AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53527

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53527.t1 MTR_1g045040 87.313 134 17 0 1 134 1 134 8.24e-78 226
MS.gene53527.t1 MTR_1g089830 76.336 131 24 2 1 130 1 125 1.24e-68 203
MS.gene53527.t1 MTR_8g089170 39.456 147 63 3 6 127 7 152 2.69e-23 89.0
MS.gene53527.t1 MTR_8g089130 36.424 151 70 3 6 130 7 157 5.67e-22 85.9
MS.gene53527.t1 MTR_8g039350 73.171 41 11 0 4 44 15 55 3.68e-17 70.9
MS.gene53527.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 1.84e-12 59.7
MS.gene53527.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 3.22e-11 59.7
MS.gene53527.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 4.83e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.2:+27867025 MS.gene53527:CDS
CGCTTGTGGACTACATTTCA+AGG 0.405648 1.2:+27866429 MS.gene53527:CDS
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27866542 None:intergenic
CCACAAGCGTTACATAGTAT+TGG 0.448818 1.2:-27866415 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27866379 MS.gene53527:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.2:+27866504 MS.gene53527:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.2:+27866436 MS.gene53527:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27866462 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.2:+27867114 MS.gene53527:CDS
CATAGTATTGGCTTCTCATA+CGG 0.490978 1.2:-27866403 None:intergenic
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27866993 MS.gene53527:CDS
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27866541 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.2:+27867120 MS.gene53527:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27866991 None:intergenic
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27867026 MS.gene53527:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.2:-27867120 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27866544 MS.gene53527:CDS
CCAATACTATGTAACGCTTG+TGG 0.608782 1.2:+27866415 MS.gene53527:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27866461 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27866996 MS.gene53527:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTTAATTTTTTGTAGAA+AGG + chr1.2:27866965-27866984 MS.gene53527:intron 15.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27866605-27866624 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27866604-27866623 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27866710-27866729 MS.gene53527:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27866945-27866964 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27866659-27866678 MS.gene53527:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.2:27866606-27866625 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27866565-27866584 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27866804-27866823 MS.gene53527:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27866803-27866822 MS.gene53527:intron 20.0%
! ATTCATTCAAAACCTAATAC+CGG - chr1.2:27866795-27866814 None:intergenic 25.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27866750-27866769 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27866853-27866872 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27866751-27866770 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27866805-27866824 MS.gene53527:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27866670-27866689 MS.gene53527:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27866371-27866390 MS.gene53527:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27866558-27866577 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27867025-27867044 MS.gene53527:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27867026-27867045 MS.gene53527:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27866847-27866866 MS.gene53527:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27866993-27867012 MS.gene53527:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27866758-27866777 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27866994-27867013 None:intergenic 30.0%
TTCATTCAAAACCTAATACC+GGG - chr1.2:27866794-27866813 None:intergenic 30.0%
!! GTCTGATAACTGATTTTGTT+GGG - chr1.2:27866491-27866510 None:intergenic 30.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27866464-27866483 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27866379-27866398 MS.gene53527:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27866996-27867015 MS.gene53527:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27866932-27866951 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27866465-27866484 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27867114-27867133 MS.gene53527:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27866811-27866830 MS.gene53527:intron 35.0%
! TGATTTTGTTGGGATGTCTT+CGG - chr1.2:27866481-27866500 None:intergenic 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27866406-27866425 None:intergenic 35.0%
!! GGTCTGATAACTGATTTTGT+TGG - chr1.2:27866492-27866511 None:intergenic 35.0%
AGCATTCATTTGAGTAGACC+CGG + chr1.2:27866773-27866792 MS.gene53527:intron 40.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.2:27866504-27866523 MS.gene53527:CDS 40.0%
ATTTGAGTAGACCCGGTATT+AGG + chr1.2:27866780-27866799 MS.gene53527:intron 40.0%
CCAATACTATGTAACGCTTG+TGG + chr1.2:27866415-27866434 MS.gene53527:CDS 40.0%
CCACAAGCGTTACATAGTAT+TGG - chr1.2:27866418-27866437 None:intergenic 40.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.2:27866436-27866455 MS.gene53527:CDS 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.2:27866513-27866532 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27866545-27866564 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.2:27867120-27867139 MS.gene53527:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.2:27867123-27867142 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27866544-27866563 MS.gene53527:CDS 45.0%
! CGCTTGTGGACTACATTTCA+AGG + chr1.2:27866429-27866448 MS.gene53527:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27866544-27866563 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27866367 27867188 27866367 ID=MS.gene53527
chr1.2 mRNA 27866367 27867188 27866367 ID=MS.gene53527.t1;Parent=MS.gene53527
chr1.2 exon 27866367 27866565 27866367 ID=MS.gene53527.t1.exon1;Parent=MS.gene53527.t1
chr1.2 CDS 27866367 27866565 27866367 ID=cds.MS.gene53527.t1;Parent=MS.gene53527.t1
chr1.2 exon 27866983 27867188 27866983 ID=MS.gene53527.t1.exon2;Parent=MS.gene53527.t1
chr1.2 CDS 27866983 27867188 27866983 ID=cds.MS.gene53527.t1;Parent=MS.gene53527.t1
Gene Sequence

>MS.gene53527

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAACGCTTGTGGACTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAACAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACCCGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATGAGTGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTGAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene53527.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNNCIPSNEIGIGCTLLKTDVTSKKSA