295438-11295457 MS.gene20050:intron 25.0%
!!! TTTTTTTTTTGTTGCTCTTG+GGG + chr7.2:11296250-11296269 MS.gene20050:intron 25.0%
AAAAGAAGATGAAAAAGGAG+AGG + chr7.2:11296428-11296447 MS.gene20050:CDS 30.0%
AGACATAGAATATGAGAAAG+GGG - chr7.2:11295286-11295305 None:intergenic 30.0%
AGTGAAAGAATCCTGATTTA+TGG + chr7.2:11295901-11295920 MS.gene20050:intron 30.0%
ATAACTGAAAAACTCAGTGA+TGG - chr7.2:11295373-11295392 None:intergenic 30.0%
ATTCTCAAATAAGTCTGTGT+TGG + chr7.2:11295798-11295817 MS.gene20050:intron 30.0%
ATTGCAGAGCAAATAAAGAA+TGG - chr7.2:11296108-11296127 None:intergenic 30.0%
ATTGTATTGTACACGTGTTA+AGG + chr7.2:11295836-11295855 MS.gene20050:intron 30.0%
TATGAATAGATCCACAAGTA+AGG - chr7.2:11295401-11295420 None:intergenic 30.0%
! TTTTGTGGAGACATACAAAA+GGG - chr7.2:11295935-11295954 None:intergenic 30.0%
! TTTTTGTGGAGACATACAAA+AGG - chr7.2:11295936-11295955 None:intergenic 30.0%
!! TGCATTTTGATGATAAAACC+TGG - chr7.2:11295742-11295761 None:intergenic 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr7.2:11296421-11296440 None:intergenic 30.0%
AGAAAATCGGATCTAAGAAG+AGG - chr7.2:11295191-11295210 None:intergenic 35.0%
AGTTATATACGCCTTACTTG+TGG + chr7.2:11295387-11295406 MS.gene20050:intron 35.0%
TAAAACCTGGAAAACCTTGA+TGG - chr7.2:11295729-11295748 None:intergenic 35.0%
TAAGTTTACCAATGCCATCA+AGG + chr7.2:11295712-11295731 MS.gene20050:intron 35.0%
TATACATGGATGATTGTGAG+TGG + chr7.2:11296143-11296162 MS.gene20050:intron 35.0%
TTGATTGTTCTCCTGGTTAT+TGG + chr7.2:11296313-11296332 MS.gene20050:CDS 35.0%
! AAGTAGAATCTCTGATTTGC+AGG - chr7.2:11296002-11296021 None:intergenic 35.0%
! CCTTTGTTTCAAAGAATCTC+TGG + chr7.2:11296050-11296069 MS.gene20050:intron 35.0%
! TTGCTGTTGACATTTCTCAT+TGG + chr7.2:11296340-11296359 MS.gene20050:CDS 35.0%
! TTTAGAATGCTGGATCTCAA+GGG + chr7.2:11296278-11296297 MS.gene20050:intron 35.0%
! TTTGAAACAAAGGAGAGAAG+TGG - chr7.2:11296043-11296062 None:intergenic 35.0%
!! CCAGAGATTCTTTGAAACAA+AGG - chr7.2:11296053-11296072 None:intergenic 35.0%
AGAAGAGGAGAGAAGAATAC+CGG - chr7.2:11295176-11295195 None:intergenic 40.0%
ATTGTTCTCCTGGTTATTGG+TGG + chr7.2:11296316-11296335 MS.gene20050:CDS 40.0%
TGAATACACAGAAGATGCTC+TGG + chr7.2:11295869-11295888 MS.gene20050:intron 40.0%
TTGTTCTCCTGGTTATTGGT+GGG + chr7.2:11296317-11296336 MS.gene20050:CDS 40.0%
! GTTTAGAATGCTGGATCTCA+AGG + chr7.2:11296277-11296296 MS.gene20050:intron 40.0%
! TGGGGAAATGTTTAGAATGC+TGG + chr7.2:11296268-11296287 MS.gene20050:intron 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr7.2:11296403-11296422 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr7.2:11296402-11296421 None:intergenic 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG - chr7.2:11296398-11296417 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr7.2:11296406-11296425 None:intergenic 40.0%
AAAAAGGAGAGGCTGAAGCA+AGG + chr7.2:11296439-11296458 MS.gene20050:CDS 45.0%
AAGAGGAGAGAAGAATACCG+GGG - chr7.2:11295174-11295193 None:intergenic 45.0%
ACATGGATGATTGTGAGTGG+TGG + chr7.2:11296146-11296165 MS.gene20050:intron 45.0%
GAAGAGGAGAGAAGAATACC+GGG - chr7.2:11295175-11295194 None:intergenic 45.0%
GCTCTACGTTTATGCACAGA+AGG + chr7.2:11296372-11296391 MS.gene20050:CDS 45.0%
GGGACTGTGAACCATAAATC+AGG - chr7.2:11295915-11295934 None:intergenic 45.0%
! ATATGAGAAAGGGGCATGCA+AGG - chr7.2:11295277-11295296 None:intergenic 45.0%
! CAATGCCATCAAGGTTTTCC+AGG + chr7.2:11295721-11295740 MS.gene20050:intron 45.0%
! CTGGAAAACCTTGATGGCAT+TGG - chr7.2:11295723-11295742 None:intergenic 45.0%
! TATGAGAAAGGGGCATGCAA+GGG - chr7.2:11295276-11295295 None:intergenic 45.0%
!! CTCAGTGATGGATCTTCATC+TGG - chr7.2:11295361-11295380 None:intergenic 45.0%
!! GTGATGGATCTTCATCTGGA+AGG - chr7.2:11295357-11295376 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG - chr7.2:11296399-11296418 None:intergenic 45.0%
ACAGCAACCCACCAATAACC+AGG - chr7.2:11296327-11296346 None:intergenic 50.0%
ACCAGGAGAACAATCAAGCC+TGG - chr7.2:11296310-11296329 None:intergenic 50.0%
AGAGGAGAGAAGAATACCGG+GGG - chr7.2:11295173-11295192 None:intergenic 50.0%
CCAGGAGAACAATCAAGCCT+GGG - chr7.2:11296309-11296328 None:intergenic 50.0%
GAATACCGGGGGGACTTTAT+CGG - chr7.2:11295162-11295181 None:intergenic 50.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr7.2:11296454-11296473 MS.gene20050:CDS 55.0%
CCCAGGCTTGATTGTTCTCC+TGG + chr7.2:11296306-11296325 MS.gene20050:CDS 55.0%
GAGGAGAGAAGAATACCGGG+GGG - chr7.2:11295172-11295191 None:intergenic 55.0%
GGATCTCAAGGGTTCAACCC+AGG + chr7.2:11296289-11296308 MS.gene20050:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 11295155 11296483 11295155 ID=MS.gene20050
chr7.2 mRNA 11295155 11296483 11295155 ID=MS.gene20050.t1;Parent=MS.gene20050
chr7.2 exon 11295155 11295175 11295155 ID=MS.gene20050.t1.exon1;Parent=MS.gene20050.t1
chr7.2 CDS 11295155 11295175 11295155 ID=cds.MS.gene20050.t1;Parent=MS.gene20050.t1
chr7.2 exon 11296283 11296483 11296283 ID=MS.gene20050.t1.exon2;Parent=MS.gene20050.t1
chr7.2 CDS 11296283 11296483 11296283 ID=cds.MS.gene20050.t1;Parent=MS.gene20050.t1
Gene Sequence

>MS.gene20050

ATGGCCGATAAAGTCCCCCCGGTATTCTTCTCTCCTCTTCTTAGATCCGATTTTCTTCAAATCAATTCCCACATTCTTCATTATTTATTTTTTCAGATCTTAAAATTTCATGAATCAACCCTTGCATGCCCCTTTCTCATATTCTATGTCTTTTGCTCTTTCATACTTTCAATCATCATCAAATTTGCTTAATTTTTTACCTTCCAGATGAAGATCCATCACTGAGTTTTTCAGTTATATACGCCTTACTTGTGGATCTATTCATAATTAAATTAGGATTTTTTTTTATTCACATTCAGGTTAAGGTTAATTTCACATTTAGATTTAAAAATTTAATGATACTTATCTGCTTGTTTTGCTTTATTAGACACTTTTAAGGTTTTTGTTACATTGCTGTCTCTGTAAAAATATAACTTTTATTTAATGCATTGCTGTTTAATGTTGATCTAATCTATGATTTAGATTTTAGATGATGATGATGATGATGATGTAAATATAACTTTTATTTAATGCACCGCTTGTTTGTATTTTTTGATTCATAAAATTCATTTTTGAGCTAAGTTTACCAATGCCATCAAGGTTTTCCAGGTTTTATCATCAAAATGCATTTTCCATATTGATGTTATTTGTAACCCTTATTGTTATTCTCAAATAAGTCTGTGTTGGAAGATTGTACACAAGATTGTATTGTACACGTGTTAAGGATCAAAGATATGAATACACAGAAGATGCTCTGGAAAGTAAATAGTGAAAGAATCCTGATTTATGGTTCACAGTCCCTTTTGTATGTCTCCACAAAAACATTCTCAAATTAAGAAAACAAGTTTTGTTAATTGTCGATCATCCTGCAAATCAGAGATTCTACTTTGAATATAATGGGAAAAACCACTTCTCTCCTTTGTTTCAAAGAATCTCTGGTTGATTAAGAAGATTGCACTTGCACATTGTAGCCATTCTTTATTTGCTCTGCAATTCATATTACTATTTGTATACATGGATGATTGTGAGTGGTGGTTAATTACATTTACATGTCAATTTTCCTTTGGAAATATTTTTTTATTGCTTTTTGCTCTGTTATATGACCTTATTTAAGTGTTTTTTTTTTGTTGCTCTTGGGGAAATGTTTAGAATGCTGGATCTCAAGGGTTCAACCCAGGCTTGATTGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTTCTCATTGGAAATTATGCGCTCTACGTTTATGCACAGAAGGCCCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGGCTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>MS.gene20050.t1

MADKVPPNAGSQGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKALPPRKKKPVSKKKMKKERLKQGVSAPGE