AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53007

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53007.t1 MTR_1g089830 59.146 164 29 1 1 164 1 126 1.52e-57 177
MS.gene53007.t1 MTR_1g045040 54.601 163 41 2 1 163 1 130 1.62e-44 143
MS.gene53007.t1 MTR_1g075130 73.494 83 18 1 86 168 7 85 8.90e-28 99.8
MS.gene53007.t1 MTR_8g089170 36.585 164 83 3 3 160 4 152 3.80e-26 97.4
MS.gene53007.t1 MTR_8g089130 35.503 169 86 4 3 163 4 157 1.68e-24 93.6
MS.gene53007.t1 MTR_8g039350 70.455 44 13 0 3 46 14 57 5.14e-15 66.2
MS.gene53007.t1 MTR_4g028990 43.478 92 45 3 73 164 13 97 2.32e-13 62.8
MS.gene53007.t1 MTR_5g013370 53.846 52 23 1 4 55 13 63 6.14e-11 60.1
MS.gene53007.t1 MTR_5g013370 53.846 52 23 1 4 55 13 63 8.61e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTTGTGGTTTACATTTCA+AGG 0.339580 1.1:+56180531 MS.gene53007:CDS
ATTGGTGTCGGCATCTCTAT+TGG 0.346524 1.1:-56181500 None:intergenic
ATTGGTGTCGGCGTCTCTAT+TGG 0.349108 1.1:-56181518 None:intergenic
CCACAAGCGTTACACAATAT+TGG 0.380139 1.1:-56180517 None:intergenic
TTTCAACAGAAACTCAAGTT+TGG 0.389578 1.1:+56180473 MS.gene53007:CDS
AATCTTTCAAACCAAACTTC+AGG 0.411413 1.1:+56180646 MS.gene53007:CDS
CCAAGCAATGAGATAGGTCT+TGG 0.425187 1.1:+56181647 MS.gene53007:CDS
CACAATATTGGCGTCTCGTA+TGG 0.440494 1.1:-56180505 None:intergenic
TCAAACAACAAAATATCGTC+AGG 0.502407 1.1:-56181605 None:intergenic
TCTTGGATGCATTCGTCTAA+AGG 0.502885 1.1:+56181664 MS.gene53007:CDS
TTTATACCAAGCAATGAGAT+AGG 0.511374 1.1:+56181641 MS.gene53007:CDS
CCAATATTGTGTAACGCTTG+TGG 0.532300 1.1:+56180517 MS.gene53007:CDS
CCAAGACCTATCTCATTGCT+TGG 0.545705 1.1:-56181647 None:intergenic
GAAACTCAAGTTTGGCGCAA+GGG 0.554208 1.1:+56180481 MS.gene53007:CDS
GGTTTACATTTCAAGGCGAA+AGG 0.567422 1.1:+56180538 MS.gene53007:CDS
AATAGAGACGCCGACACCAA+TGG 0.575440 1.1:+56181520 MS.gene53007:CDS
GTCGGCGTCTCTATTGGTGT+CGG 0.578211 1.1:-56181512 None:intergenic
TCTTCGGGAGATAGTTAGCA+AGG 0.579240 1.1:-56180564 None:intergenic
AAAAGCGTTCATTTGTAGAG+AGG 0.581892 1.1:+56181453 MS.gene53007:CDS
GGAAACTCATCCATTGGTGT+CGG 0.599667 1.1:-56181530 None:intergenic
AGCCCTGCAAAATCAGTCAT+CGG 0.602139 1.1:+56180588 MS.gene53007:CDS
GATACTTCTACAGATCAAGA+TGG 0.615323 1.1:+56181692 MS.gene53007:CDS
AGAAACTCAAGTTTGGCGCA+AGG 0.616630 1.1:+56180480 MS.gene53007:CDS
CTTCGGGAGATAGTTAGCAA+GGG 0.642252 1.1:-56180563 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAGATGATATAAATTGA+AGG - chr1.1:56180748-56180767 None:intergenic 15.0%
!! AATAGATGATATAAATTGAA+GGG - chr1.1:56180747-56180766 None:intergenic 15.0%
!! TTAAAATATGAAACTTCATT+TGG - chr1.1:56181122-56181141 None:intergenic 15.0%
!!! ACATTGTAAGAATATTTTTA+AGG + chr1.1:56180933-56180952 MS.gene53007:intron 15.0%
!!! ATTGTAAGAATATTTTTAAG+GGG + chr1.1:56180935-56180954 MS.gene53007:intron 15.0%
!!! CATTGTAAGAATATTTTTAA+GGG + chr1.1:56180934-56180953 MS.gene53007:intron 15.0%
!!! AATTTTTATTACCTGAAGTT+TGG - chr1.1:56180660-56180679 None:intergenic 20.0%
! ACAAATATCTCCATAAATGT+AGG - chr1.1:56181216-56181235 None:intergenic 25.0%
! CGATTGAAAATGAAAATGTT+GGG + chr1.1:56180853-56180872 MS.gene53007:intron 25.0%
! GTGGGAAAAATACAAATTTA+TGG + chr1.1:56181411-56181430 MS.gene53007:CDS 25.0%
! TCGATTGAAAATGAAAATGT+TGG + chr1.1:56180852-56180871 MS.gene53007:intron 25.0%
!! AATAACTTGTGCTTTACATT+TGG - chr1.1:56180718-56180737 None:intergenic 25.0%
!! ATGGGTATTGTTATAATTCA+GGG + chr1.1:56180966-56180985 MS.gene53007:intron 25.0%
!! CTTTACATTTGGTGAAATAT+GGG - chr1.1:56180707-56180726 None:intergenic 25.0%
!! TTTACATTTGGTGAAATATG+GGG - chr1.1:56180706-56180725 None:intergenic 25.0%
AATCTTTCAAACCAAACTTC+AGG + chr1.1:56180646-56180665 MS.gene53007:CDS 30.0%
AATGACAACTAAAGAAGAGT+TGG + chr1.1:56181244-56181263 MS.gene53007:intron 30.0%
ACTCATAAGTAGTGTAGAAT+GGG + chr1.1:56180880-56180899 MS.gene53007:intron 30.0%
ACTCTATATGCCTACATTTA+TGG + chr1.1:56181203-56181222 MS.gene53007:intron 30.0%
CACATTAGCTAGTATTCTTA+TGG + chr1.1:56181303-56181322 MS.gene53007:intron 30.0%
CTAGCTAATGTGTAACTATA+AGG - chr1.1:56181295-56181314 None:intergenic 30.0%
TCAAACAACAAAATATCGTC+AGG - chr1.1:56181608-56181627 None:intergenic 30.0%
TTTATACCAAGCAATGAGAT+AGG + chr1.1:56181641-56181660 MS.gene53007:CDS 30.0%
TTTCAACAGAAACTCAAGTT+TGG + chr1.1:56180473-56180492 MS.gene53007:CDS 30.0%
! CATGGGTATTGTTATAATTC+AGG + chr1.1:56180965-56180984 MS.gene53007:intron 30.0%
! GCTTTACATTTGGTGAAATA+TGG - chr1.1:56180708-56180727 None:intergenic 30.0%
! TGGGTATTGTTATAATTCAG+GGG + chr1.1:56180967-56180986 MS.gene53007:intron 30.0%
!! ATTTTAAGTAGACACAGCAT+TGG + chr1.1:56181135-56181154 MS.gene53007:intron 30.0%
!! ATTTTTCCTTTTCTAGTGCA+TGG + chr1.1:56180764-56180783 MS.gene53007:intron 30.0%
!! TTTTAAGGGGTACAATTCAT+GGG + chr1.1:56180948-56180967 MS.gene53007:intron 30.0%
!! TTTTTAAGGGGTACAATTCA+TGG + chr1.1:56180947-56180966 MS.gene53007:intron 30.0%
!! TTTTTCCTTTTCTAGTGCAT+GGG + chr1.1:56180765-56180784 MS.gene53007:intron 30.0%
!!! ACAAATGAACGCTTTTTTTG+AGG - chr1.1:56181449-56181468 None:intergenic 30.0%
!!! CAGATGTTTTTTCAATGTCA+AGG - chr1.1:56180615-56180634 None:intergenic 30.0%
!!! CATTAGTACCTTATTTTCTC+AGG + chr1.1:56181389-56181408 MS.gene53007:intron 30.0%
GACTCATAAGTAGTGTAGAA+TGG + chr1.1:56180879-56180898 MS.gene53007:intron 35.0%
GATACTTCTACAGATCAAGA+TGG + chr1.1:56181692-56181711 MS.gene53007:CDS 35.0%
TAAAACCCATGCACTAGAAA+AGG - chr1.1:56180773-56180792 None:intergenic 35.0%
! TATAGACTGAGAAGCTTTTG+TGG - chr1.1:56181554-56181573 None:intergenic 35.0%
! TCGTTGCAATGTGGATTAAA+GGG + chr1.1:56181085-56181104 MS.gene53007:intron 35.0%
! TTTTCCCACCTGAGAAAATA+AGG - chr1.1:56181400-56181419 None:intergenic 35.0%
! TTTTGTGGAAACTCATCCAT+TGG - chr1.1:56181539-56181558 None:intergenic 35.0%
!! AAAAGCGTTCATTTGTAGAG+AGG + chr1.1:56181453-56181472 MS.gene53007:CDS 35.0%
!!! AGTACCTTATTTTCTCAGGT+GGG + chr1.1:56181393-56181412 MS.gene53007:intron 35.0%
!!! TAGTACCTTATTTTCTCAGG+TGG + chr1.1:56181392-56181411 MS.gene53007:intron 35.0%
ATAAGTAGTGTAGAATGGGC+AGG + chr1.1:56180884-56180903 MS.gene53007:intron 40.0%
CCAATATTGTGTAACGCTTG+TGG + chr1.1:56180517-56180536 MS.gene53007:CDS 40.0%
CCACAAGCGTTACACAATAT+TGG - chr1.1:56180520-56180539 None:intergenic 40.0%
CGCTTGTGGTTTACATTTCA+AGG + chr1.1:56180531-56180550 MS.gene53007:CDS 40.0%
GGTTTACATTTCAAGGCGAA+AGG + chr1.1:56180538-56180557 MS.gene53007:CDS 40.0%
TCTTGGATGCATTCGTCTAA+AGG + chr1.1:56181664-56181683 MS.gene53007:CDS 40.0%
! ACGCTGCTAAAGTTTTCTAC+GGG - chr1.1:56181012-56181031 None:intergenic 40.0%
! CACGCTGCTAAAGTTTTCTA+CGG - chr1.1:56181013-56181032 None:intergenic 40.0%
! GTCGTTGCAATGTGGATTAA+AGG + chr1.1:56181084-56181103 MS.gene53007:intron 40.0%
!! GTGCATGGGTTTTAATGTAG+CGG + chr1.1:56180779-56180798 MS.gene53007:intron 40.0%
!! GTGGATTAAAGGGTGTTTGA+GGG + chr1.1:56181095-56181114 MS.gene53007:intron 40.0%
!! TGTGGATTAAAGGGTGTTTG+AGG + chr1.1:56181094-56181113 MS.gene53007:intron 40.0%
AGAAACTCAAGTTTGGCGCA+AGG + chr1.1:56180480-56180499 MS.gene53007:CDS 45.0%
AGCCCTGCAAAATCAGTCAT+CGG + chr1.1:56180588-56180607 MS.gene53007:CDS 45.0%
CACAATATTGGCGTCTCGTA+TGG - chr1.1:56180508-56180527 None:intergenic 45.0%
CCAAGACCTATCTCATTGCT+TGG - chr1.1:56181650-56181669 None:intergenic 45.0%
CCAAGCAATGAGATAGGTCT+TGG + chr1.1:56181647-56181666 MS.gene53007:CDS 45.0%
CTTCGGGAGATAGTTAGCAA+GGG - chr1.1:56180566-56180585 None:intergenic 45.0%
GAAACTCAAGTTTGGCGCAA+GGG + chr1.1:56180481-56180500 MS.gene53007:CDS 45.0%
GGAAACTCATCCATTGGTGT+CGG - chr1.1:56181533-56181552 None:intergenic 45.0%
TCTTCGGGAGATAGTTAGCA+AGG - chr1.1:56180567-56180586 None:intergenic 45.0%
TGAGAGTTGTCGTTGCAATG+TGG + chr1.1:56181076-56181095 MS.gene53007:intron 45.0%
! CGCTGCTAAAGTTTTCTACG+GGG - chr1.1:56181011-56181030 None:intergenic 45.0%
! TGATTTTGCAGGGCTCTCTT+CGG - chr1.1:56180583-56180602 None:intergenic 45.0%
!! ATTGGTGTCGGCATCTCTAT+TGG - chr1.1:56181503-56181522 None:intergenic 45.0%
!! GTCCGATGACTGATTTTGCA+GGG - chr1.1:56180593-56180612 None:intergenic 45.0%
AATAGAGACGCCGACACCAA+TGG + chr1.1:56181520-56181539 MS.gene53007:CDS 50.0%
! GATTTTGCAGGGCTCTCTTC+GGG - chr1.1:56180582-56180601 None:intergenic 50.0%
!! ATTGGTGTCGGCGTCTCTAT+TGG - chr1.1:56181521-56181540 None:intergenic 50.0%
!! GGTCCGATGACTGATTTTGC+AGG - chr1.1:56180594-56180613 None:intergenic 50.0%
GTCGGCGTCTCTATTGGTGT+CGG - chr1.1:56181515-56181534 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 56180469 56181718 56180469 ID=MS.gene53007
chr1.1 mRNA 56180469 56181718 56180469 ID=MS.gene53007.t1;Parent=MS.gene53007
chr1.1 exon 56180469 56180667 56180469 ID=MS.gene53007.t1.exon1;Parent=MS.gene53007.t1
chr1.1 CDS 56180469 56180667 56180469 ID=cds.MS.gene53007.t1;Parent=MS.gene53007.t1
chr1.1 exon 56181411 56181718 56181411 ID=MS.gene53007.t1.exon2;Parent=MS.gene53007.t1
chr1.1 CDS 56181411 56181718 56181411 ID=cds.MS.gene53007.t1;Parent=MS.gene53007.t1
Gene Sequence

>MS.gene53007

ATGGTTTCAACAGAAACTCAAGTTTGGCGCAAGGGACCATACGAGACGCCAATATTGTGTAACGCTTGTGGTTTACATTTCAAGGCGAAAGGAACCCTTGCTAACTATCTCCCGAAGAGAGCCCTGCAAAATCAGTCATCGGACCTTGACATTGAAAAAACATCTGAAAGTAATGCAAATCTTTCAAACCAAACTTCAGGTAATAAAAATTGCAATAAGTTAATTAAATGTTCACCCCATATTTCACCAAATGTAAAGCACAAGTTATTCATTTTCCCTTCAATTTATATCATCTATTTTTCCTTTTCTAGTGCATGGGTTTTAATGTAGCGGTTGAGAAAGTCATTTGTTGCTTAATTTTTTGAAATATCTAAATAAATTTATCGATTGAAAATGAAAATGTTGGGTATGACTCATAAGTAGTGTAGAATGGGCAGGACAAGCAAGACAAGTGAGCAAGAAAGACATTGTAAGAATATTTTTAAGGGGTACAATTCATGGGTATTGTTATAATTCAGGGGTATTGATTTCTTGCAATACCCCGTAGAAAACTTTAGCAGCGTGTTTTGATTTCTTTGATTTCTTGCATAACTTAAAGATGATTCTATGAGAGTTGTCGTTGCAATGTGGATTAAAGGGTGTTTGAGGGACCAAATGAAGTTTCATATTTTAAGTAGACACAGCATTGGATTTTGAATCAATTATATTGTTGTGCATTATAAAACGCACATACAACTCTATATGCCTACATTTATGGAGATATTTGTGCTAATACAATGACAACTAAAGAAGAGTTGGTATAAGATTGATCGATCAATCTTAGCCTTATAGTTACACATTAGCTAGTATTCTTATGGTAATACAAATAAATGATTATTCATTAATATGTAGCGTGTATGATGTATAAATATTTTTTTTATCATTAGTACCTTATTTTCTCAGGTGGGAAAAATACAAATTTATGGAACGTCAAAATTCCTCAAAAAAAGCGTTCATTTGTAGAGAGGCATTCATCGACTGTGATGCAGACACCAATAGAGATGCCGACACCAATAGAGACGCCGACACCAATGGATGAGTTTCCACAAAAGCTTCTCAGTCTATATGAATCTGAGAAAGAAGAAAATGAATCATCTCCTGACGATATTTTGTTGTTTGAGAAAATGAACAACTTTATACCAAGCAATGAGATAGGTCTTGGATGCATTCGTCTAAAGGCAGATGATACTTCTACAGATCAAGATGGTTAA
Protein sequence

>MS.gene53007.t1

MVSTETQVWRKGPYETPILCNACGLHFKAKGTLANYLPKRALQNQSSDLDIEKTSESNANLSNQTSGGKNTNLWNVKIPQKKRSFVERHSSTVMQTPIEMPTPIETPTPMDEFPQKLLSLYESEKEENESSPDDILLFEKMNNFIPSNEIGLGCIRLKADDTSTDQDG