AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028849

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028849.t1 MTR_2g090900 91.775 231 11 2 1 231 11 233 3.96e-128 366
MS.gene028849.t1 MTR_2g090900 91.775 231 11 2 1 231 11 233 6.52e-128 364
MS.gene028849.t1 MTR_4g079500 54.959 242 80 9 1 231 13 236 2.92e-66 208
MS.gene028849.t1 MTR_2g078370 41.667 168 81 6 34 195 58 214 3.01e-27 104
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028849.t1 AT3G58120 50.000 244 96 7 2 231 13 244 8.31e-65 202
MS.gene028849.t1 AT3G58120 50.000 244 96 7 2 231 13 244 1.86e-64 203
MS.gene028849.t1 AT2G42380 48.673 226 101 5 1 225 11 222 8.60e-54 173
MS.gene028849.t1 AT2G42380 48.673 226 101 5 1 225 11 222 8.60e-54 173
MS.gene028849.t1 AT2G42380 47.414 232 107 5 1 231 11 228 1.03e-53 174
MS.gene028849.t1 AT2G42380 48.133 241 92 6 1 231 11 228 1.20e-53 175
MS.gene028849.t1 AT2G42380 47.807 228 86 6 1 218 11 215 1.85e-48 161

Find 36 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGTAGTGACAATGTTAT+TGG 0.263094 2.3:+9499867 None:intergenic
GCATTAGAATCTTGGCAAAT+AGG 0.275046 2.3:-9498946 MS.gene028849:intron
GAGAAGAAGGAGAATGATTT+AGG 0.291281 2.3:-9499523 MS.gene028849:CDS
GCGTAGTGTAACTTCATTAC+AGG 0.313139 2.3:-9498870 MS.gene028849:intron
GTGTAATGTATAGTGGAATT+TGG 0.331218 2.3:-9498763 MS.gene028849:intron
CATTGGCTTTCTACCTCATC+AGG 0.351950 2.3:+9499457 None:intergenic
GACAATGTTATTGGTTGAAA+TGG 0.385822 2.3:+9499876 None:intergenic
GAAGAATAAACAAGAGAAGA+AGG 0.396694 2.3:-9499536 MS.gene028849:CDS
ACCAATGCTTGATGATTGTC+GGG 0.399558 2.3:-9499734 MS.gene028849:CDS
GCATTGTTGTTATTACTTTG+AGG 0.430433 2.3:+9499415 None:intergenic
ATCAGAATCAGAACCCTTCA+TGG 0.433073 2.3:-9499840 MS.gene028849:CDS
CAAGGCGAGGCGCTCATAGA+AGG 0.460166 2.3:-9499789 MS.gene028849:CDS
CACCAATGCTTGATGATTGT+CGG 0.462711 2.3:-9499735 MS.gene028849:CDS
GGTAGAAAGCCAATGCAAAC+AGG 0.488493 2.3:-9499449 MS.gene028849:CDS
ATGTTCAGTGATGAAATATC+TGG 0.505923 2.3:-9499646 MS.gene028849:CDS
TTATTGGTTGAAATGGATGT+TGG 0.515770 2.3:+9499883 None:intergenic
TTGACAAAATTCTGATCTGA+AGG 0.516864 2.3:+9499577 None:intergenic
CCCCGACAATCATCAAGCAT+TGG 0.530465 2.3:+9499733 None:intergenic
TTTAGGAGAGATGAAGAAAG+AGG 0.538946 2.3:-9499506 MS.gene028849:CDS
AGGAACTCATCCACCCATGA+AGG 0.539506 2.3:+9499826 None:intergenic
AGATATTTCATCACTGAACA+TGG 0.569631 2.3:+9499648 None:intergenic
CTGATCCAAAGAGAGTCAAA+AGG 0.572655 2.3:-9499369 MS.gene028849:intron
TTCGATGAAGACAACGTTGG+TGG 0.575587 2.3:+9499610 None:intergenic
TCCCAAACATGTCACCAAGT+TGG 0.580152 2.3:-9499939 None:intergenic
GAATCAGAACCCTTCATGGG+TGG 0.607660 2.3:-9499836 MS.gene028849:CDS
ATTGAAATATGAACCTGATG+AGG 0.608223 2.3:-9499470 MS.gene028849:CDS
TCAGAATCAGAACCCTTCAT+GGG 0.609308 2.3:-9499839 MS.gene028849:CDS
GGAACTCATCCACCCATGAA+GGG 0.626852 2.3:+9499827 None:intergenic
CAAATAGGCAATCAGCACAA+AGG 0.647617 2.3:-9498931 MS.gene028849:CDS
ATGAGCGCCTCGCCTTGCCG+AGG 0.647953 2.3:+9499795 None:intergenic
CAGCACAAAGGTCACGTGTG+AGG 0.661809 2.3:-9498919 MS.gene028849:CDS
GCGAGGCGCTCATAGAAGGT+CGG 0.662721 2.3:-9499785 MS.gene028849:CDS
GCCTTGCCGAGGAAAAGTCG+AGG 0.688307 2.3:+9499806 None:intergenic
GATTGTCGGGGTAAACACGA+TGG 0.708511 2.3:-9499721 MS.gene028849:CDS
GTGTTCGATGAAGACAACGT+TGG 0.718712 2.3:+9499607 None:intergenic
CCAATGCTTGATGATTGTCG+GGG 0.745183 2.3:-9499733 MS.gene028849:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATAAAAATTAAAACATGT+AGG - chr2.3:9499361-9499380 MS.gene028849:intron 15.0%
!! AATTGAAATATTGTTGATCT+TGG - chr2.3:9499605-9499624 MS.gene028849:CDS 20.0%
!! ATTTGCAGTACTATAATATA+TGG - chr2.3:9499885-9499904 MS.gene028849:CDS 20.0%
!!! ATGTTGGCATAATATTTTTT+TGG + chr2.3:9498784-9498803 None:intergenic 20.0%
!!! CATAATATTTTTTTGGTGTT+TGG + chr2.3:9498777-9498796 None:intergenic 20.0%
!!! TTTTTTTTGCATTAGAATCT+TGG - chr2.3:9499726-9499745 MS.gene028849:CDS 20.0%
! ATTTGATGTGTAATGTATAG+TGG - chr2.3:9499910-9499929 MS.gene028849:CDS 25.0%
AGATATTTCATCACTGAACA+TGG + chr2.3:9499035-9499054 None:intergenic 30.0%
ATGTTCAGTGATGAAATATC+TGG - chr2.3:9499034-9499053 MS.gene028849:intron 30.0%
ATTGAAATATGAACCTGATG+AGG - chr2.3:9499210-9499229 MS.gene028849:intron 30.0%
GAAGAATAAACAAGAGAAGA+AGG - chr2.3:9499144-9499163 MS.gene028849:intron 30.0%
GAATCAGTTACAAAACTCAA+AGG + chr2.3:9499692-9499711 None:intergenic 30.0%
GTTTGTAGTGACAATGTTAT+TGG + chr2.3:9498816-9498835 None:intergenic 30.0%
TTGACAAAATTCTGATCTGA+AGG + chr2.3:9499106-9499125 None:intergenic 30.0%
! GACAATGTTATTGGTTGAAA+TGG + chr2.3:9498807-9498826 None:intergenic 30.0%
! GCATTGTTGTTATTACTTTG+AGG + chr2.3:9499268-9499287 None:intergenic 30.0%
! GTGTAATGTATAGTGGAATT+TGG - chr2.3:9499917-9499936 MS.gene028849:CDS 30.0%
! TTATTGGTTGAAATGGATGT+TGG + chr2.3:9498800-9498819 None:intergenic 30.0%
!! AATTACCTTTTGACTCTCTT+TGG + chr2.3:9499319-9499338 None:intergenic 30.0%
!! TTGAGTTTTGTAACTGATTC+TGG - chr2.3:9499692-9499711 MS.gene028849:CDS 30.0%
!!! TTTTGGTGTTTGGAAAAATC+TGG + chr2.3:9498767-9498786 None:intergenic 30.0%
ACTCCAAAATCATGTCATGT+GGG + chr2.3:9499500-9499519 None:intergenic 35.0%
GAGAAGAAGGAGAATGATTT+AGG - chr2.3:9499157-9499176 MS.gene028849:intron 35.0%
GCATTAGAATCTTGGCAAAT+AGG - chr2.3:9499734-9499753 MS.gene028849:CDS 35.0%
TTTAGGAGAGATGAAGAAAG+AGG - chr2.3:9499174-9499193 MS.gene028849:intron 35.0%
! GTGAATTTTCCTGTTTGCAT+TGG + chr2.3:9499243-9499262 None:intergenic 35.0%
ATCAGAATCAGAACCCTTCA+TGG - chr2.3:9498840-9498859 MS.gene028849:intron 40.0%
CAAATAGGCAATCAGCACAA+AGG - chr2.3:9499749-9499768 MS.gene028849:CDS 40.0%
CACTCCAAAATCATGTCATG+TGG + chr2.3:9499501-9499520 None:intergenic 40.0%
CTGATCCAAAGAGAGTCAAA+AGG - chr2.3:9499311-9499330 MS.gene028849:intron 40.0%
GCGTAGTGTAACTTCATTAC+AGG - chr2.3:9499810-9499829 MS.gene028849:CDS 40.0%
TCAGAATCAGAACCCTTCAT+GGG - chr2.3:9498841-9498860 MS.gene028849:intron 40.0%
TTGGAAAAATCTGGCCAACT+TGG + chr2.3:9498758-9498777 None:intergenic 40.0%
! ACCAATGCTTGATGATTGTC+GGG - chr2.3:9498946-9498965 MS.gene028849:intron 40.0%
! ATGCCCACATGACATGATTT+TGG - chr2.3:9499494-9499513 MS.gene028849:CDS 40.0%
! CACCAATGCTTGATGATTGT+CGG - chr2.3:9498945-9498964 MS.gene028849:intron 40.0%
GGTAGAAAGCCAATGCAAAC+AGG - chr2.3:9499231-9499250 MS.gene028849:intron 45.0%
GTGTTCGATGAAGACAACGT+TGG + chr2.3:9499076-9499095 None:intergenic 45.0%
TTCGATGAAGACAACGTTGG+TGG + chr2.3:9499073-9499092 None:intergenic 45.0%
! CCAATGCTTGATGATTGTCG+GGG - chr2.3:9498947-9498966 MS.gene028849:intron 45.0%
! TGAGTTCCTCGACTTTTCCT+CGG - chr2.3:9498868-9498887 MS.gene028849:intron 45.0%
!! CATTGGCTTTCTACCTCATC+AGG + chr2.3:9499226-9499245 None:intergenic 45.0%
AGGAACTCATCCACCCATGA+AGG + chr2.3:9498857-9498876 None:intergenic 50.0%
CCCCGACAATCATCAAGCAT+TGG + chr2.3:9498950-9498969 None:intergenic 50.0%
GAATCAGAACCCTTCATGGG+TGG - chr2.3:9498844-9498863 MS.gene028849:intron 50.0%
GATTGTCGGGGTAAACACGA+TGG - chr2.3:9498959-9498978 MS.gene028849:intron 50.0%
GGAACTCATCCACCCATGAA+GGG + chr2.3:9498856-9498875 None:intergenic 50.0%
CAGCACAAAGGTCACGTGTG+AGG - chr2.3:9499761-9499780 MS.gene028849:CDS 55.0%
! TCCTCGACTTTTCCTCGGCA+AGG - chr2.3:9498873-9498892 MS.gene028849:CDS 55.0%
GCCTTGCCGAGGAAAAGTCG+AGG + chr2.3:9498877-9498896 None:intergenic 60.0%
! CAAGGCGAGGCGCTCATAGA+AGG - chr2.3:9498891-9498910 MS.gene028849:CDS 60.0%
! GACTTTTCCTCGGCAAGGCG+AGG - chr2.3:9498878-9498897 MS.gene028849:CDS 60.0%
! GCGAGGCGCTCATAGAAGGT+CGG - chr2.3:9498895-9498914 MS.gene028849:CDS 60.0%
ATGAGCGCCTCGCCTTGCCG+AGG + chr2.3:9498888-9498907 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 9498749 9499953 9498749 ID=MS.gene028849
chr2.3 mRNA 9498749 9499953 9498749 ID=MS.gene028849.t1;Parent=MS.gene028849
chr2.3 exon 9499370 9499953 9499370 ID=MS.gene028849.t1.exon1;Parent=MS.gene028849.t1
chr2.3 CDS 9499370 9499953 9499370 ID=cds.MS.gene028849.t1;Parent=MS.gene028849.t1
chr2.3 exon 9498871 9498961 9498871 ID=MS.gene028849.t1.exon2;Parent=MS.gene028849.t1
chr2.3 CDS 9498871 9498961 9498871 ID=cds.MS.gene028849.t1;Parent=MS.gene028849.t1
chr2.3 exon 9498749 9498772 9498749 ID=MS.gene028849.t1.exon3;Parent=MS.gene028849.t1
chr2.3 CDS 9498749 9498772 9498749 ID=cds.MS.gene028849.t1;Parent=MS.gene028849.t1
Gene Sequence

>MS.gene028849

ATGTCACCAAGTTGGCCAGATTTTTCCAAACACCAAAAAAATATTATGCCAACATCCATTTCAACCAATAACATTGTCACTACAAACAATTATCAGAATCAGAACCCTTCATGGGTGGATGAGTTCCTCGACTTTTCCTCGGCAAGGCGAGGCGCTCATAGAAGGTCGGTGAGCGATTCAGTCACATTCTTAGAAACACCAATGCTTGATGATTGTCGGGGTAAACACGATGGTAACAACAATGACAACGAGTTCGACAAGTTTGATGATGAACAATTTTTGTCCATGTTCAGTGATGAAATATCTGGTGTCAATAACATGCCACCAACGTTGTCTTCATCGAACACTTCGAGTCCTTCAGATCAGAATTTTGTCAATGATGATAATGAGAAAGAGAAGAATAAACAAGAGAAGAAGGAGAATGATTTAGGAGAGATGAAGAAAGAGGAAGATGAGAAGCAATTGAAATATGAACCTGATGAGGTAGAAAGCCAATGCAAACAGGAAAATTCACAGCCTCAAAGTAATAACAACAATGCTACTTCTTCAAATGATAGAATTACTGATCCAAAGAGAGTCAAAAGGTAATTATCAAACACTTCTATATAATATAGATAAAAATTAAAACATGTAGGATGAAATTTAAAACATTTTTTTTTCTTCTAATTTTCTTGCATAATTCAACTTTTTCTAATAGTATATTTTTATCTATATACATATGCTTAATTTTGCTAATAAACTTGCAATGCCCACATGACATGATTTTGGAGTGCTTCATTATTGTAGATTTTTTTTTAAGCATGATTTTGATATTCTAGTTGTAATTGTTGATTAGTTTTCATGCATTTCTCTTTATAATTGAAATATTGTTGATCTTGGTTTCTTGAACTGTTTTTTTTTTTTTTTCTTTGTTTGTAAAGTGAAAATAAAGCATTTTTTACCTTTGAGTTTTGTAACTGATTCTGGTTTTTTTTTTTTTTTTTTTGCATTAGAATCTTGGCAAATAGGCAATCAGCACAAAGGTCACGTGTGAGGAAGCTGCAATACATATCAGAGCTTGAGCGTAGTGTAACTTCATTACAGGTTTGTCACGTAACATAACATAGCATGATTTCACTATAATTTTTATATTATTTATTTGCAGTACTATAATATATGGAAATTTGATGTGTAATGTATAGTGGAATTTGGAAATGATCAAATAA
Protein sequence

>MS.gene028849.t1

MSPSWPDFSKHQKNIMPTSISTNNIVTTNNYQNQNPSWVDEFLDFSSARRGAHRRSVSDSVTFLETPMLDDCRGKHDGNNNDNEFDKFDDEQFLSMFSDEISGVNNMPPTLSSSNTSSPSDQNFVNDDNEKEKNKQEKKENDLGEMKKEEDEKQLKYEPDEVESQCKQENSQPQSNNNNATSSNDRITDPKRVKRILANRQSAQRSRVRKLQYISELERSVTSLQWNLEMIK