AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068452


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068452.t1 MTR_4g029740 83.673 98 16 0 1 98 104 201 1.36e-57 182
MS.gene068452.t1 MTR_2g026970 82.353 68 12 0 118 185 3 70 3.29e-33 116
MS.gene068452.t1 MTR_3g463980 83.871 62 10 0 124 185 73 134 3.38e-26 98.6
MS.gene068452.t1 MTR_3g005890 92.000 50 4 0 136 185 18 67 2.04e-21 85.1
MS.gene068452.t1 MTR_1g077860 41.228 114 64 2 59 172 2 112 3.87e-17 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCAGACAACTTCATCTTCT+TGG 0.215709 6.3:-64819018 MS.gene068452:CDS
GTACCCGATACATTGTATTT+TGG 0.222822 6.3:+64819914 None:intergenic
AAAATTGGGAAGATAGTAAA+TGG 0.294207 6.3:-64819834 MS.gene068452:CDS
AATAATGAACTGTCTGTTAC+AGG 0.299759 6.3:-64820612 None:intergenic
TCTATGTCTTGCTCATGTTC+AGG 0.345935 6.3:+64819970 None:intergenic
GAAAGGACACATATATGGTT+TGG 0.371434 6.3:-64818973 MS.gene068452:CDS
AAAGGACACATATATGGTTT+GGG 0.378346 6.3:-64818972 MS.gene068452:CDS
GACAAGAAAGGACACATATA+TGG 0.391600 6.3:-64818978 MS.gene068452:CDS
TTCATCTTCTTGGACGTAGT+TGG 0.429547 6.3:-64819008 MS.gene068452:CDS
ATGGTCCATTGCACACTTGT+GGG 0.458304 6.3:-64819768 MS.gene068452:CDS
CATCTGAATATGAGCATATG+AGG 0.460761 6.3:-64818893 MS.gene068452:CDS
TATGGTTTGGGGACAGAGGC+AGG 0.462107 6.3:-64818960 MS.gene068452:CDS
GATGGTCCATTGCACACTTG+TGG 0.470798 6.3:-64819769 MS.gene068452:CDS
ATCTTCTTGGACGTAGTTGG+AGG 0.475318 6.3:-64819005 MS.gene068452:CDS
AGAGAAGACTTATCATCATA+AGG 0.476174 6.3:-64819950 MS.gene068452:CDS
TCTTCATCCAGATCATTTGA+CGG 0.487821 6.3:-64818924 MS.gene068452:CDS
TGAAATGCCGTCAAATGATC+TGG 0.505157 6.3:+64818917 None:intergenic
GGTACCAAAATACAATGTAT+CGG 0.506345 6.3:-64819918 MS.gene068452:CDS
TATTGCAGAGGATATATAAG+TGG 0.513050 6.3:-64819996 MS.gene068452:intron
GTACCAAAATACAATGTATC+GGG 0.520464 6.3:-64819917 MS.gene068452:CDS
ACAATGTATCGGGTACGAAA+AGG 0.523365 6.3:-64819907 MS.gene068452:CDS
TATCATCATAAGGCATCTGA+TGG 0.529469 6.3:-64819940 MS.gene068452:CDS
GTGTAGGATGAATATGAAAG+AGG 0.541573 6.3:-64819098 MS.gene068452:intron
GTTGGAGGAGTCGACAAGAA+AGG 0.560231 6.3:-64818990 MS.gene068452:CDS
TGTAGGATGAATATGAAAGA+GGG 0.565349 6.3:-64819097 MS.gene068452:intron
TAAAATGTCAGCTGAAAACA+TGG 0.565653 6.3:-64818859 MS.gene068452:CDS
ATGAAAGAGGGATCTTTGAA+AGG 0.571397 6.3:-64819085 MS.gene068452:CDS
CTGAAAACATGGAACTCTCA+AGG 0.572053 6.3:-64818848 MS.gene068452:CDS
CTCATATGCTCATATTCAGA+TGG 0.573783 6.3:+64818894 None:intergenic
TTGGGAAGATAGTAAATGGA+AGG 0.581599 6.3:-64819830 MS.gene068452:CDS
AAGGAATAGACAAAGGCGAA+TGG 0.591694 6.3:-64819888 MS.gene068452:CDS
AGTGTGCAATGGACCATCAG+AGG 0.611168 6.3:+64819774 None:intergenic
CAAAATAGAAGATCCTCTGA+TGG 0.614529 6.3:-64819787 MS.gene068452:CDS
AGGAACTCACAACAAACAGA+GGG 0.614725 6.3:-64819065 MS.gene068452:CDS
ATCATCATAAGGCATCTGAT+GGG 0.619211 6.3:-64819939 MS.gene068452:CDS
CATATATGGTTTGGGGACAG+AGG 0.629154 6.3:-64818964 MS.gene068452:CDS
ATAGACCCACAAGTGTGCAA+TGG 0.640134 6.3:+64819763 None:intergenic
AAGGACACATATATGGTTTG+GGG 0.644659 6.3:-64818971 MS.gene068452:CDS
AGATGAAGTTGTCTGACTGA+TGG 0.649405 6.3:+64819024 None:intergenic
AACATGGAACTCTCAAGGAG+CGG 0.660939 6.3:-64818843 MS.gene068452:CDS
GTACGAAAAGGAATAGACAA+AGG 0.669707 6.3:-64819895 MS.gene068452:CDS
AAGGAACTCACAACAAACAG+AGG 0.682264 6.3:-64819066 MS.gene068452:CDS
AGATAGTAAATGGAAGGACA+AGG 0.688548 6.3:-64819824 MS.gene068452:CDS
GAACTCACAACAAACAGAGG+GGG 0.692900 6.3:-64819063 MS.gene068452:CDS
GGAACTCACAACAAACAGAG+GGG 0.755288 6.3:-64819064 MS.gene068452:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACAATGTAAATAATAT+AGG + chr6.3:64819432-64819451 None:intergenic 10.0%
!! AAATAAATAGATTAGTATTA+TGG + chr6.3:64819786-64819805 None:intergenic 10.0%
!! ATGCATAACATTAAAAACTA+TGG + chr6.3:64820203-64820222 None:intergenic 20.0%
!! GTAAATAATATAGGTTAAAC+CGG + chr6.3:64819423-64819442 None:intergenic 20.0%
!! TGAAAAATTGGAACAAAATT+GGG - chr6.3:64819599-64819618 MS.gene068452:intron 20.0%
!!! AAGTTTTCTAATGTAGTTAT+TGG - chr6.3:64819244-64819263 MS.gene068452:intron 20.0%
!!! AGTTTTCTAATGTAGTTATT+GGG - chr6.3:64819245-64819264 MS.gene068452:intron 20.0%
!!! TTTTATGTTTATTTGACAGA+AGG + chr6.3:64819964-64819983 None:intergenic 20.0%
! AAAACAATTATAGCACATGA+TGG + chr6.3:64820135-64820154 None:intergenic 25.0%
! AAAATTGGGAAGATAGTAAA+TGG - chr6.3:64819613-64819632 MS.gene068452:intron 25.0%
! AAGTCAGTTGAACAATTAAA+AGG + chr6.3:64819289-64819308 None:intergenic 25.0%
! AGCAACAAAGAATGATAAAA+AGG + chr6.3:64818929-64818948 None:intergenic 25.0%
! AGTCAGTTGAACAATTAAAA+GGG + chr6.3:64819288-64819307 None:intergenic 25.0%
! ATAAAGACACACAAAATGAA+AGG - chr6.3:64819861-64819880 MS.gene068452:CDS 25.0%
! CAACAAAGAATGATAAAAAG+GGG + chr6.3:64818927-64818946 None:intergenic 25.0%
! CTAGAATTAGTTATATCCTT+TGG - chr6.3:64820002-64820021 MS.gene068452:intron 25.0%
! GCAACAAAGAATGATAAAAA+GGG + chr6.3:64818928-64818947 None:intergenic 25.0%
! GTGAAAAATTGGAACAAAAT+TGG - chr6.3:64819598-64819617 MS.gene068452:intron 25.0%
! TTTATTCTGTTAAAGTCAGT+TGG + chr6.3:64819321-64819340 None:intergenic 25.0%
!! TCATGTGCTATAATTGTTTT+TGG - chr6.3:64820135-64820154 MS.gene068452:intron 25.0%
!!! TTACATTGTTTTTATTGCAG+AGG - chr6.3:64819439-64819458 MS.gene068452:intron 25.0%
AAAGGACACATATATGGTTT+GGG - chr6.3:64820475-64820494 MS.gene068452:intron 30.0%
AGAGAAGACTTATCATCATA+AGG - chr6.3:64819497-64819516 MS.gene068452:intron 30.0%
GAATTAGTTATATCCTTTGG+TGG - chr6.3:64820005-64820024 MS.gene068452:intron 30.0%
GGTACCAAAATACAATGTAT+CGG - chr6.3:64819529-64819548 MS.gene068452:intron 30.0%
GTACCAAAATACAATGTATC+GGG - chr6.3:64819530-64819549 MS.gene068452:intron 30.0%
GTCTTATGTAAATGCAAATG+TGG - chr6.3:64819017-64819036 MS.gene068452:CDS 30.0%
TAAAATGTCAGCTGAAAACA+TGG - chr6.3:64820588-64820607 MS.gene068452:intron 30.0%
TATTGCAGAGGATATATAAG+TGG - chr6.3:64819451-64819470 MS.gene068452:intron 30.0%
TGATCTTATGTTTCTTCACT+TGG - chr6.3:64820262-64820281 MS.gene068452:intron 30.0%
TGTAGGATGAATATGAAAGA+GGG - chr6.3:64820350-64820369 MS.gene068452:intron 30.0%
TGTTCAATTGCGTGAAAAAT+TGG - chr6.3:64819587-64819606 MS.gene068452:intron 30.0%
! AATTTTTCACGCAATTGAAC+AGG + chr6.3:64819588-64819607 None:intergenic 30.0%
! ATTTTTCACGCAATTGAACA+GGG + chr6.3:64819587-64819606 None:intergenic 30.0%
! TATGCTATGATAATGTTGTC+TGG - chr6.3:64819127-64819146 MS.gene068452:intron 30.0%
!!! CTTTTAAAATGCTCGATTGT+TGG + chr6.3:64819711-64819730 None:intergenic 30.0%
AAAAACTATGGCACAAAAGC+AGG + chr6.3:64820191-64820210 None:intergenic 35.0%
AAATGTGGCATCTAATTGTG+TGG - chr6.3:64819032-64819051 MS.gene068452:CDS 35.0%
AAGACGAACTCTAATTGTGT+AGG - chr6.3:64820333-64820352 MS.gene068452:intron 35.0%
AAGGACACATATATGGTTTG+GGG - chr6.3:64820476-64820495 MS.gene068452:intron 35.0%
AGATAGTAAATGGAAGGACA+AGG - chr6.3:64819623-64819642 MS.gene068452:intron 35.0%
ATGAAAGAGGGATCTTTGAA+AGG - chr6.3:64820362-64820381 MS.gene068452:intron 35.0%
ATGTTTATTTGACAGAAGGC+TGG + chr6.3:64819960-64819979 None:intergenic 35.0%
CAAAATAGAAGATCCTCTGA+TGG - chr6.3:64819660-64819679 MS.gene068452:intron 35.0%
CATCTGAATATGAGCATATG+AGG - chr6.3:64820554-64820573 MS.gene068452:intron 35.0%
CTCATATGCTCATATTCAGA+TGG + chr6.3:64820556-64820575 None:intergenic 35.0%
GAAAGGACACATATATGGTT+TGG - chr6.3:64820474-64820493 MS.gene068452:intron 35.0%
GAAAGGTGATCCATCAAATT+GGG - chr6.3:64819878-64819897 MS.gene068452:CDS 35.0%
GACAAGAAAGGACACATATA+TGG - chr6.3:64820469-64820488 MS.gene068452:intron 35.0%
GTACGAAAAGGAATAGACAA+AGG - chr6.3:64819552-64819571 MS.gene068452:intron 35.0%
GTGTAGGATGAATATGAAAG+AGG - chr6.3:64820349-64820368 MS.gene068452:intron 35.0%
TACAATGATCCTGCAGATTA+AGG + chr6.3:64819203-64819222 None:intergenic 35.0%
TCTTCATCCAGATCATTTGA+CGG - chr6.3:64820523-64820542 MS.gene068452:intron 35.0%
TGAAAGGTGATCCATCAAAT+TGG - chr6.3:64819877-64819896 MS.gene068452:CDS 35.0%
TTGGGAAGATAGTAAATGGA+AGG - chr6.3:64819617-64819636 MS.gene068452:intron 35.0%
TTTGTTCATCCTTAATCTGC+AGG - chr6.3:64819191-64819210 MS.gene068452:intron 35.0%
! ATCATCATAAGGCATCTGAT+GGG - chr6.3:64819508-64819527 MS.gene068452:intron 35.0%
! GTACCCGATACATTGTATTT+TGG + chr6.3:64819536-64819555 None:intergenic 35.0%
! TATCATCATAAGGCATCTGA+TGG - chr6.3:64819507-64819526 MS.gene068452:intron 35.0%
AAAGCTCCTAGTTTGATGTC+CGG - chr6.3:64819401-64819420 MS.gene068452:intron 40.0%
AAGGAACTCACAACAAACAG+AGG - chr6.3:64820381-64820400 MS.gene068452:intron 40.0%
AAGGAATAGACAAAGGCGAA+TGG - chr6.3:64819559-64819578 MS.gene068452:intron 40.0%
ACAATGTATCGGGTACGAAA+AGG - chr6.3:64819540-64819559 MS.gene068452:intron 40.0%
AGATGAAGTTGTCTGACTGA+TGG + chr6.3:64820426-64820445 None:intergenic 40.0%
AGCATGCATCAATACACATG+AGG + chr6.3:64820095-64820114 None:intergenic 40.0%
AGGAACTCACAACAAACAGA+GGG - chr6.3:64820382-64820401 MS.gene068452:intron 40.0%
CAAACATGATTCCAAGCTAC+TGG - chr6.3:64819830-64819849 MS.gene068452:CDS 40.0%
CTCCAAATCTCAAATGGTTG+CGG - chr6.3:64819905-64819924 MS.gene068452:CDS 40.0%
CTGAAAACATGGAACTCTCA+AGG - chr6.3:64820599-64820618 MS.gene068452:intron 40.0%
GGTATCCTCCAAATCTCAAA+TGG - chr6.3:64819899-64819918 MS.gene068452:CDS 40.0%
GGTTTACCAGATCTCATATC+AGG + chr6.3:64818970-64818989 None:intergenic 40.0%
GTCAGACAACTTCATCTTCT+TGG - chr6.3:64820429-64820448 MS.gene068452:intron 40.0%
GTTAAACCGGACATCAAACT+AGG + chr6.3:64819410-64819429 None:intergenic 40.0%
TATATACACCTCCAGTAGCT+TGG + chr6.3:64819844-64819863 None:intergenic 40.0%
TCTATGTCTTGCTCATGTTC+AGG + chr6.3:64819480-64819499 None:intergenic 40.0%
TCTCTACCTGATATGAGATC+TGG - chr6.3:64818961-64818980 MS.gene068452:CDS 40.0%
TGAAATGCCGTCAAATGATC+TGG + chr6.3:64820533-64820552 None:intergenic 40.0%
TGGTGGAAAGTCAAGGTAAT+TGG - chr6.3:64820039-64820058 MS.gene068452:intron 40.0%
TTCATCTTCTTGGACGTAGT+TGG - chr6.3:64820439-64820458 MS.gene068452:intron 40.0%
TTGGAGGATACCCAATTTGA+TGG + chr6.3:64819891-64819910 None:intergenic 40.0%
! TACCGCAACCATTTGAGATT+TGG + chr6.3:64819910-64819929 None:intergenic 40.0%
!! GTTATATCCTTTGGTGGACT+TGG - chr6.3:64820011-64820030 MS.gene068452:intron 40.0%
AACATGGAACTCTCAAGGAG+CGG - chr6.3:64820604-64820623 MS.gene068452:intron 45.0%
ACATGATTCCAAGCTACTGG+AGG - chr6.3:64819833-64819852 MS.gene068452:CDS 45.0%
ATAGACCCACAAGTGTGCAA+TGG + chr6.3:64819687-64819706 None:intergenic 45.0%
ATCTTCTTGGACGTAGTTGG+AGG - chr6.3:64820442-64820461 MS.gene068452:intron 45.0%
ATGGTCCATTGCACACTTGT+GGG - chr6.3:64819679-64819698 MS.gene068452:intron 45.0%
GAACTCACAACAAACAGAGG+GGG - chr6.3:64820384-64820403 MS.gene068452:intron 45.0%
GGAACTCACAACAAACAGAG+GGG - chr6.3:64820383-64820402 MS.gene068452:intron 45.0%
TCAAACTAGGAGCTTTGCTC+TGG + chr6.3:64819397-64819416 None:intergenic 45.0%
TTATTGGGTCCAACTGTCGT+CGG - chr6.3:64819260-64819279 MS.gene068452:intron 45.0%
! CATATATGGTTTGGGGACAG+AGG - chr6.3:64820483-64820502 MS.gene068452:intron 45.0%
! CGCAACCATTTGAGATTTGG+AGG + chr6.3:64819907-64819926 None:intergenic 45.0%
AGTGTGCAATGGACCATCAG+AGG + chr6.3:64819676-64819695 None:intergenic 50.0%
CAGCATACCAAGTCCACCAA+AGG + chr6.3:64820021-64820040 None:intergenic 50.0%
GATGGTCCATTGCACACTTG+TGG - chr6.3:64819678-64819697 MS.gene068452:intron 50.0%
GGTATGCTGGTGGAAAGTCA+AGG - chr6.3:64820032-64820051 MS.gene068452:intron 50.0%
GTTGGAGGAGTCGACAAGAA+AGG - chr6.3:64820457-64820476 MS.gene068452:intron 50.0%
TGTTGTCTGGCATGTGCGAA+TGG - chr6.3:64819140-64819159 MS.gene068452:intron 50.0%
! TGCACACAAGAGTGCAGTCA+TGG + chr6.3:64818991-64819010 None:intergenic 50.0%
!! AAAAGGGTACCGACGACAGT+TGG + chr6.3:64819272-64819291 None:intergenic 50.0%
!! CTTTGGTGGACTTGGTATGC+TGG - chr6.3:64820019-64820038 MS.gene068452:intron 50.0%
! TATGGTTTGGGGACAGAGGC+AGG - chr6.3:64820487-64820506 MS.gene068452:intron 55.0%
!! TGGTGGACTTGGTATGCTGG+TGG - chr6.3:64820022-64820041 MS.gene068452:intron 55.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 64818839 64820630 64818839 ID=MS.gene068452
chr6.3 mRNA 64818839 64820630 64818839 ID=MS.gene068452.t1;Parent=MS.gene068452
chr6.3 exon 64820613 64820630 64820613 ID=MS.gene068452.t1.exon1;Parent=MS.gene068452.t1
chr6.3 CDS 64820613 64820630 64820613 ID=cds.MS.gene068452.t1;Parent=MS.gene068452.t1
chr6.3 exon 64819735 64820010 64819735 ID=MS.gene068452.t1.exon2;Parent=MS.gene068452.t1
chr6.3 CDS 64819735 64820010 64819735 ID=cds.MS.gene068452.t1;Parent=MS.gene068452.t1
chr6.3 exon 64818839 64819114 64818839 ID=MS.gene068452.t1.exon3;Parent=MS.gene068452.t1
chr6.3 CDS 64818839 64819114 64818839 ID=cds.MS.gene068452.t1;Parent=MS.gene068452.t1
Gene Sequence

>MS.gene068452

ATGAACTGTCTGTTACAGGTCTGTGATTTTCTTGTGATGAACTGTCTGTGATTTTCTTGTGTTCAAGCTCTTCTTTCTTTATCTTCCCCTTTTTATCATTCTTTGTTGCTAGTGTTTCATTGTCTCTACCTGATATGAGATCTGGTAAACCATGACTGCACTCTTGTGTGCACTCTTAGTCTTATGTAAATGCAAATGTGGCATCTAATTGTGTGGCTTGTGATTTATCAGAAGCATGTTTTGTAGTAGCATTCATTTTAAGCACTTCAATTGCAGTATACATAATTATATGCTATGATAATGTTGTCTGGCATGTGCGAATGGAGTTAATAATCATTGTTTGATTTATGTGTTTGTTCATCCTTAATCTGCAGGATCATTGTAGCTTTTTTCACAGTACTAGAAAAGTTTTCTAATGTAGTTATTGGGTCCAACTGTCGTCGGTACCCTTTTAATTGTTCAACTGACTTTAATAGTGTCCAACTGACTTTAACAGAATAAATCAATAGAAACAAGAGAATAGTGAATATTAATAACTCACAAGAGTTACAAGTTCCAGAGCAAAGCTCCTAGTTTGATGTCCGGTTTAACCTATATTATTTACATTGTTTTTATTGCAGAGGATATATAAGTGGCTTCCTGAACATGAGCAAGACATAGAGAAGACTTATCATCATAAGGCATCTGATGGGTACCAAAATACAATGTATCGGGTACGAAAAGGAATAGACAAAGGCGAATGGATCCCTGTTCAATTGCGTGAAAAATTGGAACAAAATTGGGAAGATAGTAAATGGAAGGACAAGGCAGAAGTTAATAAGCAAAATAGAAGATCCTCTGATGGTCCATTGCACACTTGTGGGTCTATTCCAACAATCGAGCATTTTAAAAGATTAGTAAGTAAACAAATTTTATTTGCAGTAAAGCATAGTGATTTAAATTAACCATAATACTAATCTATTTATTTATTTTGTACTATAGAAAACTGACTCAAACATGATTCCAAGCTACTGGAGGTGTATATAAAGACACACAAAATGAAAGGTGATCCATCAAATTGGGTATCCTCCAAATCTCAAATGGTTGCGGTAAGTTACAATTCGACAAGATTATCATTTCCAGCCTTCTGTCAAATAAACATAAAACAATTGAAAATTAATTTTCTAGAATTAGTTATATCCTTTGGTGGACTTGGTATGCTGGTGGAAAGTCAAGGTAATTGGAAAAACTTTAAAATTAGTATTTATAACTGTCCTCATGTGTATTGATGCATGCTGCTACACTATAACTCTGCCATCATGTGCTATAATTGTTTTTGGTTATCTAATCATGTTTATTGTTGTATGTTACCTGCTTTTGTGCCATAGTTTTTAATGTTATGCATGCTTATTATTGTTCATCAAGTTCTGACATCTGAACATGATGATCTTATGTTTCTTCACTTGGAAAGAAGTCATGATAACTTAGTTATTAATTAAAAGCTAGATAAGAATTAAGACGAACTCTAATTGTGTAGGATGAATATGAAAGAGGGATCTTTGAAAGGAACTCACAACAAACAGAGGGGGATGATGTGTCTAATGACCATCAGTCAGACAACTTCATCTTCTTGGACGTAGTTGGAGGAGTCGACAAGAAAGGACACATATATGGTTTGGGGACAGAGGCAGGAAAATACAAGTCTTCTTCATCCAGATCATTTGACGGCATTTCACCATCTGAATATGAGCATATGAGGACTGCAATATCTAAAATGTCAGCTGAAAACATGGAACTCTCAAGGAGCGGTTGA

Protein sequence

>MS.gene068452.t1

MNCLLQRIYKWLPEHEQDIEKTYHHKASDGYQNTMYRVRKGIDKGEWIPVQLREKLEQNWEDSKWKDKAEVNKQNRRSSDGPLHTCGSIPTIEHFKRLDEYERGIFERNSQQTEGDDVSNDHQSDNFIFLDVVGGVDKKGHIYGLGTEAGKYKSSSSRSFDGISPSEYEHMRTAISKMSAENMELSRSG