AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49786


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49786.t1 MTR_6g029250 92.797 236 9 1 1 236 1 228 7.25e-153 424
MS.gene49786.t1 MTR_7g085790 48.077 260 98 9 1 233 1 250 1.33e-65 204
MS.gene49786.t1 MTR_7g085790 44.400 250 83 10 1 233 1 211 5.72e-54 173
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49786.t1 AT3G03870 37.184 277 117 15 1 233 1 264 2.94e-31 116
MS.gene49786.t1 AT5G18130 44.186 172 60 8 91 233 114 278 1.18e-30 115
MS.gene49786.t1 AT3G03870 32.645 242 107 14 1 199 1 229 2.88e-14 70.1
MS.gene49786.t1 AT5G18130 37.857 140 52 7 91 202 114 246 6.31e-14 69.3

Find 36 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAATAGTGGTTTCAATTTA+TGG 0.126095 6.3:+20325986 MS.gene49786:CDS
GTTATGTGAGCTCTTGTTAT+TGG 0.194388 6.3:-20327147 None:intergenic
TCTTTCTCAATAATCATTCT+TGG 0.230298 6.3:-20325919 None:intergenic
AAGATTAAGGAAAATGAAAT+TGG 0.238321 6.3:+20325841 MS.gene49786:CDS
GTTGGTGCTATTTGCACTTT+TGG 0.279828 6.3:+20326027 MS.gene49786:CDS
ATTATTGAGAAAGATGATTT+TGG 0.285258 6.3:+20325928 MS.gene49786:CDS
TTACCAAGTTTGAGGTCTAA+TGG 0.382258 6.3:-20325730 None:intergenic
TAACACCTCAAATGATGTTA+TGG 0.383015 6.3:+20325750 MS.gene49786:CDS
GTGGTTTCAATTTATGGAAG+TGG 0.411257 6.3:+20325992 MS.gene49786:CDS
GAAGCAATTTCTGTTGTAAG+AGG 0.414220 6.3:+20327120 MS.gene49786:CDS
GGTCTAATGGAATTTGTAAA+GGG 0.426783 6.3:-20325717 None:intergenic
TTATGGAAGTGGAGTCTTAG+TGG 0.445021 6.3:+20326003 MS.gene49786:CDS
TTGAGGTGTTACCAAGTTTG+AGG 0.452496 6.3:-20325738 None:intergenic
AGGTCTAATGGAATTTGTAA+AGG 0.463571 6.3:-20325718 None:intergenic
TGGGAAGTAGAGGACAATAG+TGG 0.465059 6.3:+20325973 MS.gene49786:CDS
TTCAGAAGGATCAGAAGAAT+AGG 0.469303 6.3:+20326106 MS.gene49786:CDS
TTGAACCATAACATCATTTG+AGG 0.471724 6.3:-20325755 None:intergenic
TCTTTGCTACTACTTGACTT+TGG 0.472978 6.3:-20325883 None:intergenic
TGGAGATGGATCTTGATGAA+TGG 0.483700 6.3:+20325557 None:intergenic
GAATTTGTAAAGGGACAAGT+TGG 0.486114 6.3:-20325708 None:intergenic
GGAGATGGATCTTGATGAAT+GGG 0.498676 6.3:+20325558 None:intergenic
ATTCCATTAGACCTCAAACT+TGG 0.502699 6.3:+20325727 MS.gene49786:CDS
CAAAGAAGAGGATTCAAGTT+GGG 0.511674 6.3:+20325954 MS.gene49786:CDS
TATATTGATTTCAATGAAGA+TGG 0.511704 6.3:+20325601 MS.gene49786:CDS
TGTTCTTTGGAAGCCAACAT+AGG 0.514724 6.3:+20326076 MS.gene49786:CDS
AAGCAATTTCTGTTGTAAGA+GGG 0.518875 6.3:+20327121 MS.gene49786:CDS
GGATTCAAGTTGGGAAGTAG+AGG 0.539605 6.3:+20325963 MS.gene49786:CDS
AGCAATTTCTGTTGTAAGAG+GGG 0.561387 6.3:+20327122 MS.gene49786:CDS
ATTTCAGAGGATTAAGCAAG+TGG 0.575069 6.3:+20327074 MS.gene49786:intron
AAGTGGAGTCTTAGTGGTGT+TGG 0.575334 6.3:+20326009 MS.gene49786:CDS
ACAAGAGCTCACATAACAGT+TGG 0.586253 6.3:+20327153 MS.gene49786:CDS
ACAAAGAAGAGGATTCAAGT+TGG 0.588072 6.3:+20325953 MS.gene49786:CDS
AGAGCTCACATAACAGTTGG+TGG 0.589518 6.3:+20327156 MS.gene49786:CDS
TGGGAATCAATCTCTAGTGA+TGG 0.593054 6.3:+20325577 MS.gene49786:CDS
ATCAGAAAGTGCTTTAGACA+TGG 0.600275 6.3:+20325651 MS.gene49786:CDS
TCAAATCTATGCTGATGACA+AGG 0.621211 6.3:+20326131 MS.gene49786:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCAAATCATATATATTTTTT+TGG + chr6.3:20326172-20326191 MS.gene49786:intron 10.0%
!!! TTTTAGTCATTATATTGTTA+AGG + chr6.3:20326421-20326440 MS.gene49786:intron 15.0%
!!! TTTTGATTCGAAAAATAAAT+TGG - chr6.3:20326690-20326709 None:intergenic 15.0%
!! AAGATTAAGGAAAATGAAAT+TGG + chr6.3:20325841-20325860 MS.gene49786:CDS 20.0%
!! ATCATTTATTCAAGAAATAC+CGG + chr6.3:20326789-20326808 MS.gene49786:intron 20.0%
!! TTCATAAAGTCAATTATAAG+TGG - chr6.3:20326759-20326778 None:intergenic 20.0%
!!! AAATAAATTGGAGTATCAAT+TGG - chr6.3:20326678-20326697 None:intergenic 20.0%
!!! ACAAGTTTTCTTTAAGATTA+AGG + chr6.3:20325828-20325847 MS.gene49786:CDS 20.0%
!!! ATTATTGAGAAAGATGATTT+TGG + chr6.3:20325928-20325947 MS.gene49786:CDS 20.0%
!!! GGATGGAATTTTATTATATT+TGG + chr6.3:20326997-20327016 MS.gene49786:intron 20.0%
!!! TATATTGATTTCAATGAAGA+TGG + chr6.3:20325601-20325620 MS.gene49786:CDS 20.0%
!!! TTTTACTCTATAGTATTTCT+GGG - chr6.3:20326957-20326976 None:intergenic 20.0%
!!! TTTTTACTCTATAGTATTTC+TGG - chr6.3:20326958-20326977 None:intergenic 20.0%
! AAAAAAAGTTTCCTAGGAAA+AGG + chr6.3:20325628-20325647 MS.gene49786:CDS 25.0%
! ACAATAGTGGTTTCAATTTA+TGG + chr6.3:20325986-20326005 MS.gene49786:CDS 25.0%
! CGAATGTCATCAATATTTAT+CGG - chr6.3:20326553-20326572 None:intergenic 25.0%
! TCATTTATTCAAGAAATACC+GGG + chr6.3:20326790-20326809 MS.gene49786:intron 25.0%
! TCTTTCTCAATAATCATTCT+TGG - chr6.3:20325922-20325941 None:intergenic 25.0%
! TTGTATATTGAACTAAACCT+TGG + chr6.3:20327046-20327065 MS.gene49786:intron 25.0%
!! AGAATCTGGTTTAGTATAAA+TGG + chr6.3:20326270-20326289 MS.gene49786:intron 25.0%
!! TCAAGATTTTAAATTGCTCT+TGG + chr6.3:20326335-20326354 MS.gene49786:intron 25.0%
!! TTTTCGAATCAAAACAATCA+GGG + chr6.3:20326696-20326715 MS.gene49786:intron 25.0%
!!! ATTGATGATTCTTTAGAGTT+GGG + chr6.3:20326491-20326510 MS.gene49786:intron 25.0%
!!! GTAAAAAAGTGTTAACTTTG+TGG + chr6.3:20326971-20326990 MS.gene49786:intron 25.0%
!!! TCTATTTGTGTTTTGTTCTT+TGG + chr6.3:20326063-20326082 MS.gene49786:CDS 25.0%
!!! TTTTTCGAATCAAAACAATC+AGG + chr6.3:20326695-20326714 MS.gene49786:intron 25.0%
AAAGTCAATTATAAGTGGCA+TGG - chr6.3:20326754-20326773 None:intergenic 30.0%
AAGCAATTTCTGTTGTAAGA+GGG + chr6.3:20327121-20327140 MS.gene49786:CDS 30.0%
ACATAGGAAAAAACTTCAGA+AGG + chr6.3:20326092-20326111 MS.gene49786:CDS 30.0%
AGGTCTAATGGAATTTGTAA+AGG - chr6.3:20325721-20325740 None:intergenic 30.0%
CTTAGTCATTTGATCTTGAT+CGG + chr6.3:20326590-20326609 MS.gene49786:intron 30.0%
GAATCATCAATCAACTAACA+AGG - chr6.3:20326482-20326501 None:intergenic 30.0%
GACAAGGTTAGTAAATTTCT+TGG + chr6.3:20326147-20326166 MS.gene49786:intron 30.0%
GGTCTAATGGAATTTGTAAA+GGG - chr6.3:20325720-20325739 None:intergenic 30.0%
TAACACCTCAAATGATGTTA+TGG + chr6.3:20325750-20325769 MS.gene49786:CDS 30.0%
TTGAACCATAACATCATTTG+AGG - chr6.3:20325758-20325777 None:intergenic 30.0%
!! GATTGATGATTCTTTAGAGT+TGG + chr6.3:20326490-20326509 MS.gene49786:intron 30.0%
!! TTGATGATTCTTTAGAGTTG+GGG + chr6.3:20326492-20326511 MS.gene49786:intron 30.0%
!!! ACAAGTTGGTTTTGTTTTCT+TGG - chr6.3:20325697-20325716 None:intergenic 30.0%
!!! TCTGAAGTTTTTTCCTATGT+TGG - chr6.3:20326092-20326111 None:intergenic 30.0%
AAGAAATACCGGGAAATACT+TGG + chr6.3:20326800-20326819 MS.gene49786:intron 35.0%
ACAAAGAAGAGGATTCAAGT+TGG + chr6.3:20325953-20325972 MS.gene49786:CDS 35.0%
AGAAATACCGGGAAATACTT+GGG + chr6.3:20326801-20326820 MS.gene49786:intron 35.0%
AGCAATTTCTGTTGTAAGAG+GGG + chr6.3:20327122-20327141 MS.gene49786:CDS 35.0%
ATTCCATTAGACCTCAAACT+TGG + chr6.3:20325727-20325746 MS.gene49786:CDS 35.0%
ATTTCAGAGGATTAAGCAAG+TGG + chr6.3:20327074-20327093 MS.gene49786:intron 35.0%
GAAGCAATTTCTGTTGTAAG+AGG + chr6.3:20327120-20327139 MS.gene49786:CDS 35.0%
GAATTTGTAAAGGGACAAGT+TGG - chr6.3:20325711-20325730 None:intergenic 35.0%
GGTGAGAAAAAAAGTTTCCT+AGG + chr6.3:20325622-20325641 MS.gene49786:CDS 35.0%
GTGGTTTCAATTTATGGAAG+TGG + chr6.3:20325992-20326011 MS.gene49786:CDS 35.0%
TCAAATCTATGCTGATGACA+AGG + chr6.3:20326131-20326150 MS.gene49786:CDS 35.0%
TCTTTGCTACTACTTGACTT+TGG - chr6.3:20325886-20325905 None:intergenic 35.0%
TGTCAATGACTGATGTTTGT+CGG + chr6.3:20326247-20326266 MS.gene49786:intron 35.0%
TTCAGAAGGATCAGAAGAAT+AGG + chr6.3:20326106-20326125 MS.gene49786:CDS 35.0%
! AAAGTGTTAACTTTGTGGCA+AGG + chr6.3:20326976-20326995 MS.gene49786:intron 35.0%
! CAAAGAAGAGGATTCAAGTT+GGG + chr6.3:20325954-20325973 MS.gene49786:CDS 35.0%
! GTTATGTGAGCTCTTGTTAT+TGG - chr6.3:20327150-20327169 None:intergenic 35.0%
! TTACCAAGTTTGAGGTCTAA+TGG - chr6.3:20325733-20325752 None:intergenic 35.0%
!! AAATACTTGGGTGCCATTAA+TGG + chr6.3:20326813-20326832 MS.gene49786:intron 35.0%
!! ATCAGAAAGTGCTTTAGACA+TGG + chr6.3:20325651-20325670 MS.gene49786:CDS 35.0%
!! ATCCTCTGAAATCAAAACCA+AGG - chr6.3:20327066-20327085 None:intergenic 35.0%
!! TACTCTATAGTATTTCTGGG+TGG - chr6.3:20326954-20326973 None:intergenic 35.0%
!! TGATTTTGGTGACAAAGAAG+AGG + chr6.3:20325942-20325961 MS.gene49786:CDS 35.0%
!!! AACCTTGGTTTTGATTTCAG+AGG + chr6.3:20327061-20327080 MS.gene49786:intron 35.0%
!!! AGTTGGTTTTGTTTTCTTGG+TGG - chr6.3:20325694-20325713 None:intergenic 35.0%
!!! TTTTGTTTTCTTGGTGGTGA+AGG - chr6.3:20325688-20325707 None:intergenic 35.0%
ACAAGAGCTCACATAACAGT+TGG + chr6.3:20327153-20327172 MS.gene49786:CDS 40.0%
ACACACACATCCACAATGTT+TGG - chr6.3:20326873-20326892 None:intergenic 40.0%
CACACACATCCACAATGTTT+GGG - chr6.3:20326872-20326891 None:intergenic 40.0%
GGAGTCATAGTTAGCATGTA+TGG + chr6.3:20326522-20326541 MS.gene49786:intron 40.0%
TGGGAATCAATCTCTAGTGA+TGG + chr6.3:20325577-20325596 MS.gene49786:CDS 40.0%
TGTTAACTTTGTGGCAAGGA+TGG + chr6.3:20326980-20326999 MS.gene49786:intron 40.0%
TTATGGAAGTGGAGTCTTAG+TGG + chr6.3:20326003-20326022 MS.gene49786:CDS 40.0%
TTGTTAAGGCTGCAATCACA+TGG + chr6.3:20326435-20326454 MS.gene49786:intron 40.0%
! CACTTTCTGATCCTTTTCCT+AGG - chr6.3:20325642-20325661 None:intergenic 40.0%
! TGTTCTTTGGAAGCCAACAT+AGG + chr6.3:20326076-20326095 MS.gene49786:CDS 40.0%
! TTGAGGTGTTACCAAGTTTG+AGG - chr6.3:20325741-20325760 None:intergenic 40.0%
!! CTTTAGAGTTGGGGAATTTG+TGG + chr6.3:20326501-20326520 MS.gene49786:intron 40.0%
!! TAATGGCATGGTGCCATTAA+TGG + chr6.3:20326918-20326937 MS.gene49786:intron 40.0%
!!! GTTGGTGCTATTTGCACTTT+TGG + chr6.3:20326027-20326046 MS.gene49786:CDS 40.0%
AAGTGGAGTCTTAGTGGTGT+TGG + chr6.3:20326009-20326028 MS.gene49786:CDS 45.0%
AATGGCACCCAAGTATTTCC+CGG - chr6.3:20326811-20326830 None:intergenic 45.0%
AGAGCTCACATAACAGTTGG+TGG + chr6.3:20327156-20327175 MS.gene49786:CDS 45.0%
CATCAATGGCCAGGATGTAA+TGG - chr6.3:20326846-20326865 None:intergenic 45.0%
CATTACATCCTGGCCATTGA+TGG + chr6.3:20326844-20326863 MS.gene49786:intron 45.0%
CTGATGTTTGTCGGAGAATC+TGG + chr6.3:20326256-20326275 MS.gene49786:intron 45.0%
GTTGAATCTCAGTCGATCGT+GGG + chr6.3:20326718-20326737 MS.gene49786:intron 45.0%
TGGGAAGTAGAGGACAATAG+TGG + chr6.3:20325973-20325992 MS.gene49786:CDS 45.0%
! CAATGTTTGGGTGCCATCAA+TGG - chr6.3:20326860-20326879 None:intergenic 45.0%
! CTGCAATCACATGGCAGTTT+TGG + chr6.3:20326444-20326463 MS.gene49786:intron 45.0%
! TGTGTGTGGTGGAGATCTAA+TGG + chr6.3:20326901-20326920 MS.gene49786:intron 45.0%
! TTGATGGCACCCAAACATTG+TGG + chr6.3:20326860-20326879 MS.gene49786:intron 45.0%
!! AGTATTTCTGGGTGGCACTT+TGG - chr6.3:20326946-20326965 None:intergenic 45.0%
!! GGATTCAAGTTGGGAAGTAG+AGG + chr6.3:20325963-20325982 MS.gene49786:CDS 45.0%
!! TAATGGCACGGTGCCATTAA+TGG - chr6.3:20326829-20326848 None:intergenic 45.0%
!! TGGCACTTTGGTGCCATTAA+TGG - chr6.3:20326934-20326953 None:intergenic 45.0%
ATGGCCAGGATGTAATGGCA+CGG - chr6.3:20326841-20326860 None:intergenic 50.0%
GGTTGAATCTCAGTCGATCG+TGG + chr6.3:20326717-20326736 MS.gene49786:intron 50.0%
GTGTGTGTGATGTGTGTGTG+TGG + chr6.3:20326887-20326906 MS.gene49786:intron 50.0%
TGTGTGATGTGTGTGTGTGG+TGG + chr6.3:20326890-20326909 MS.gene49786:intron 50.0%
! GTGGTGGAGATCTAATGGCA+TGG + chr6.3:20326906-20326925 MS.gene49786:intron 50.0%
! TTTGGGTGCCATCAATGGCC+AGG - chr6.3:20326855-20326874 None:intergenic 55.0%
! GGCACCGTGCCATTACATCC+TGG + chr6.3:20326834-20326853 MS.gene49786:intron 60.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 20325562 20327200 20325562 ID=MS.gene49786
chr6.3 mRNA 20325562 20327200 20325562 ID=MS.gene49786.t1;Parent=MS.gene49786
chr6.3 exon 20325562 20326152 20325562 ID=MS.gene49786.t1.exon1;Parent=MS.gene49786.t1
chr6.3 CDS 20325562 20326152 20325562 ID=cds.MS.gene49786.t1;Parent=MS.gene49786.t1
chr6.3 exon 20327081 20327200 20327081 ID=MS.gene49786.t1.exon2;Parent=MS.gene49786.t1
chr6.3 CDS 20327081 20327200 20327081 ID=cds.MS.gene49786.t1;Parent=MS.gene49786.t1
Gene Sequence

>MS.gene49786

ATGGATCTTGATGAATGGGAATCAATCTCTAGTGATGGCTATATTGATTTCAATGAAGATGGTGAGAAAAAAAGTTTCCTAGGAAAAGGATCAGAAAGTGCTTTAGACATGGAATATTTGTATCCTTCACCACCAAGAAAACAAAACCAACTTGTCCCTTTACAAATTCCATTAGACCTCAAACTTGGTAACACCTCAAATGATGTTATGGTTCAAGACATCACAAAGAATCAATCTCTTGAAGCTGATCAAGAAGAAAATGTGTCACAAGTTTTCTTTAAGATTAAGGAAAATGAAATTGGTGACATGAAAATTGAATCACCAAAGTCAAGTAGTAGCAAAGAGTTTATTACTTCTCCAAGAATGATTATTGAGAAAGATGATTTTGGTGACAAAGAAGAGGATTCAAGTTGGGAAGTAGAGGACAATAGTGGTTTCAATTTATGGAAGTGGAGTCTTAGTGGTGTTGGTGCTATTTGCACTTTTGGTGTTGTTGCTGCTTCTATTTGTGTTTTGTTCTTTGGAAGCCAACATAGGAAAAAACTTCAGAAGGATCAGAAGAATAGGTTTCAAATCTATGCTGATGACAAGGTTAGTAAATTTCTTGGTTTCAAATCATATATATTTTTTTGGTTTGCTTATAAATTAATTTGTTTGATTAATAGTACGAAGTATCTATCAACTTTGTCAATGACTGATGTTTGTCGGAGAATCTGGTTTAGTATAAATGGTTTAAATTATAGAAATTTATATTGATTTAGTATAGAATTTAGTCAAGATTTTAAATTGCTCTTGGTGTTACACTAATATACTTGAAAATAAGAAAAATTATAGACAAACAAAGTTTATGTAGCAATGATTTTAGTCATTATATTGTTAAGGCTGCAATCACATGGCAGTTTTGGAGACTTATGAAACCTTGTTAGTTGATTGATGATTCTTTAGAGTTGGGGAATTTGTGGAGTCATAGTTAGCATGTATGGATCATCCGATAAATATTGATGACATTCGTTTATCAAATTTAAAATCTTAGTCATTTGATCTTGATCGGATATATTTGACTAATTGACTATGTGACTGTATAGATTCTCTAACTTTATGAAATTTGAATCTCCAATTGATACTCCAATTTATTTTTCGAATCAAAACAATCAGGGTTGAATCTCAGTCGATCGTGGGAGCAAAATCACCATGCCACTTATAATTGACTTTATGAAACACAACTGTATCATTTATTCAAGAAATACCGGGAAATACTTGGGTGCCATTAATGGCACCGTGCCATTACATCCTGGCCATTGATGGCACCCAAACATTGTGGATGTGTGTGTGTGATGTGTGTGTGTGGTGGAGATCTAATGGCATGGTGCCATTAATGGCACCAAAGTGCCACCCAGAAATACTATAGAGTAAAAAAGTGTTAACTTTGTGGCAAGGATGGAATTTTATTATATTTGGTTAAATATTCAATTGATTATGAGTTATTGTATATTGAACTAAACCTTGGTTTTGATTTCAGAGGATTAAGCAAGTGGTGCAGCATGCAACAAAATTGAATGAAGCAATTTCTGTTGTAAGAGGGGTTCCAATAACAAGAGCTCACATAACAGTTGGTGGCAACTATGATTTCTTTGATTGA

Protein sequence

>MS.gene49786.t1

MDLDEWESISSDGYIDFNEDGEKKSFLGKGSESALDMEYLYPSPPRKQNQLVPLQIPLDLKLGNTSNDVMVQDITKNQSLEADQEENVSQVFFKIKENEIGDMKIESPKSSSSKEFITSPRMIIEKDDFGDKEEDSSWEVEDNSGFNLWKWSLSGVGAICTFGVVAASICVLFFGSQHRKKLQKDQKNRFQIYADDKRIKQVVQHATKLNEAISVVRGVPITRAHITVGGNYDFFD