AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71531

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71531.t1 MTR_3g083050 90.476 210 17 2 1 209 1 208 1.12e-128 361
MS.gene71531.t1 MTR_3g083030 77.489 231 30 2 1 209 1 231 2.00e-124 351
MS.gene71531.t1 MTR_3g083080 58.019 212 81 3 1 209 1 207 3.36e-81 241
MS.gene71531.t1 MTR_3g082340 35.398 226 123 6 1 207 1 222 3.37e-33 119
MS.gene71531.t1 MTR_3g082420 36.449 214 114 6 11 207 13 221 1.19e-32 117
MS.gene71531.t1 MTR_3g083150 37.788 217 121 6 1 208 1 212 3.57e-29 108
MS.gene71531.t1 MTR_3g086030 56.471 85 37 0 49 133 18 102 1.43e-25 97.4
MS.gene71531.t1 MTR_3g080680 40.244 164 83 7 54 207 40 198 3.52e-21 87.0
MS.gene71531.t1 MTR_8g461300 36.408 206 95 10 22 207 9 198 2.47e-20 85.1
MS.gene71531.t1 MTR_3g083100 38.889 126 59 4 101 208 49 174 4.43e-17 75.9
MS.gene71531.t1 MTR_4g055800 34.568 162 84 6 42 191 122 273 3.69e-15 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 48 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCTTTCATCGCAGCTTTC+TGG 0.028678 3.4:-78238922 None:intergenic
TTGCAGAATGTCGACAAATT+TGG 0.208783 3.4:+78238867 None:intergenic
GCGCTTTATTTACAAGAATA+AGG 0.246265 3.4:+78239089 MS.gene71531:CDS
CGCGCGCATATAAACATAAA+AGG 0.298624 3.4:-78239069 None:intergenic
CAGCCCTGTTATATCTTTCC+AGG 0.337582 3.4:+78239574 MS.gene71531:CDS
TCATCGCAGCTTTCTGGAGC+TGG 0.351234 3.4:-78238916 None:intergenic
CAATTACAATGCTGAGAATC+AGG 0.359881 3.4:+78239369 MS.gene71531:CDS
AAAGAGGGAAGCGGGTGAAA+TGG 0.363098 3.4:+78238938 MS.gene71531:CDS
TCCAGGCCGAAGTCAGGAAT+TGG 0.401904 3.4:+78239591 MS.gene71531:CDS
TCGGCCTGGAAAGATATAAC+AGG 0.404862 3.4:-78239578 None:intergenic
ATAGAAACCACCAGGTCTAT+AGG 0.424873 3.4:-78239516 None:intergenic
AATTTCTTCTTGTGCTTGAA+AGG 0.458380 3.4:-78239546 None:intergenic
ATGGCACATGACTTGATGAT+AGG 0.460123 3.4:-78239626 None:intergenic
AGGCGAAGGTCATCGGTCAT+AGG 0.477086 3.4:-78239313 None:intergenic
AAGAGGGAAGCGGGTGAAAT+GGG 0.477294 3.4:+78238939 MS.gene71531:CDS
TATCTTTCCAGGCCGAAGTC+AGG 0.478343 3.4:+78239585 MS.gene71531:CDS
AAAGATATAACAGGGCTGTT+GGG 0.481315 3.4:-78239569 None:intergenic
TCCAATTCCTGACTTCGGCC+TGG 0.483561 3.4:-78239592 None:intergenic
GAAAGATATAACAGGGCTGT+TGG 0.497566 3.4:-78239570 None:intergenic
CGCAGCTTTCTGGAGCTGGT+CGG 0.524358 3.4:-78238912 None:intergenic
GAAGGTCATCGGTCATAGGA+AGG 0.529164 3.4:-78239309 None:intergenic
TGTCTAACGCAAGGTGGCAG+AGG 0.530284 3.4:-78239348 None:intergenic
AAGGTCATCGGTCATAGGAA+GGG 0.538907 3.4:-78239308 None:intergenic
TAGTTCAAGGCGAAGGTCAT+CGG 0.539626 3.4:-78239320 None:intergenic
GTCTAACGCAAGGTGGCAGA+GGG 0.542570 3.4:-78239347 None:intergenic
CCAGAAAGCTGCGATGAAAG+AGG 0.543643 3.4:+78238922 MS.gene71531:CDS
AGGTCATCGGTCATAGGAAG+GGG 0.548021 3.4:-78239307 None:intergenic
CTGCGATGAAAGAGGGAAGC+GGG 0.550268 3.4:+78238930 MS.gene71531:CDS
GGCAGAGGGGAATTAGTTCA+AGG 0.553169 3.4:-78239333 None:intergenic
TGGTCGGTTGACACTGAACA+AGG 0.584593 3.4:-78238896 None:intergenic
CAGAAAGCTGCGATGAAAGA+GGG 0.588588 3.4:+78238923 MS.gene71531:CDS
GTCGGTTGACACTGAACAAG+GGG 0.589765 3.4:-78238894 None:intergenic
TAAGGAGATTGAAGTAGCCA+TGG 0.591215 3.4:+78239128 MS.gene71531:CDS
AGGCCGAAGTCAGGAATTGG+AGG 0.613344 3.4:+78239594 MS.gene71531:CDS
ACTCCTCCAATTCCTGACTT+CGG 0.621511 3.4:-78239597 None:intergenic
GGGGAATTAGTTCAAGGCGA+AGG 0.625929 3.4:-78239327 None:intergenic
GTCAAGACAACCTATAGACC+TGG 0.629319 3.4:+78239506 MS.gene71531:CDS
GCACTCATCATACTCAGCCA+TGG 0.631008 3.4:-78239145 None:intergenic
CGGCCTGGAAAGATATAACA+GGG 0.637548 3.4:-78239577 None:intergenic
CATTGTAATTGTCTAACGCA+AGG 0.644983 3.4:-78239357 None:intergenic
GCTGCGATGAAAGAGGGAAG+CGG 0.653611 3.4:+78238929 MS.gene71531:CDS
GGTCGGTTGACACTGAACAA+GGG 0.674801 3.4:-78238895 None:intergenic
GCACATGACTTGATGATAGG+TGG 0.677186 3.4:-78239623 None:intergenic
TGTAATTGTCTAACGCAAGG+TGG 0.687008 3.4:-78239354 None:intergenic
GTAATGTAATAGAAACCACC+AGG 0.687557 3.4:-78239524 None:intergenic
AAGACAACCTATAGACCTGG+TGG 0.716471 3.4:+78239509 MS.gene71531:CDS
TCTAACGCAAGGTGGCAGAG+GGG 0.742244 3.4:-78239346 None:intergenic
TCGGTTGACACTGAACAAGG+GGG 0.768468 3.4:-78238893 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATTTTAATGATTCATTC+TGG + chr3.4:78239211-78239230 MS.gene71531:intron 15.0%
!! GAAATCGAAAAAATATGAAT+GGG + chr3.4:78238984-78239003 MS.gene71531:CDS 20.0%
!!! CATTCATATTTTTTCGATTT+CGG - chr3.4:78238985-78239004 None:intergenic 20.0%
! CGAAATCGAAAAAATATGAA+TGG + chr3.4:78238983-78239002 MS.gene71531:CDS 25.0%
!!! TATTTTTTCGATTTCGGTTT+TGG - chr3.4:78238979-78238998 None:intergenic 25.0%
!!! TTTTTCTGAGATTTTTGGAA+CGG - chr3.4:78239272-78239291 None:intergenic 25.0%
AAAATCTCAGAAAAATGTGG+CGG + chr3.4:78239277-78239296 MS.gene71531:CDS 30.0%
AATTTCTTCTTGTGCTTGAA+AGG - chr3.4:78239549-78239568 None:intergenic 30.0%
ACGTCAACAAAAACGAAATT+TGG - chr3.4:78239485-78239504 None:intergenic 30.0%
CCAAAAATCTCAGAAAAATG+TGG + chr3.4:78239274-78239293 MS.gene71531:CDS 30.0%
TAGTTGAGTTACTTACACTT+AGG - chr3.4:78239179-78239198 None:intergenic 30.0%
! CTCCTTATCTTTTTGAATCT+GGG - chr3.4:78239115-78239134 None:intergenic 30.0%
! TCTCCTTATCTTTTTGAATC+TGG - chr3.4:78239116-78239135 None:intergenic 30.0%
!! GCGCTTTATTTACAAGAATA+AGG + chr3.4:78239089-78239108 MS.gene71531:CDS 30.0%
!!! CCACATTTTTCTGAGATTTT+TGG - chr3.4:78239277-78239296 None:intergenic 30.0%
!!! TTTTCTGAGATTTTTGGAAC+GGG - chr3.4:78239271-78239290 None:intergenic 30.0%
AAAGATATAACAGGGCTGTT+GGG - chr3.4:78239572-78239591 None:intergenic 35.0%
CAATTACAATGCTGAGAATC+AGG + chr3.4:78239369-78239388 MS.gene71531:CDS 35.0%
CATTGTAATTGTCTAACGCA+AGG - chr3.4:78239360-78239379 None:intergenic 35.0%
GTAATGTAATAGAAACCACC+AGG - chr3.4:78239527-78239546 None:intergenic 35.0%
!!! TTCGATTTCGGTTTTGGTTT+TGG - chr3.4:78238973-78238992 None:intergenic 35.0%
!!! TTCGGTTTTGGTTTTGGTTT+TGG - chr3.4:78238967-78238986 None:intergenic 35.0%
!!! TTTCTGAGATTTTTGGAACG+GGG - chr3.4:78239270-78239289 None:intergenic 35.0%
ATAGAAACCACCAGGTCTAT+AGG - chr3.4:78239519-78239538 None:intergenic 40.0%
CGCGCGCATATAAACATAAA+AGG - chr3.4:78239072-78239091 None:intergenic 40.0%
GAAAGATATAACAGGGCTGT+TGG - chr3.4:78239573-78239592 None:intergenic 40.0%
GGCCCAGATTCAAAAAGATA+AGG + chr3.4:78239110-78239129 MS.gene71531:CDS 40.0%
TAAGGAGATTGAAGTAGCCA+TGG + chr3.4:78239128-78239147 MS.gene71531:CDS 40.0%
TGTAATTGTCTAACGCAAGG+TGG - chr3.4:78239357-78239376 None:intergenic 40.0%
! ATGGCACATGACTTGATGAT+AGG - chr3.4:78239629-78239648 None:intergenic 40.0%
AAGACAACCTATAGACCTGG+TGG + chr3.4:78239509-78239528 MS.gene71531:CDS 45.0%
AAGGTCATCGGTCATAGGAA+GGG - chr3.4:78239311-78239330 None:intergenic 45.0%
ACTCCTCCAATTCCTGACTT+CGG - chr3.4:78239600-78239619 None:intergenic 45.0%
CAGAAAGCTGCGATGAAAGA+GGG + chr3.4:78238923-78238942 MS.gene71531:CDS 45.0%
CAGCCCTGTTATATCTTTCC+AGG + chr3.4:78239574-78239593 MS.gene71531:CDS 45.0%
CGGCCTGGAAAGATATAACA+GGG - chr3.4:78239580-78239599 None:intergenic 45.0%
GTCAAGACAACCTATAGACC+TGG + chr3.4:78239506-78239525 MS.gene71531:CDS 45.0%
TACAATGCTGAGAATCAGGC+AGG + chr3.4:78239373-78239392 MS.gene71531:intron 45.0%
TAGTTCAAGGCGAAGGTCAT+CGG - chr3.4:78239323-78239342 None:intergenic 45.0%
TCAGAAAAATGTGGCGGTGT+CGG + chr3.4:78239283-78239302 MS.gene71531:CDS 45.0%
TCGGCCTGGAAAGATATAAC+AGG - chr3.4:78239581-78239600 None:intergenic 45.0%
TGGACAACACAACACAACAC+AGG + chr3.4:78239231-78239250 MS.gene71531:intron 45.0%
! GCACATGACTTGATGATAGG+TGG - chr3.4:78239626-78239645 None:intergenic 45.0%
!!! ATATACTATTTTTATTTTTT+AGG + chr3.4:78239457-78239476 MS.gene71531:intron 5.0%
!!! TATACTATTTTTATTTTTTA+GGG + chr3.4:78239458-78239477 MS.gene71531:intron 5.0%
AAAGAGGGAAGCGGGTGAAA+TGG + chr3.4:78238938-78238957 MS.gene71531:CDS 50.0%
AAGAGGGAAGCGGGTGAAAT+GGG + chr3.4:78238939-78238958 MS.gene71531:CDS 50.0%
AGGTCATCGGTCATAGGAAG+GGG - chr3.4:78239310-78239329 None:intergenic 50.0%
CCAGAAAGCTGCGATGAAAG+AGG + chr3.4:78238922-78238941 MS.gene71531:CDS 50.0%
CCTCTTTCATCGCAGCTTTC+TGG - chr3.4:78238925-78238944 None:intergenic 50.0%
GAAGGTCATCGGTCATAGGA+AGG - chr3.4:78239312-78239331 None:intergenic 50.0%
GCACTCATCATACTCAGCCA+TGG - chr3.4:78239148-78239167 None:intergenic 50.0%
GGCAGAGGGGAATTAGTTCA+AGG - chr3.4:78239336-78239355 None:intergenic 50.0%
GGGGAATTAGTTCAAGGCGA+AGG - chr3.4:78239330-78239349 None:intergenic 50.0%
GGTCGGTTGACACTGAACAA+GGG - chr3.4:78238898-78238917 None:intergenic 50.0%
GTCGGTTGACACTGAACAAG+GGG - chr3.4:78238897-78238916 None:intergenic 50.0%
TATCTTTCCAGGCCGAAGTC+AGG + chr3.4:78239585-78239604 MS.gene71531:CDS 50.0%
TCGGTTGACACTGAACAAGG+GGG - chr3.4:78238896-78238915 None:intergenic 50.0%
TGGTCGGTTGACACTGAACA+AGG - chr3.4:78238899-78238918 None:intergenic 50.0%
AGGCCGAAGTCAGGAATTGG+AGG + chr3.4:78239594-78239613 MS.gene71531:CDS 55.0%
AGGCGAAGGTCATCGGTCAT+AGG - chr3.4:78239316-78239335 None:intergenic 55.0%
CTGCGATGAAAGAGGGAAGC+GGG + chr3.4:78238930-78238949 MS.gene71531:CDS 55.0%
GCTGCGATGAAAGAGGGAAG+CGG + chr3.4:78238929-78238948 MS.gene71531:CDS 55.0%
GTCTAACGCAAGGTGGCAGA+GGG - chr3.4:78239350-78239369 None:intergenic 55.0%
TCCAATTCCTGACTTCGGCC+TGG - chr3.4:78239595-78239614 None:intergenic 55.0%
TCCAGGCCGAAGTCAGGAAT+TGG + chr3.4:78239591-78239610 MS.gene71531:CDS 55.0%
TCTAACGCAAGGTGGCAGAG+GGG - chr3.4:78239349-78239368 None:intergenic 55.0%
TGTCTAACGCAAGGTGGCAG+AGG - chr3.4:78239351-78239370 None:intergenic 55.0%
!! TCATCGCAGCTTTCTGGAGC+TGG - chr3.4:78238919-78238938 None:intergenic 55.0%
!! CGCAGCTTTCTGGAGCTGGT+CGG - chr3.4:78238915-78238934 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 78238874 78239661 78238874 ID=MS.gene71531
chr3.4 mRNA 78238874 78239661 78238874 ID=MS.gene71531.t1;Parent=MS.gene71531
chr3.4 exon 78238874 78239182 78238874 ID=MS.gene71531.t1.exon1;Parent=MS.gene71531.t1
chr3.4 CDS 78238874 78239182 78238874 ID=cds.MS.gene71531.t1;Parent=MS.gene71531.t1
chr3.4 exon 78239253 78239390 78239253 ID=MS.gene71531.t1.exon2;Parent=MS.gene71531.t1
chr3.4 CDS 78239253 78239390 78239253 ID=cds.MS.gene71531.t1;Parent=MS.gene71531.t1
chr3.4 exon 78239479 78239661 78239479 ID=MS.gene71531.t1.exon3;Parent=MS.gene71531.t1
chr3.4 CDS 78239479 78239661 78239479 ID=cds.MS.gene71531.t1;Parent=MS.gene71531.t1
Gene Sequence

>MS.gene71531

ATGTCGACAAATTTGGATACCCCCTTGTTCAGTGTCAACCGACCAGCTCCAGAAAGCTGCGATGAAAGAGGGAAGCGGGTGAAATGGGAACCAAAACCAAAACCAAAACCGAAATCGAAAAAATATGAATGGGAATCGAAACGCGTTGAAGATCTTGAGATGAGTGACTTCTCTATGTATGACGATGACATTGAGCCTTTTATGTTTATATGCGCGCGCTTTATTTACAAGAATAAGGCCCAGATTCAAAAAGATAAGGAGATTGAAGTAGCCATGGCTGAGTATGATGAGTGCTCTCGCAACCTAAGTGTAAGTAACTCAACTATCTATCTTAATTTTAATTTTAATGATTCATTCTGGACAACACAACACAACACAGGTGTTCGATGCTATCCCCGTTCCAAAAATCTCAGAAAAATGTGGCGGTGTCGGTCCCCTTCCTATGACCGATGACCTTCGCCTTGAACTAATTCCCCTCTGCCACCTTGCGTTAGACAATTACAATGCTGAGAATCAGGCAGGTTTCAATACTTATGATGATTATAATATGTTTATGTTTATTTATTCATTCATTGATCATCTAATATACTATTTTTATTTTTTAGGGTCCAAATTTCGTTTTTGTTGACGTTGTCAAGACAACCTATAGACCTGGTGGTTTCTATTACATTACCTTTCAAGCACAAGAAGAAATTCCCAACAGCCCTGTTATATCTTTCCAGGCCGAAGTCAGGAATTGGAGGAGTCAGCCACCTATCATCAAGTCATGTGCCATTAAAACTACTTAA
Protein sequence

>MS.gene71531.t1

MSTNLDTPLFSVNRPAPESCDERGKRVKWEPKPKPKPKSKKYEWESKRVEDLEMSDFSMYDDDIEPFMFICARFIYKNKAQIQKDKEIEVAMAEYDECSRNLSVFDAIPVPKISEKCGGVGPLPMTDDLRLELIPLCHLALDNYNAENQGPNFVFVDVVKTTYRPGGFYYITFQAQEEIPNSPVISFQAEVRNWRSQPPIIKSCAIKTT