AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052376


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052376.t1 MTR_4g076090 96.825 63 2 0 1 63 1 63 5.61e-40 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052376.t1 AT3G22210 62.295 61 22 1 5 65 6 65 7.04e-20 76.6

Find 22 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAATTCGCTCTTCCAGTTT+TGG 0.231911 4.2:-33048225 MS.gene052376:CDS
TGATGTGTGGCGAGCATTAC+TGG 0.309464 4.2:-33047030 MS.gene052376:CDS
GTCTTCTAGCTCGCCTCTCT+CGG 0.346161 4.2:+33047995 None:intergenic
GACAGAAATCACTTCAAGAT+TGG 0.349085 4.2:-33048065 MS.gene052376:intron
GCTGCAACAATGCCCAAAAC+TGG 0.365881 4.2:+33048212 None:intergenic
AGCATTAAACTTTATTATCA+AGG 0.372958 4.2:+33046949 None:intergenic
AGCTCGCCTCTCTCGGGAGC+TGG 0.374844 4.2:+33048002 None:intergenic
CTCTCTCGGGAGCTGGATGT+TGG 0.452110 4.2:+33048009 None:intergenic
GGTCATCTTCATCACCATAC+TGG 0.459278 4.2:-33046998 MS.gene052376:CDS
TTGATACTCGTAATCCAGTA+TGG 0.459701 4.2:+33046984 None:intergenic
ACAGAAATCACTTCAAGATT+GGG 0.482353 4.2:-33048064 MS.gene052376:intron
ATTGAAACTCACTGCATAGA+AGG 0.485260 4.2:+33048178 None:intergenic
TCTTCTAGCTCGCCTCTCTC+GGG 0.500761 4.2:+33047996 None:intergenic
AAACTTTATTATCAAGGGAA+GGG 0.504724 4.2:+33046955 None:intergenic
TAAACTTTATTATCAAGGGA+AGG 0.509711 4.2:+33046954 None:intergenic
GCATTAAACTTTATTATCAA+GGG 0.548046 4.2:+33046950 None:intergenic
GAGCATTACTGGATTGTCTA+CGG 0.582425 4.2:-33047019 MS.gene052376:CDS
CAACATCCAGCTCCCGAGAG+AGG 0.612999 4.2:-33048008 MS.gene052376:CDS
GATGATTCTGAATCAGACAA+TGG 0.634322 4.2:-33048042 MS.gene052376:CDS
GAGTTTCAATGAGATTAGAG+AGG 0.641117 4.2:-33048165 MS.gene052376:intron
GATTCTGAATCAGACAATGG+AGG 0.655225 4.2:-33048039 MS.gene052376:CDS
CTCGATATAACACTGATGTG+TGG 0.707696 4.2:-33047043 MS.gene052376:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGAATAGTATTTTTTTTTT+TGG - chr4.2:33047782-33047801 MS.gene052376:intron 10.0%
!! ATAACATTGAAATTTGAAAA+CGG + chr4.2:33047582-33047601 None:intergenic 15.0%
!!! ATACTCCTTTTATATTTTAA+TGG - chr4.2:33047600-33047619 MS.gene052376:intron 15.0%
!!! TACATTTTTCTAATAGAAAA+TGG + chr4.2:33047411-33047430 None:intergenic 15.0%
!! AAAATTAAGGAAAATACTTC+GGG + chr4.2:33048107-33048126 None:intergenic 20.0%
!! CAAAATTAAGGAAAATACTT+CGG + chr4.2:33048108-33048127 None:intergenic 20.0%
!! CTAGACCATTAAAATATAAA+AGG + chr4.2:33047608-33047627 None:intergenic 20.0%
!! TAACATTGAAATTTGAAAAC+GGG + chr4.2:33047581-33047600 None:intergenic 20.0%
!! TGATCACTAAAAAGTAATAT+CGG - chr4.2:33047923-33047942 MS.gene052376:intron 20.0%
!! TGTCAAAAAGAAAAACATAT+AGG + chr4.2:33047700-33047719 None:intergenic 20.0%
!!! AGTATTTTCCTTAATTTTGT+TGG - chr4.2:33048109-33048128 MS.gene052376:intron 20.0%
!!! ATAGTAGTTTTTTATTACGT+CGG - chr4.2:33047812-33047831 MS.gene052376:intron 20.0%
!!! ATTTCTTTATTTTTGATGCT+TGG - chr4.2:33047291-33047310 MS.gene052376:intron 20.0%
!!! TTTTTTGGATAATAATACGT+AGG - chr4.2:33047838-33047857 MS.gene052376:intron 20.0%
! AAACTTTATTATCAAGGGAA+GGG + chr4.2:33048237-33048256 None:intergenic 25.0%
! AACATTGAAATTTGAAAACG+GGG + chr4.2:33047580-33047599 None:intergenic 25.0%
! GATCACTAAAAAGTAATATC+GGG - chr4.2:33047924-33047943 MS.gene052376:intron 25.0%
! TAAACTTTATTATCAAGGGA+AGG + chr4.2:33048238-33048257 None:intergenic 25.0%
! TCTCATTGCTAATATAGTTT+AGG + chr4.2:33047731-33047750 None:intergenic 25.0%
!! AAATGAACATGCAACTATTT+TGG + chr4.2:33047528-33047547 None:intergenic 25.0%
!!! TTATTACGTCGGTTTTTTTT+TGG - chr4.2:33047823-33047842 MS.gene052376:intron 25.0%
!!! TTGCTGTTGAAGTTATTTTT+TGG + chr4.2:33047235-33047254 None:intergenic 25.0%
AAGAACAGGTGACTTAAATT+TGG - chr4.2:33047876-33047895 MS.gene052376:intron 30.0%
AAGTTGAGCCAACAAAATTA+AGG + chr4.2:33048120-33048139 None:intergenic 30.0%
ACAGAAATCACTTCAAGATT+GGG - chr4.2:33047125-33047144 MS.gene052376:intron 30.0%
ACATTGAAATTTGAAAACGG+GGG + chr4.2:33047579-33047598 None:intergenic 30.0%
ACCAACAAGAACTATTGAAA+AGG + chr4.2:33047365-33047384 None:intergenic 30.0%
AGTAGCAAATTGTTTGTACT+AGG - chr4.2:33047331-33047350 MS.gene052376:intron 30.0%
! ACCTTTTCAATAGTTCTTGT+TGG - chr4.2:33047361-33047380 MS.gene052376:intron 30.0%
!!! ACATTTTTTGTGTTTTCTCC+AGG - chr4.2:33047463-33047482 MS.gene052376:intron 30.0%
!!! CATTTTTTGTGTTTTCTCCA+GGG - chr4.2:33047464-33047483 MS.gene052376:intron 30.0%
ATTGAAACTCACTGCATAGA+AGG + chr4.2:33047014-33047033 None:intergenic 35.0%
GACAGAAATCACTTCAAGAT+TGG - chr4.2:33047124-33047143 MS.gene052376:intron 35.0%
GAGTTTCAATGAGATTAGAG+AGG - chr4.2:33047024-33047043 MS.gene052376:CDS 35.0%
GATGATTCTGAATCAGACAA+TGG - chr4.2:33047147-33047166 MS.gene052376:intron 35.0%
TCTCATTATTTCCTCTTGAG+AGG - chr4.2:33047632-33047651 MS.gene052376:intron 35.0%
TTGATACTCGTAATCCAGTA+TGG + chr4.2:33048208-33048227 None:intergenic 35.0%
ATGAGAAAGTAAACACGCCA+AGG - chr4.2:33047745-33047764 MS.gene052376:intron 40.0%
CTCGATATAACACTGATGTG+TGG - chr4.2:33048146-33048165 MS.gene052376:intron 40.0%
GACTTAAATTTGGTCCGTTG+AGG - chr4.2:33047886-33047905 MS.gene052376:intron 40.0%
GAGCATTACTGGATTGTCTA+CGG - chr4.2:33048170-33048189 MS.gene052376:CDS 40.0%
GATCTTAATCCCACACTTGA+GGG - chr4.2:33047654-33047673 MS.gene052376:intron 40.0%
GATTCTGAATCAGACAATGG+AGG - chr4.2:33047150-33047169 MS.gene052376:intron 40.0%
TGTACAGTCGATGAAAGAAC+AGG - chr4.2:33047862-33047881 MS.gene052376:intron 40.0%
! CAATTCGCTCTTCCAGTTTT+GGG - chr4.2:33046965-33046984 MS.gene052376:CDS 40.0%
!! CTTCGGGTAACTTTGAGTTT+TGG + chr4.2:33048091-33048110 None:intergenic 40.0%
!!! CATGCAACTATTTTGGTCTC+TGG + chr4.2:33047521-33047540 None:intergenic 40.0%
ACACTTGAGGGTGAGAATGT+CGG - chr4.2:33047666-33047685 MS.gene052376:intron 45.0%
ACATTCTCACCCTCAAGTGT+GGG + chr4.2:33047666-33047685 None:intergenic 45.0%
CGGGGGAGAAAAGTCATTTA+AGG + chr4.2:33047562-33047581 None:intergenic 45.0%
GGATCTTAATCCCACACTTG+AGG - chr4.2:33047653-33047672 MS.gene052376:intron 45.0%
GGGATTAAGATCCTCTCAAG+AGG + chr4.2:33047646-33047665 None:intergenic 45.0%
GGTCATCTTCATCACCATAC+TGG - chr4.2:33048191-33048210 MS.gene052376:CDS 45.0%
TAAATTTGGTCCGTTGAGGC+TGG - chr4.2:33047890-33047909 MS.gene052376:intron 45.0%
! CTACGTCTGTTGCTTATCCT+TGG + chr4.2:33047765-33047784 None:intergenic 45.0%
! GCAATTCGCTCTTCCAGTTT+TGG - chr4.2:33046964-33046983 MS.gene052376:CDS 45.0%
GACATTCTCACCCTCAAGTG+TGG + chr4.2:33047667-33047686 None:intergenic 50.0%
GCTGCAACAATGCCCAAAAC+TGG + chr4.2:33046980-33046999 None:intergenic 50.0%
TGATGTGTGGCGAGCATTAC+TGG - chr4.2:33048159-33048178 MS.gene052376:intron 50.0%
CACTGTCAGACCAGCCTCAA+CGG + chr4.2:33047903-33047922 None:intergenic 55.0%
! GTGAGACTAGTCACTGACCC+TGG + chr4.2:33047484-33047503 None:intergenic 55.0%
!! GTCTTCTAGCTCGCCTCTCT+CGG + chr4.2:33047197-33047216 None:intergenic 55.0%
!! TCTTCTAGCTCGCCTCTCTC+GGG + chr4.2:33047196-33047215 None:intergenic 55.0%
CAACATCCAGCTCCCGAGAG+AGG - chr4.2:33047181-33047200 MS.gene052376:intron 60.0%
CTCTCTCGGGAGCTGGATGT+TGG + chr4.2:33047183-33047202 None:intergenic 60.0%
AGCTCGCCTCTCTCGGGAGC+TGG + chr4.2:33047190-33047209 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 33046953 33048258 33046953 ID=MS.gene052376
chr4.2 mRNA 33046953 33048258 33046953 ID=MS.gene052376.t1;Parent=MS.gene052376
chr4.2 exon 33048166 33048258 33048166 ID=MS.gene052376.t1.exon1;Parent=MS.gene052376.t1
chr4.2 CDS 33048166 33048258 33048166 ID=cds.MS.gene052376.t1;Parent=MS.gene052376.t1
chr4.2 exon 33047989 33048082 33047989 ID=MS.gene052376.t1.exon2;Parent=MS.gene052376.t1
chr4.2 CDS 33047989 33048082 33047989 ID=cds.MS.gene052376.t1;Parent=MS.gene052376.t1
chr4.2 exon 33046953 33047068 33046953 ID=MS.gene052376.t1.exon3;Parent=MS.gene052376.t1
chr4.2 CDS 33046953 33047068 33046953 ID=cds.MS.gene052376.t1;Parent=MS.gene052376.t1
Gene Sequence

>MS.gene052376

ATGGATGCAATGCAATTCGCTCTTCCAGTTTTGGGCATTGTTGCAGCTGCAGCTGTGACCTTCTATGCAGTGAGTTTCAATGAGATTAGAGAGGTAAGTCACTAAGCAGCATCATCAACTATGTAATATATATTACTTGATATCTTTATCAATCTTATAAAATTGAATTATGACAGAAATCACTTCAAGATTGGGATGATTCTGAATCAGACAATGGAGGTTTTAGACCAACATCCAGCTCCCGAGAGAGGCGAGCTAGAAGACAAGCTAGTAAAAATACCAAAAAATAACTTCAACAGCAACGATAATTACTCTCTTTAAATGTTATGTTGTCTTTCATTTCTTTATTTTTGATGCTTGGTTTTATACTAAATAAATAGTAGCAAATTGTTTGTACTAGGTTGAGTGACCTTTTCAATAGTTCTTGTTGGTGCTCGTTGAATAGTGCTCGTGTTCCATTTTCTATTAGAAAAATGTAGAAAATTGTGTATCAAATTTGAGTTAGAAGTCACATTTTTTGTGTTTTCTCCAGGGTCAGTGACTAGTCTCACAACAAGTTGCACATCCAGAGACCAAAATAGTTGCATGTTCATTTTTACATCTCATCCTTAAATGACTTTTCTCCCCCGTTTTCAAATTTCAATGTTATACTCCTTTTATATTTTAATGGTCTAGATTCTCTCATTATTTCCTCTTGAGAGGATCTTAATCCCACACTTGAGGGTGAGAATGTCGGTTAGATTACCTATATGTTTTTCTTTTTGACAGTTGATTACCTAAACTATATTAGCAATGAGAAAGTAAACACGCCAAGGATAAGCAACAGACGTAGAATAGTATTTTTTTTTTTGGTCAAAAAATAGTAGTTTTTTATTACGTCGGTTTTTTTTTGGATAATAATACGTAGGTTGTACAGTCGATGAAAGAACAGGTGACTTAAATTTGGTCCGTTGAGGCTGGTCTGACAGTGTGATCACTAAAAAGTAATATCGGGTGTCTTTTATTGTGCATCACAAATCTGATTTAGTTTTACATTGCTTGTGTTTTGTGTTTTTTTTTTTTAGCTTGTGTTTTGTGTTTTTTTTTTTTAGAAGATATTAGTTTAATCATTCGTATGTCAATTAAATATAAGTCACCAAAACTCAAAGTTACCCGAAGTATTTTCCTTAATTTTGTTGGCTCAACTTCAGATGCTCGATATAACACTGATGTGTGGCGAGCATTACTGGATTGTCTACGGTCATCTTCATCACCATACTGGATTACGAGTATCAATCTCATCCCTTCCCTTGATAATAAAGTTTAA

Protein sequence

>MS.gene052376.t1

MDAMQFALPVLGIVAAAAVTFYAVSFNEIREKSLQDWDDSESDNGGFRPTSSSRERRARRQANARYNTDVWRALLDCLRSSSSPYWITSINLIPSLDNKV