AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09705

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09705.t1 MTR_5g013515 85.057 87 12 1 31 117 1 86 2.64e-48 154
MS.gene09705.t1 MTR_5g013530 67.797 118 29 4 1 117 1 110 5.10e-44 144
MS.gene09705.t1 MTR_5g013520 63.636 88 25 2 30 117 1 81 6.38e-31 110
MS.gene09705.t1 MTR_5g013530 67.778 90 20 4 29 117 7 88 1.15e-29 107
MS.gene09705.t1 MTR_2g042900 47.692 65 30 1 34 98 101 161 5.75e-14 68.6
MS.gene09705.t1 MTR_2g042900 47.692 65 30 1 34 98 101 161 6.78e-14 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTACAAGAGGTTTCAAATT+TGG 0.130518 5.2:+5521512 MS.gene09705:CDS
CCATCCACACCTGTTATTTA+TGG 0.168614 5.2:+5521924 MS.gene09705:CDS
CTACAAGAGGTTTCAAATTT+GGG 0.272831 5.2:+5521513 MS.gene09705:CDS
AGAGGTAGTAGTTCCTTTCT+TGG 0.282086 5.2:-5521808 None:intergenic
CATCATAAAATATTGTCATT+TGG 0.312886 5.2:-5521725 None:intergenic
ATTGTCATTTGGGCACTTCT+AGG 0.314984 5.2:-5521714 None:intergenic
ATCATAAAATATTGTCATTT+GGG 0.325400 5.2:-5521724 None:intergenic
ACGAAGGATGGCAGAGAATC+TGG 0.335118 5.2:-5522427 None:intergenic
ATATTTAATTCAAGGTTGAT+TGG 0.378488 5.2:-5522530 None:intergenic
TTTCAAATTTGGGACATTCC+AGG 0.386089 5.2:+5521523 MS.gene09705:CDS
GAAAGAGATGAGGAGCTTGT+TGG 0.425523 5.2:-5521491 None:intergenic
GGTGAAGATATCGTATCTAT+AGG 0.437981 5.2:-5522326 None:intergenic
GAATTTCTAGCAAGAAATGA+TGG 0.446507 5.2:-5521879 None:intergenic
TCAAGGTTGATTGGTATCCA+TGG 0.473689 5.2:-5522521 None:intergenic
TGGTACTTGAAGAGAATTGT+AGG 0.475609 5.2:-5521904 None:intergenic
CAAGGTTGATTGGTATCCAT+GGG 0.484519 5.2:-5522520 None:intergenic
TCCTCATCTCTTTCTACAAG+AGG 0.490417 5.2:+5521500 MS.gene09705:CDS
TTCGTTGTAGTGGTGATGAT+AGG 0.501093 5.2:-5522456 None:intergenic
GAAGGCTAATAGTATTATCA+AGG 0.508788 5.2:+5521686 MS.gene09705:CDS
GATAGGTGGCGGACGAAGGA+TGG 0.545293 5.2:-5522439 None:intergenic
GATGGTGAAGATGCATGAAT+TGG 0.549510 5.2:-5522372 None:intergenic
GCGAAAGCTTCTTCACCCCA+TGG 0.571900 5.2:+5522504 MS.gene09705:CDS
AAGCATAGTTGTTATTGTTG+TGG 0.572885 5.2:-5521836 None:intergenic
ACCTCTTGTAGAAAGAGATG+AGG 0.589295 5.2:-5521501 None:intergenic
CCATAAATAACAGGTGTGGA+TGG 0.595900 5.2:-5521924 None:intergenic
TTTACCATAAATAACAGGTG+TGG 0.596443 5.2:-5521928 None:intergenic
GTTGTAGTGGTGATGATAGG+TGG 0.631625 5.2:-5522453 None:intergenic
AATTTCTAGCAAGAAATGAT+GGG 0.637681 5.2:-5521878 None:intergenic
TGATGATAGGTGGCGGACGA+AGG 0.645109 5.2:-5522443 None:intergenic
TTCTAGCAAGAAATGATGGG+TGG 0.652275 5.2:-5521875 None:intergenic
ATAAAGCTGAATCTGTGCGA+TGG 0.703445 5.2:-5522390 None:intergenic
GTATCTACAAGTTAATACGA+TGG 0.710495 5.2:-5522347 None:intergenic
GTAGTGGTGATGATAGGTGG+CGG 0.722498 5.2:-5522450 None:intergenic
AAGGTTGATTGGTATCCATG+GGG 0.724094 5.2:-5522519 None:intergenic
CAACGAAAAGAGAATCTCTG+CGG 0.767900 5.2:+5522472 MS.gene09705:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATGGTAAAAATAATAAT+TGG + chr5.2:5521940-5521959 MS.gene09705:intron 10.0%
!!! AAATGACAATATTTTATGAT+GGG + chr5.2:5521727-5521746 MS.gene09705:CDS 15.0%
!!! ATCATAAAATATTGTCATTT+GGG - chr5.2:5521727-5521746 None:intergenic 15.0%
!!! GAATTTTCCTATATATAAAT+AGG - chr5.2:5522068-5522087 None:intergenic 15.0%
!!! GTTTAATTTTGATTTAATCA+AGG - chr5.2:5522248-5522267 None:intergenic 15.0%
!!! TGGATATCTTTTTTTTTTTT+TGG + chr5.2:5521960-5521979 MS.gene09705:intron 15.0%
!!! TTATTTTTACCATAAATAAC+AGG - chr5.2:5521936-5521955 None:intergenic 15.0%
!!! TTTTTGGTACAAATAATAAT+TGG + chr5.2:5521976-5521995 MS.gene09705:intron 15.0%
!! CATCATAAAATATTGTCATT+TGG - chr5.2:5521728-5521747 None:intergenic 20.0%
!! TGACTTTCCTATTTATATAT+AGG + chr5.2:5522058-5522077 MS.gene09705:intron 20.0%
!! TGCAATAAGTAAAAATATAG+TGG - chr5.2:5522218-5522237 None:intergenic 20.0%
!!! CAAATGACAATATTTTATGA+TGG + chr5.2:5521726-5521745 MS.gene09705:CDS 20.0%
! AGTAGCTAAAAAAATGTTGA+TGG - chr5.2:5521583-5521602 None:intergenic 25.0%
! ATACACAAATGCATTATGAT+TGG - chr5.2:5522139-5522158 None:intergenic 25.0%
! CATGATTCATGTTTATAACA+TGG + chr5.2:5521615-5521634 MS.gene09705:intron 25.0%
! TAATTGGATATCTATTTGAG+TGG + chr5.2:5521992-5522011 MS.gene09705:intron 25.0%
!!! AATTTCTAGCAAGAAATGAT+GGG - chr5.2:5521881-5521900 None:intergenic 25.0%
!!! AGTCGTTAAAATGACTTTTT+TGG + chr5.2:5522096-5522115 MS.gene09705:intron 25.0%
!!! GTTTTATTACAGTGTAATGA+AGG + chr5.2:5521668-5521687 MS.gene09705:intron 25.0%
CTACAAGAGGTTTCAAATTT+GGG + chr5.2:5521513-5521532 MS.gene09705:CDS 30.0%
GAAGGCTAATAGTATTATCA+AGG + chr5.2:5521686-5521705 MS.gene09705:CDS 30.0%
GTATCTACAAGTTAATACGA+TGG - chr5.2:5522350-5522369 None:intergenic 30.0%
TCTACAAGAGGTTTCAAATT+TGG + chr5.2:5521512-5521531 MS.gene09705:CDS 30.0%
TTTACCATAAATAACAGGTG+TGG - chr5.2:5521931-5521950 None:intergenic 30.0%
! AAGCATAGTTGTTATTGTTG+TGG - chr5.2:5521839-5521858 None:intergenic 30.0%
!! GAATTTCTAGCAAGAAATGA+TGG - chr5.2:5521882-5521901 None:intergenic 30.0%
ATGCGCAGTAAAATTTGATG+TGG - chr5.2:5522172-5522191 None:intergenic 35.0%
GGTGAAGATATCGTATCTAT+AGG - chr5.2:5522329-5522348 None:intergenic 35.0%
TGAAAAAGTCAACGACATCA+TGG + chr5.2:5521779-5521798 MS.gene09705:CDS 35.0%
TGGTACTTGAAGAGAATTGT+AGG - chr5.2:5521907-5521926 None:intergenic 35.0%
! AGATTCTCTTTTCGTTGTAG+TGG - chr5.2:5522469-5522488 None:intergenic 35.0%
! ATCATGGTCTTTTCCAAGAA+AGG + chr5.2:5521795-5521814 MS.gene09705:CDS 35.0%
! TTTCAAATTTGGGACATTCC+AGG + chr5.2:5521523-5521542 MS.gene09705:CDS 35.0%
!!! GTTATTGTTGTGGTTTTGAG+AGG - chr5.2:5521829-5521848 None:intergenic 35.0%
ACCTCTTGTAGAAAGAGATG+AGG - chr5.2:5521504-5521523 None:intergenic 40.0%
AGAGGTAGTAGTTCCTTTCT+TGG - chr5.2:5521811-5521830 None:intergenic 40.0%
ATAAAGCTGAATCTGTGCGA+TGG - chr5.2:5522393-5522412 None:intergenic 40.0%
CAACGAAAAGAGAATCTCTG+CGG + chr5.2:5522472-5522491 MS.gene09705:CDS 40.0%
CCATAAATAACAGGTGTGGA+TGG - chr5.2:5521927-5521946 None:intergenic 40.0%
GATGGTGAAGATGCATGAAT+TGG - chr5.2:5522375-5522394 None:intergenic 40.0%
GCATCGTACATTTGCTCATA+TGG + chr5.2:5522188-5522207 MS.gene09705:intron 40.0%
GTAGCAAAAGAACATGTACC+TGG - chr5.2:5521544-5521563 None:intergenic 40.0%
TCCTCATCTCTTTCTACAAG+AGG + chr5.2:5521500-5521519 MS.gene09705:CDS 40.0%
! AAGGTTGATTGGTATCCATG+GGG - chr5.2:5522522-5522541 None:intergenic 40.0%
! ATTGTCATTTGGGCACTTCT+AGG - chr5.2:5521717-5521736 None:intergenic 40.0%
! CAAGGTTGATTGGTATCCAT+GGG - chr5.2:5522523-5522542 None:intergenic 40.0%
! CCATCCACACCTGTTATTTA+TGG + chr5.2:5521924-5521943 MS.gene09705:CDS 40.0%
! TCAAGGTTGATTGGTATCCA+TGG - chr5.2:5522524-5522543 None:intergenic 40.0%
! TTCGTTGTAGTGGTGATGAT+AGG - chr5.2:5522459-5522478 None:intergenic 40.0%
! TTCTAGCAAGAAATGATGGG+TGG - chr5.2:5521878-5521897 None:intergenic 40.0%
!!! ATGTCGTTGACTTTTTCAGC+TGG - chr5.2:5521777-5521796 None:intergenic 40.0%
GAAAGAGATGAGGAGCTTGT+TGG - chr5.2:5521494-5521513 None:intergenic 45.0%
! GTTGTAGTGGTGATGATAGG+TGG - chr5.2:5522456-5522475 None:intergenic 45.0%
ACGAAGGATGGCAGAGAATC+TGG - chr5.2:5522430-5522449 None:intergenic 50.0%
! GTAGTGGTGATGATAGGTGG+CGG - chr5.2:5522453-5522472 None:intergenic 50.0%
GCGAAAGCTTCTTCACCCCA+TGG + chr5.2:5522504-5522523 MS.gene09705:CDS 55.0%
!! TGATGATAGGTGGCGGACGA+AGG - chr5.2:5522446-5522465 None:intergenic 55.0%
!! GATAGGTGGCGGACGAAGGA+TGG - chr5.2:5522442-5522461 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 5521459 5522543 5521459 ID=MS.gene09705
chr5.2 mRNA 5521459 5522543 5521459 ID=MS.gene09705.t1;Parent=MS.gene09705
chr5.2 exon 5521459 5521544 5521459 ID=MS.gene09705.t1.exon1;Parent=MS.gene09705.t1
chr5.2 CDS 5521459 5521544 5521459 ID=cds.MS.gene09705.t1;Parent=MS.gene09705.t1
chr5.2 exon 5521680 5521945 5521680 ID=MS.gene09705.t1.exon2;Parent=MS.gene09705.t1
chr5.2 CDS 5521680 5521945 5521680 ID=cds.MS.gene09705.t1;Parent=MS.gene09705.t1
chr5.2 exon 5522326 5522543 5522326 ID=MS.gene09705.t1.exon3;Parent=MS.gene09705.t1
chr5.2 CDS 5522326 5522543 5522326 ID=cds.MS.gene09705.t1;Parent=MS.gene09705.t1
Gene Sequence

>MS.gene09705

ATGAATCACTACAAACGTACACGTATGAATTTCCAACAAGCTCCTCATCTCTTTCTACAAGAGGTTTCAAATTTGGGACATTCCAGGTACATGTTCTTTTGCTACTTTTAACTTGTCAAGTCCATCAACATTTTTTTAGCTACTAAATCATGAATTCATGATTCATGTTTATAACATGGTCAATTTGCATTAAATTAATTGTTAATGTTGTTTTATTACAGTGTAATGAAGGCTAATAGTATTATCAAGGAAGAGCCTAGAAGTGCCCAAATGACAATATTTTATGATGGGAAAGTAATTGTGTTTGATGATATTCCAGCTGAAAAAGTCAACGACATCATGGTCTTTTCCAAGAAAGGAACTACTACCTCTCAAAACCACAACAATAACAACTATGCTTTCAGATTTGCTCAGAGCCACCCATCATTTCTTGCTAGAAATTCTGCCTACAATTCTCTTCAAGTACCATCCACACCTGTTATTTATGGTAAAAATAATAATTGGATATCTTTTTTTTTTTTTGGTACAAATAATAATTGGATATCTATTTGAGTGGTGCTTGATTTGTGTAATGATTTTATGTGTGTTTTTCATATTCATGACTTTCCTATTTATATATAGGAAAATTCTACAGTGAAGTCGTTAAAATGACTTTTTTGGTGAAGTCATTAGAATGACCAATCATAATGCATTTGTGTATTTAATGCATGCCACATCAAATTTTACTGCGCATCGTACATTTGCTCATATGGTGTACCACTATATTTTTACTTATTGCAATTGTGTCCTTGATTAAATCAAAATTAAACATTTTTTTATATTATTTTTTACTTTTTATTCTTAAAACTTATAGTGTTTCAGTTTCAGCCTATAGATACGATATCTTCACCATCGTATTAACTTGTAGATACGACCAATTCATGCATCTTCACCATCGCACAGATTCAGCTTTATCAATCATCAAAATTCCAGATTCTCTGCCATCCTTCGTCCGCCACCTATCATCACCACTACAACGAAAAGAGAATCTCTGCGGCGAGCTTCAGCGAAAGCTTCTTCACCCCATGGATACCAATCAACCTTGA
Protein sequence

>MS.gene09705.t1

MNHYKRTRMNFQQAPHLFLQEVSNLGHSSVMKANSIIKEEPRSAQMTIFYDGKVIVFDDIPAEKVNDIMVFSKKGTTTSQNHNNNNYAFRFAQSHPSFLARNSAYNSLQVPSTPVIYAYRYDIFTIVLTCRYDQFMHLHHRTDSALSIIKIPDSLPSFVRHLSSPLQRKENLCGELQRKLLHPMDTNQP